Octet System Data Acquisition User Guide

Octet System Data



Acquisition User Guide

Release 7.1

ForteBio, Inc.



1360 Willow Road, Suite 201



Menlo Park, CA 94025



888.OCTET-QK



650.322.1360

 www.fortebio.com

Copyright 2011© ForteBio, Inc. All rights reserved

page 1

Table of Contents

Chapter 1:



Welcome. . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

About the Octet System. . . . . . . . . . . . . . . . . . .8

What’s New in the Octet System Data

Acquisition Software, Release 7.1 . . . . . . . . .8

What’s New in the Octet System Data

Acquisition software, Release 7.0 . . . . . . . 12

Conventions and Symbols Used in This Guide

13

ForteBio Technical Support . . . . . . . . . . . . . 13

Chapter 2:



Octet System Specifications. . . . . . . . . 15

Octet RED96 System Specifications . . . . . 16

Octet RED384 System Specifications . . . . 18

Octet QK

e

System Specifications . . . . . . . . 21

Octet QK System Specifications . . . . . . . . . 23

Octet QK384 System Specifications . . . . . 25

Chapter 3:



Getting Started. . . . . . . . . . . . . . . . . . . . . 29

Starting the Octet System and Data

Acquisition Software . . . . . . . . . . . . . . . . . . . 30

Software Overview . . . . . . . . . . . . . . . . . . . . . 31

Main Menu and Toolbar . . . . . . . . . . . . 31

View Menu. . . . . . . . . . . . . . . . . . . . . . . . . . 34

Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Instrument Status Window. . . . . . . . . . 39

Experiment Wizard . . . . . . . . . . . . . . . . . 40

Octet System Data Acquisition Options . 40

Setting the Plate Temperature . . . . . . . . . . .43

Changing the Plate Temperature for

Individual Experiments . . . . . . . . . . . . . .43

Defining a New Default Sample Plate

Temperature . . . . . . . . . . . . . . . . . . . . . . . .44

Monitoring Experiments Remotely. . . . . . .45

Managing Biosensor Types . . . . . . . . . . . . . .48

Viewing Available Biosensor Types . . .48

Adding a Biosensor Type . . . . . . . . . . . . .49

Removing a Biosensor Type . . . . . . . . . .49

Chapter 4:



21 CFR Part 11 Compliance . . . . . . . . . .51

21 CFR Part 11 Software . . . . . . . . . . . . . . . . .52

ForteBio GxP Server Module . . . . . . . . . . . . .52

Selecting a Server Location . . . . . . . . . . . . . .52

Starting a User Session . . . . . . . . . . . . . . . . . .56

Compliance Features. . . . . . . . . . . . . . . . . . . .59

Experiment and Method File Compliance

59

Verifying Digital Signatures . . . . . . . . . .60

Viewing the Audit Trail. . . . . . . . . . . . . . .62

Changing Projects During a User Session

64

Changing the User Password. . . . . . . . .65

Locking the Application. . . . . . . . . . . . . .65

Ending a User Session. . . . . . . . . . . . . . . .66

Octet System Data Acquisition User Guide, Release 7.1

page 2

Chapter 5:



Quantitation Experiments:



Octet RED96, QK e

and QK . . . . . . . . . . . 67

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Starting a Quantitation Experiment . . . . 69

Starting an Experiment Using the

Experiment Wizard . . . . . . . . . . . . . . . . . 69

Defining the Sample Plate . . . . . . . . . . . . . . 70

Designating Samples . . . . . . . . . . . . . . . 71

Selecting Wells in the Sample Plate Map

73

Designating Standards . . . . . . . . . . . . . 73

Designating Unknowns . . . . . . . . . . . . . 78

Designating Controls or Reference Wells

81

Annotating Samples . . . . . . . . . . . . . . . . 82

Replicate Groups. . . . . . . . . . . . . . . . . . . . 84

Managing Sample Plate Definitions . . . . 88

Exporting a Plate Definition . . . . . . . . . 88

Importing a Plate Definition. . . . . . . . . 89

Managing Assay Parameter Settings. . . . 91

Modifying Assay Parameter Settings 91

Viewing User-Modifiable Assay Parameter

Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Assigning Biosensors to Samples. . . . . . . . 96

Biosensor Assignment in Single-Analyte

Experiments . . . . . . . . . . . . . . . . . . . . . . . . 96

Biosensor Assignment in Multiple Analyte

Experiments . . . . . . . . . . . . . . . . . . . . . . . . 99

Biosensor Regeneration. . . . . . . . . . . . 111

Using Partial Biosensor Trays . . . . . . 112

Reviewing Experiments. . . . . . . . . . . . . . . . 114

Saving Experiments . . . . . . . . . . . . . . . . . . . 114

Running a Quantitation Experiment . . . 116

Loading the Biosensor Tray and Sample

Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

Starting an Experiment . . . . . . . . . . . . 117

Run Experiment Window Settings . . 119

Stopping an Experiment . . . . . . . . . . . 122

Managing Runtime Binding Charts . . . . 122

Opening a Runtime Binding Chart . 123

Viewing Reference-Subtracted Data 123

Viewing Inverted Data . . . . . . . . . . . . . 125

Magnifying the Runtime Binding Chart.

125

Scaling a Runtime Binding Chart . . . 126

Adding a Runtime Binding Chart Title126

Selecting a Runtime Binding Chart Legend

126

Viewing Multiple Runtime Binding Charts

127

Exporting or Printing the Runtime Binding

Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Managing Experiment Method Files . . . 128

Custom Quantitation Assays . . . . . . . . . . 129

Defining a Custom Assay . . . . . . . . . . 129

Editing Assay Parameters . . . . . . . . . . 131


page 3

Selecting a Custom Assay . . . . . . . . . . 137

Chapter 6:



Quantitation Experiments:



Octet RED384 and QK384 . . . . . . . . . . 139

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . 140

Starting a Quantitation Experiment . . . 141


Experiment Wizard . . . . . . . . . . . . . . . . 141

Defining the Sample Plate . . . . . . . . . . . . . 142

Read Head Configuration and Plate

Layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Changing the Plate Format . . . . . . . . 144

Designating Samples . . . . . . . . . . . . . . 144


148

Designating Standards . . . . . . . . . . . . 148

Designating Unknowns . . . . . . . . . . . . 153

Designating Controls or Reference Wells

156

Annotating Samples . . . . . . . . . . . . . . . 157

Replicate Groups. . . . . . . . . . . . . . . . . . . 159

Managing Sample Plate Definitions . . . 163

Exporting a Plate Definition . . . . . . . . 163

Importing a Plate Definition. . . . . . . . 164

Working with a Reagent Plate . . . . . . . . . 165

Saving a Reagent Plate Definition . . 167

Managing Assay Parameter Settings. . . 167

Modifying Assay Parameter Settings167

Viewing User-Modifiable Assay Parameter

Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

Assigning Biosensors to Samples . . . . . . 173

Biosensor Assignment in Single-Analyte

Experiments . . . . . . . . . . . . . . . . . . . . . . . 173

Biosensor Assignment in Multiple Analyte

Experiments . . . . . . . . . . . . . . . . . . . . . . . 177

Biosensor Regeneration. . . . . . . . . . . . 188

Using Partial Biosensor Trays . . . . . . 189



Running a Quantitation Experiment . . . 193

Loading the Biosensor Tray, Sample and

Reagent Plates. . . . . . . . . . . . . . . . . . . . . 193

Starting an Experiment . . . . . . . . . . . . 194



Managing Runtime Binding Charts . . . . 199

Opening a Runtime Binding Chart . 200




202




203


204


page 4


Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204


Custom Quantitation Assays . . . . . . . . . . 206

Defining a Custom Assay. . . . . . . . . . . 206

Editing Assay Parameters . . . . . . . . . . 208

Selecting a Custom Assay . . . . . . . . . . 214

Chapter 7:



Kinetics Experiments:



Octet RED96, QK e

and QK . . . . . . . . . . 215

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Starting a Basic Kinetics Experiment . . . 217






219

Designating Well Types . . . . . . . . . . . . 219

Entering Sample Information . . . . . . 221


Editing the Sample Table. . . . . . . . . . . 231




Defining a Kinetic Assay . . . . . . . . . . . . . . . 236

Defining Step Types . . . . . . . . . . . . . . . . 236

Building an Assay . . . . . . . . . . . . . . . . . . 241

Assigning Biosensors to Samples . . . . . . 249



Saving an Experiment to the Template

Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260

Running a Kinetics Experiment . . . . . . . . 260

Loading the Biosensor Tray and Sample

Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260

Starting the Experiment. . . . . . . . . . . . 261



Managing the Runtime Binding Chart . 267

Opening the Runtime Binding Chart268



Aligning Data by a Selected Step . . . 270

Extending or Skipping an Assay Step270

Terminating a Step to Begin the Next Step

271


271




271


272


Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272


page 5


Chapter 8:



Kinetics Experiments:



Octet RED384 and QK384 . . . . . . . . . . 275

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . 276

Starting a Basic Kinetics Experiment . . . 277




Read Head Configuration and Plate

Layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278

Changing the Sample Plate Format 280



281

Designating Well Types . . . . . . . . . . . . 282

Entering Sample Information . . . . . . 283


Editing the Sample Table. . . . . . . . . . . 295




Working with a Reagent Plate . . . . . . . . . 299

Saving a Reagent Plate Definition . . 301

Defining a Kinetic Assay . . . . . . . . . . . . . . . 302

Defining Step Types . . . . . . . . . . . . . . . . 302

Building an Assay . . . . . . . . . . . . . . . . . . 306

Assigning Biosensors to Samples. . . . . . . 313



Saving an Experiment to the Template

Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324

Running a Kinetics Experiment . . . . . . . . 324

Loading the Biosensor Tray, Sample, and

Reagent Plates. . . . . . . . . . . . . . . . . . . . . 324

Starting the Experiment. . . . . . . . . . . . 325



Managing the Runtime Binding Chart . 331

Opening the Runtime Binding Chart332



Aligning Data by a Selected Step . . . 334

Extending or Skipping an Assay Step335


335




336


336


Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337



page 6

Chapter 9:



Maintenance . . . . . . . . . . . . . . . . . . . . . . 339

Octet RED96 and Octet QK Systems . . . . 340

Cleaning the Octet Instrument . . . . . 340

Emptying the Waste Container . . . . . 340

Replacing Fuses (Octet RED96 and Octet

QK

e

Systems only). . . . . . . . . . . . . . . . . . 341

Octet RED384 and Octet QK384 Systems342

Cleaning the Octet Instrument . . . . . 342

Cleaning the Biosensor Pickup Tips . 343

Replacing Fuses. . . . . . . . . . . . . . . . . . . . 343

Appendix A:



Using Octet384 Systems with an

Automation Interface . . . . . . . . . . . . . . 345

Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346

Design of the Automation Interface. . . . 346

Automation Interface Control Setup346

Automation Client Example Application

348

Automation Commands. . . . . . . . . . . . . . . 349

Typical Automation Session. . . . . . . . 351

Advanced Automation Session . . . . . 353

Automation API.H . . . . . . . . . . . . . . . . . 356

Analysis Automation API . . . . . . . . . . . 361

Appendix B:



21 CFR Part 11 Software Administrator

Options . . . . . . . . . . . . . . . . . . . . . . . . . . 365

Installing the Data Acquisition 7.0 21 CFR Part

11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . 366

Installing the Data Analysis 7.0 21 CFR Part 11

Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369

Installing the ForteBio GxP Server Module371

Administrator Account Setup. . . . . . . . . . 374

Starting an Administrator User Session 378

Accessing Administrator Options . . . . . . 381

Administrator Tabs . . . . . . . . . . . . . . . . 383

User Account Administration . . . . . . 384

Group Administration . . . . . . . . . . . . . 388

Project Administration . . . . . . . . . . . . . 390

Administrator Constants. . . . . . . . . . . 392

Event Log. . . . . . . . . . . . . . . . . . . . . . . . . . 394

Accessing the GxP Server Module Directly396

Restarting the GxP Server Module . . . . . 398


page 7

CHAPTER 1:

Welcome



About the Octet System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

What’s New in the Octet System Data Acquisition Software, Release 7.1 . . . . . . . . . . . . . . . . . 8

What’s New in the Octet System Data Acquisition software, Release 7.0 . . . . . . . . . . . . . . . . . 12

Conventions and Symbols Used in This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

ForteBio Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Welcome to the ForteBio Octet System Data Acquisition User Guide. This guide explains how to:

• Operate the Octet instrument.

• Set up and run quantitation and kinetics experiments on the Octet instrument.

• Maintain the Octet instrument.

• Use the optional Octet system 21 CFR Part 11 Compliance Validation module.


page 8

Chapter 1:

Welcome

ABOUT THE OCTET SYSTEM

The Octet system enables real-time quantitation or kinetic characterization of biomolecular interactions. A system includes the Octet instrument with the following components:

• Computer

• Hardware

• Software Modules—Data Acquisition and Data Analysis (see Table 1-1)

For more details on the Data Analysis software, see the Data Analysis User Guide.

Table 1-1:

Octet System Functions

Octet Software Functions

Data Acquisition • Define a quantitation or kinetic experiment and save the experiment for future use.

• Define custom assays.

• Run the experiment and acquire binding data.

• View and save binding data to a user-specified location.

Data Analysis • Analyze binding data and view analysis results.

• Export or copy analysis results.

• Generate a report of quantitation or kinetic results in table and graph formats.

For information on preparing samples for quantitation or kinetics experiments, please see the appropriate ForteBio Octet Biosensor product instructions.

WHAT’S NEW IN THE OCTET SYSTEM DATA ACQUISITION SOFTWARE,

RELEASE 7.1

The following features are new for the Octet Pro Data Acquisition software, Release 7.1:

1.

Multiple instruments can co-exist on the same computer.

2.

The .fmf file is saved in the experiment folder as read-only.

3.

Added the Sample Plate and Sensor Tray

Print

button on the

Plate Definition

tab and the plate map.

The associated table information prints after you click

Print

(Figure 1-1).


What’s New in the Octet System Data Acquisition Software, Release 7.1

page 9

Figure 1-1:

Sample Plate and Sensor Tray Print Button

4.

Added a new

Regeneration

step that is similar to regeneration in Quantitation. a. On the


tab, assign wells as

Regeneration

or

Neutralization

(Figure 1-2).

Figure 1-2:

Regeneration Step

b. Click

Add

(Figure 1-3) to display the Add Step Definition dialog box (Figure 1-4).


page 10

Chapter 1:

Welcome

Figure 1-3:

Regeneration Step—Step Data List—Add Button

Figure 1-4:

Add Step Definition Dialog Box

c. Select the

Regeneration

radio button and click

OK

.

d. Click

Regeneration Params

(Figure 1-5).

Figure 1-5:

Regeneration Step—Step Data List—Regeneration Params Button

The

Regeneration Parameters

dialog box (Figure 1-6) displays, where you can edit

Regeneration parameters, as necessary.

Figure 1-6:

Regeneration Parameters Dialog Box

5.

Added a new feature to align a Kinetic experiment at a given time.

a. Right-click the Kinetic experiment running chart and select

Align at time...

(Figure 1-7).


What’s New in the Octet System Data Acquisition Software, Release 7.1

page 11

Figure 1-7:

Kinetic Experiment Running Chart—Align at Specified Time

The Align at Time dialog box displays (Figure 1-8).

Figure 1-8:

Align at Time Dialog Box

b. Specify the time point you want to align to and click

OK

.

The running chart aligns to the time point you specify.

6.

Made changes to only permit samples in the sample plate.

7.

Added printing for the

Assay Definition

tab via

File

>

Print & File

>

Print Preview

.


page 12

Chapter 1:

Welcome

WHAT’S NEW IN THE OCTET SYSTEM DATA ACQUISITION SOFTWARE,

RELEASE 7.0

Table 1-2 describes new features available in the Octet System Data Acquisition software,

Release 7.0.

Table 1-2:

Octet System Data Acquisition Software—New Features for Release 7.0

New Feature

User-defined default startup temperature

Description

Allows you to define the default start-up temperature for all experiments.

To access the Temperature field, click

File

>

Options

.

NOTE: To change the default setting, you must restart the Octet System Data Acquisition software after entering the new value.

Post-condition biosensors

Sample plate temperature recorded in log file

Enhanced legend options in the Runtime Binding

Chart

Multiple Runtime Binding

Charts

Post-condition biosensors after Basic Quantitation with

Regeneration or Advanced Quantitation experiments, allowing re-racked tips to be stored in a regenerated state.

The sample plate temperature is recorded in the Instrument Status window at the beginning of the experiment, as well as when each set of sensors is picked up by the manifold.

The biosensor legend displayed in the Runtime Binding

Chart provides four options for enhanced monitoring:

Sensor Location, Sample ID, Sensor Information, and Concentration/Dilution.

During data acquisition, multiple Runtime Binding Charts may be opened, allowing the comparison of different channel settings.


Conventions and Symbols Used in This Guide

page 13

CONVENTIONS AND SYMBOLS USED IN THIS GUIDE

NOTE: A note presents pertinent details on a topic.For example, general information about tips or alternate options.

IMPORTANT: An important message for instances where the assay or procedure will not work if not properly followed.

WARNING: A warning informs the user that specific actions could cause irreversible consequences or damage.

Table 9:

Octet Instrument Labels

Symbol Definition

Electrical hazard

Heat/hot

Fuse

FORTEBIO TECHNICAL SUPPORT

You can contact ForteBio technical support at any of the locations listed in Table 10.

Table 10:

ForteBio Technical Support

Main Office

ForteBio, Inc.

1360 Willow Road,



Suite 201

Menlo Park, CA 94025

USA

Tel: +1-650-322-1360

Fax: +1-650-322-1370

E-mail: [email protected]

European Office

ForteBio, UK, Ltd.

83 Victoria Street,



Suite 407

London, SW1H 0HW

UK

Tel: +44-(0)20-31784425

Fax: +44-(0)20-31787070


Asia Office

ForteBio



(Aria Biotechnology Co. Ltd.)

917 Halley Road, Bldg. 4

Zhangjiang High Tech Park

Shanghai, China 201203

Tel: +86-21-51320387



page 14

Chapter 1:

Welcome


page 15

CHAPTER 2:



Octet System Specifications

Octet RED96 System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Octet RED384 System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Octet QKe System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Octet QK System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Octet QK384 System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25


page 16

OCTET RED96 SYSTEM SPECIFICATIONS

Chapter 2:


Figure 2-1:

Octet RED96 Instrument—Door Closed (Left) or Open (Right)

Table 2-1:

Octet RED96 System Specifications

Item

Equipment



Classifications

Environmental

Compliance

Description

• Product Classification: Class 1: Detachable power cord

• Installation/Overvoltage Category: Category II

• Pollution Degree: Degree 2

• EMC Classification: Group I, Class A, ISM Equipment

(EN55011, emissions), {EN61326, immunity}

• Storage Temperature: -20 to 70 °C

• Optimum Operating Temperature: 22 ± 4 °C

• Safe Operating Temperature: 15 to 30 °C

• Humidity: Non-condensing, 10 to 80% Relative Humidity

• Indoor Use Only

• Operating Altitude: 0 to 2,000 meters

CE, CSA


Octet RED96 System Specifications

page 17

Table 2-1:

Octet RED96 System Specifications (Continued)

Item

Capabilities

Description

• Protein quantitation

• Kinetic and affinity analyses (k obs

, k a

, k d

, K

D

)

• Binding specificity and cooperativity

• Kinetic screening of proteins, peptides, and other biomolecules

• Small molecule and fragments screening and kinetic analysis

• Recommended analyte molecular weight of 150 Da or higher

Sampling Format • Required plate: 96-well, black, flat bottom polypropylene microplate (Greiner Bio-One, #655209) or similar, SBS standard microplate

• Single sample plate capacity

180–220 μL/well (96-well plate) Sampling Volume

Sample Types

Biosensor Type

Purified samples, common culture media, crude lysates

Disposable, single-use fiber optic biosensors with optional reuse by regeneration and/or re-racking

Biosensor Tray Type 8 x 12 format 96-biosensor tip tray, green color

Optics and

Mechanics

• 8-channel biosensor manifold

• Optical interferometer

• Eight spectrometers (one dedicated spectrometer per biosensor)

Throughput • Up to 8 biosensors in parallel, maximum of 96 tests unattended

• One 96-well plate and one biosensor tray at once

Static or 100–1,500 rpm Orbital Flow



Capacity

Temperature Range (Ambient + 4 °C)–40 °C, 1 °C increments

Dimensions 18.6" H x 17" W x 20.8" D (47 cm H x 43 cm W x 53 cm D)

Weight

Electrical



Requirements

63 lb (28.6 kg)

• Mains: AC 100–240 V, 5.0–2.0 A, 50/60 Hz, single phase

• Power consumption: 120 W (240 W peak)


page 18

Chapter 2:


OCTET RED384 SYSTEM SPECIFICATIONS

Biosensor tray

& rehydration plate

Sample plate stage

Automatic Sliding Door

Reagent plate stage

Figure 2-2:

Octet RED384 Instrument—Door Closed (Left) or Open (Right)

Biosensor chute to waste

Table 2-2:

Octet RED384 System Specifications

Item

Equipment



Classifications

Environmental

Compliance

Capabilities

Description










• Indoor Use Only


CE, CSA



, k a

, k d

, K

D

)


• Kinetic screening

• Small molecule kinetic analysis


Octet RED384 System Specifications

page 19

Table 2-2:


Item

Sampling Format

Sample Types

Biosensor Type

Description

• Required plates:

• 96-well, black, flat bottom polypropylene microplate

(Greiner Bio-One, #655209) or similar, SBS standard microplate

• 384-well black, flat-bottom polypropylene (Greiner

Bio-One, #781209)

• 384-well black, tilted-bottom polypropylene (ForteBio,

#18-5076 or #18-5080), SBS standard microplate

• Two plate stations

• Test volume:

• 180–300 μL in a 96-well plate, non-destructive and recoverable


• 40–100 μL in a 384-well tilted bottom microplate

(384TW), non-destructive and recoverable




Automation • Up to 16 biosensors in parallel

• Ability to integrate the Octet instrument with a laboratoryautomated robotic system for automated plate and biosensor tray handling

Optics and

Mechanics



• Sample plate platform temperature range: from 4 °C above ambient to 40 °C

• 16 spectrometers (one dedicated spectrometer per biosensor)


• Two microplates, either 96- or 384-well at once. Only one plate can be used for samples. The second plate is used for reagents.


page 20

Chapter 2:


Table 2-2:


Item

Orbital Flow



Capacity

Dimensions

Weight

Electrical



Requirements

•

•

Description

Static or 100–1,500 rpm

30.1" H x 31.5" W x 31.4" D (76.5 cm H x 80 cm W x 79.8 cm D)

150 lb (68 kg)

Mains: AC 100–240 V, 5.0–2.0 A, 50/60 Hz, single phase

Power consumption: 195 W (240 W peak)

5

6

3

4

7

Table 2-3:

Sensor Offset and Well Volumes for Octet RED384 and Octet QK384

Sensor

Offset

(mm)

Recommended Minimum Fill Volume (μL)

96-well plate

(Greiner Bio-One)

200

200

225

250

300

384-well plate


80

80

100

120

130

384-well tilted bottom plate (ForteBio, 384TW)

40

60

80

100

100


Octet QK e

System Specifications

OCTET QK

e

SYSTEM SPECIFICATIONS

page 21

Figure 2-3:

Octet QK e

Instrument—Door Closed (Left) or Open (Right)

Table 2-4:

Octet QK e

System Specifications

Item

Equipment



Classifications

Environmental

Compliance

Description









• Humidity: Non-condensing, 10 to 80% Relative

Humidity

• Indoor Use Only


CE, CSA


page 22

Chapter 2:


Table 2-4:

Octet QK e

System Specifications (Continued)

Item

Capabilities

Sampling Format

Sample Volume

Sample Types

Biosensor Type

Biosensor Tray Type

Optics and Mechanics

Throughput

Orbital Flow Capacity

Temperature Range

Dimensions

Weight

Electrical Requirements

Description



, k a

, k d

, K

D

)


• Kinetic screening of proteins, peptides and other biomolecules

• Biosensor re-racking

• Recommended analyte molecular weight of



5,000 Da or higher

• Required plate: 96-well, black, flat bottom polypropylene microplate (Greiner Bio-One, #655209), SBS standard microplate


180–220 μL/well (96-well plate)



8 x 12 format 96-biosensor tip tray, green color



• One spectrometer (shared by eight biosensors)

• Up to eight biosensors in parallel, maximum of 96 tests unattended



(Ambient + 4 °C)–40 °C, 1 °C increments

18.6" H x 17" W x 20.8" D (47 cm H x 43 cm W x 53 cm D)

54 lb (24.5 kg)

• Mains: AC 100–240 V, 5.0–2.0 A, 50/60 Hz, single phase

• Power consumption: 120 W (240 W peak)


Octet QK System Specifications

OCTET QK SYSTEM SPECIFICATIONS

page 23

Figure 2-4:

Octet QK Instrument—Door Closed (Left) or Open (Right)

Table 2-5:

Octet QK System Specifications

Item

Equipment



Classifications

Environmental

Compliance

Capabilities

Description










• Indoor Use Only


CE, CSA



, k a

, k d

, K

D

)


• Kinetic screening of proteins, peptides, and other biomolecules

• Recommended analyte molecular weight of 10,000 Da or higher


page 24

Chapter 2:


Table 2-5:

Octet QK System Specifications (Continued)

Item

Sampling Format

Description

• Required plate: 96-well, black, flat bottom polypropylene microplate (Greiner Bio-One, #655209), SBS standard microplate


180–220 μL/well (96-well plate) Sample Volume

Sample Types

Biosensor Type


Disposable, single-use fiber optic biosensors with optional reuse by regeneration


Optics and



Mechanics

•


Optical interferometer

• One spectrometer (shared by eight biosensors)



Orbital Flow



Capacity


Temperature Range (Ambient + 4 °C)–40 °C, 1 °C increments

Dimensions

Weight

Electrical



Requirements

•

•

18.6” H x 17” W x 20.8” D (47 cm H x 43 cm W x 53 cm D)

50 lb (23 kg)




Octet QK384 System Specifications

page 25

OCTET QK384 SYSTEM SPECIFICATIONS

Biosensor tray

& rehydration plate

Sample plate stage

Automatic Sliding Door

Reagent plate stage

Figure 2-5:

Octet QK384 Instrument—Door Closed (Left) or Open (Right)

Biosensor chute to waste

Table 2-6:

Octet QK384 System Specifications

Item

Equipment



Classifications

Environmental

Compliance

Capabilities

Description










• Indoor Use Only


CE, CSA



, k a

, k d

, K

D

)


• Kinetic screening


page 26

Chapter 2:


Table 2-6:

Octet QK384 System Specifications (Continued)

Item

Sampling Format

Description

• Required plates:

• 96-well, black, flat bottom polypropylene microplate

(Greiner Bio-One, #655209) or similar, SBS standard microplate

• 384-well black, flat-bottom polypropylene (Greiner

Bio-One, #781209)

• 384-well black, tilted-bottom polypropylene microplate (ForteBio, #18-5076 or



#18-5080), SBS standard microplate

• Two plate stations

• Test volume:



• 40–100 μL in a 384-well tilted bottom microplate

(384TW), non-destructive and recoverable

Sample Types

Biosensor Type




Automation

Optics and

Mechanics

• Up to 16 biosensors in parallel

• Ability to integrate the Octet instrument with a laboratoryautomated robotic system for automated plate and biosensor tray handling



• Sample plate platform temperature range: From 4 °C above ambient to 40 °C

• 2 spectrometers (one dedicated spectrometer per eight biosensors)


• Two microplates, either 96- or 384-well at once. Only one plate can be used for samples. The second plate is used for reagents.


Octet QK384 System Specifications

page 27

Table 2-6:

Octet QK384 System Specifications (Continued)

Item

Orbital Flow



Capacity

Dimensions

Weight

Electrical



Requirements

•

•

Description


30.1" H x 31.5" W x 31.4" D (76.5 cm H x 80 cm W x 79.8 cm D)

150 lb (68 kg)



5

6

3

4

7

Table 2-7:

Sensor Offset and Well Volumes for Octet RED384 and Octet QK384

Sensor

Offset

(mm)

Recommended Minimum Fill Volume (μL)

96-well plate


200

200

225

250

300

384-well plate


80

80

100

120

130

384-well tilted bottom plate (ForteBio, 384TW)

40

60

80

100

100


page 28

Chapter 2:



page 29

CHAPTER 3:



Getting Started

Starting the Octet System and Data Acquisition Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Software Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Octet System Data Acquisition Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Setting the Plate Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Monitoring Experiments Remotely . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Managing Biosensor Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

page 30

Chapter 3:

Getting Started

STARTING THE OCTET SYSTEM AND DATA ACQUISITION SOFTWARE

NOTE: The installation shall be performed by ForteBio, Inc. personnel only.



WARNING: If the Octet system is not used as specified, injury to the user and/or damage to the instrument may result.

NOTE: Do not position the Octet instrument such that it is difficult to disconnect the power.

For information about how to connect the Octet instrument to the computer, please refer to the insert sheet that is provided with the Octet instrument.

To start the system and software:

1.

Turn on the computer.

2.

Turn the Octet instrument on using the power switch located on the external electrical box.

NOTE: The instrument requires a minimum of one-hour warm-up time. It is recommended that you leave the instrument on for a minimum of eight hours prior to use.

3.

Launch the Octet System Data Acquisition software by double-clicking on the Data

Acquisition desktop icon.

Figure 3-1:

Desktop Icon


Software Overview

page 31

NOTE: When using the CFR 11 version of the Octet System Data Acquisition software, users are required to log in and start a user session before the soft-

ware will launch. Please refer to “Starting a User Session” on page 56 for more

information.

SOFTWARE OVERVIEW

Launching the application displays the Octet System Data Acquisition software

Main

Screen

. Screen components along with the default windows displayed are shown in

Figure 3-2.

Main



Menu

Toolbar

Instrument



Status



Window

Status



Bar

Experiment Wizard

Figure 3-2:

Main Screen

Main Menu and Toolbar

The Main Menu and Toolbar are located in the upper left corner of the

Main Screen

(Figure 3-3). Menu options and toolbar buttons are described in this section.


page 32

Chapter 3:

Getting Started

Figure 3-3:

Main Menu and Toolbar

NOTE: The

Security

menu is only available in the 21 CFR Part 11 version of the

Octet System Data Acquisition software.

File Menu

The

File

menu (Figure 3-4) allows users to open and save method files, view experiments,

 print files and set system and software options.



A method file (.fmf ) contains sample plate configuration, sample plate table information, sensor assignments and assay step information that allow the Octet instrument and software to run an experiment. When the run is complete, the data in the experiment folder can then be reviewed.

NOTE: When using the 21 CFR Part 11 version of the Octet System Data Acquisition software, only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened.

Files generated using the non-compliant version of the software or with a non-compliant system cannot be opened, and a message indicating this will be presented.



page 33

File History

Figure 3-4:

File Menu

Table 3-1:

File Menu Commands

Menu Command Toolbar

Button

Open Method File

Close Method File

N/A

Save Method File

Save All Method Files

Save Method File As

N/A

Open Experiment

Save Experiment

Print

Print Preview

Print Setup

N/A

N/A

N/A

N/A

N/A

Function

Opens an experiment method file (.fmf ).

Closes the active experiment method file but does not save changes.

Saves the active experiment method file

(.fmf ).

Saves all open method files (.fmf ).

Allows the active experiment method file to be saved as a new file without overwriting the original method file.

Opens an experiment folder.

Saves the active experiment.

Opens the

Print

dialog box to print a file.

Opens a print preview window of a method file.

Opens the

Print Setup

dialog box to print a file.


page 34

Chapter 3:

Getting Started

Table 3-1:

File Menu Commands (Continued)

Menu Command

File History

Options

Toolbar

Button

N/A

N/A

Exit

N/A

Function

Displays a list of previously opened files.

Opens the Options dialog box. Please refer

to “Octet System Data Acquisition Options” on page 40 for more information on chang-

ing system and software options.

Closes the application after prompting users to save any changes.

View Menu

The

View

menu allows users to show or hide the

Toolbar

and status windows. A check mark next to the menu item indicates the option is currently shown.

Figure 3-5:

View Menu

Table 3-2:

View Menu Commands

Menu Command

Toolbar

Status Bar

Instrument Status

Function

Shows or hides the

Toolbar

.

Shows or hides the

Status bar

.

Displays the


window.

Experiment Menu

The

Experiment

menu provides access to the

Experiment Wizard

, assay and experiment options as well as experiment templates.



page 35

Figure 3-6:

Experiment Menu

Table 3-3:

Experiment Menu Commands


Button

New Experiment Wizard

Edit Assay Parameters

N/A

Edit Sensor Types

Set Plate Temperature

Templates

Skip Step

N/A

N/A

N/A

N/A

Function

Opens the


.



Opens the


dialog box to define a new assay, edit an existing assay, or remove an assay from the quantita-

tion application. See “Managing Assay

Parameter Settings” on page 167 for more

information.

Opens the

Sensor Types

dialog box to view current biosensor types, add new biosensor types and remove biosensor types. See

“Managing Biosensor Types” on page 48 for

more information.

Opens the

Temperature Setting

dialog box that displays the current sample plate temperature and allows users to change the current temperature setting of the instrument.

See “Setting the Plate Temperature” on page 43 for more information. To set the

default temperature, see “Defining a New

Default Sample Plate Temperature” on page 44.

Allows users to select from a set of predefined ForteBio quantitation or kinetics method templates.

Skips the step in the method that is currently executing (kinetics experiments only).


page 36

Chapter 3:

Getting Started

Table 3-3:

Experiment Menu Commands (Continued)


Button

Function

Stop

Stops the experiment. Data from the active biosensor is not saved, but all data prior to the active biosensor will be available.

Instrument Menu

The

Instrument

menu provides direct control of Octet instrument functions.

Figure 3-7:

Instrument Menu

Table 3-4:

Instrument Menu Commands




Button

Reset

N/A

Stop Shaker

Present Stage

N/A

Function

Resets the instrument and the log in the

Instrument Status window

.

Stops the sample plate shaker.

Presents the instrument stage that houses the biosensor tray, sample and reagent plates (Octet RED384 and Octet QK384 only).

Security Menu

The

Security

menu is only available in the 21 CFR Part 11 version of the Data Acquisition

software. For complete details on menu options, please refer to “Compliance Features” on page 59.



page 37

Figure 3-8:

Security Menu

Window Menu

The

Window

menu provides display options for the open windows in the

Main Screen

.

All open windows are listed at the bottom of the menu, and a check mark indicates the window that is currently active. To view another window, select it from the list.

Open Windows

Figure 3-9:

Window Menu

Table 3-5:

Window Menu Commands

Menu Command

New Window

Cascade

Tile

Arrange Icons

Open Windows

Function

Opens a new Runtime Binding Chart window.

Organizes all windows in a cascade arrangement.

Tiles all windows vertically.

Arranges the minimized window icons in a row at the bottom of the main software screen.

Lists of windows currently open in the

Main Screen

.


page 38

Chapter 3:

Getting Started

Help Menu

The

Help

menu provides access to software and instrument support information.

Figure 3-10:

Help Menu

Table 3-6:

Help Menu Commands




Button

N/A

Data Acquisition User

Guide

ForteBio Web Site

N/A

About ForteBio Data

Acquisition

Function

Opens the online Data Acquisition

Software User Guide.

Opens a web browser and displays the ForteBio web page (www.fortebio.com).

Displays software, user and instrument information.

NOTE: Clicking on the ForteBio logo in the upper right corner of the

Main

Screen

also displays the About ForteBio Data Acquisition window.

Status Bar

The

Status Bar

is located at the bottom of the

Main Screen

and displays current instrument and experiment status as well as the plate temperature.

Figure 3-11:

Status Bar

In the 21 CFR Part 11 version of the Data Acquisition software, the

Status Bar

will also display the User and Project name entered at login.



Instrument Status Window

The


window displays a log of all instrument activity. page 39

Figure 3-12:

Instrument Status Window

Selecting the

Auto Scroll to bottom

check box will auto-scroll the log to display the most current events. Clicking

Save to File

will save a copy of the instrument log.

NOTES:



If a problem occurs during operation of the instrument, ForteBio recommends



saving a copy of the system log to better assist our technical support staff in diagnosing the issue.



The instrument log automatically resets when the Octet System Data Acquisition software application is closed.


page 40

Chapter 3:

Getting Started

Experiment Wizard

The


guides users through the complete set up of an experiment. Using the wizard is described in detail in the Quantitation and Kinetics experiment chapters.

Figure 3-13:

Experiment Wizard

OCTET SYSTEM DATA ACQUISITION OPTIONS

Acquisition options allow users to set system and data preferences for quantitation and

kinetic data acquisition. To view user options (Figure 3-14), click

File

>

Options

from the

Main Menu

.


Octet System Data Acquisition Options

page 41

Figure 3-14:

Options Dialog Box

Table 3-7:

User Options

Item

Data Files

Quantitation data

 repository

Kinetics data repository

Description

The default location where quantitation data files (.frd) are saved. Click

...

(

Browse

) to select a different folder.

NOTE: ForteBio recommends that the data be saved to the local machine first, then transferred to a network drive if needed.

The default location where kinetics data files (.frd) are saved. Click

...

(

Browse

) to select a different folder.

NOTE: ForteBio recommends that the data be saved to the local machine first, then transferred to a network drive if needed.


page 42

Chapter 3:

Getting Started

Table 3-7:

User Options (Continued)

Item

Use old 5.0 file format for

FRD files

Description

Select this option to save data in the earlier Octet RED software 5.0 format.

Use extended sample types

NOTE: Saving data in the old file format produces larger files and may result in slower data analysis.

Select this option to extend the sample types available in the right-click menu of the

Sample Plate Map

and

Sample Plate Table

to include negative and positive controls.

Startup

Temperature User-defined default startup plate temperature. This temperature is used as the default setting for all experiments.

NOTE: To change the default setting, the software must be restarted after entering the new value. This changes the startup plate temperature only, not the current plate temperature.

Data Options

Significant digits Specifies the number of significant digits for the values of

Molecular Weight, Concentration and Dilution used during data analysis.

NOTE: Six decimal places are recommended for the Protein A assay.


Setting the Plate Temperature

page 43

Table 3-7:

User Options (Continued)

Item

Simulation

Web Server

Automation

Description

If the workstation is not connected to an instrument, this option enables users to create and save an experiment to a method file (.fmf ) using the properties of the selected instrument type.

Selecting this option enables remote monitoring of the

experiment using a web browser. See “Monitoring Experiments Remotely” on page 45 for more information.

Allows users to select the appropriate connection for automation interfaces used with OctetRED384 and OctetQK384

systems only. For more information, please refer to Appendix A, Using Octet384 Systems with an Automation Interface on page 345.

SETTING THE PLATE TEMPERATURE

The settable plate temperature can range from ambient plus 4 °C to a high of 40 °C. A factory-set default plate temperature of 30 °C is used as a system startup plate temperature and the experiment default temperature. This default value can be customized by the user.

In addition, the plate temperature setting can be changed for individual experiments when needed. The current plate temperature displays in the

Status bar

at the bottom of the

Main Screen

.

Changing the Plate Temperature for Individual Experiments

To set the plate temperature to a value other than the default setting for a specific experiment:

1.

From the

Main Menu

, click

Experiment

>

Set Plate Temperature

.

2.

Click the

Set temperature to

field (Figure 3-15) to the desired value or enter the preferred temperature and click

OK

.

Figure 3-15:

Temperature Setting


page 44

Chapter 3:

Getting Started

3.

Allow sufficient time for the sample plate to equilibrate to the new temperature before beginning an experiment (approximately 5 minutes for a plate at room temperature or

15 minutes for a plate at ambient + 4 °C).

NOTE: If the Octet System Data Acquisition software is closed, the plate temperature will reset to the default startup value specified in the

Options

dialog box when the software is relaunched.

Defining a New Default Sample Plate Temperature

To define a new default temperature that will be used at startup and as the default plate temperature for all experiments:

1.

From the

Main Menu

, click

File

>

Options

.

2.

In the

Options

dialog box (Figure 3-16), select a new temperature in the

Startup

box and click

OK

. The plate temperature will then adjust to the new value, and this setting will be used as the new default startup temperature whenever the software is launched.

Figure 3-16:

Setting the Default Startup Temperature in the Options Dialog Box

3.

Allow sufficient time for the sample plate to equilibrate to the new temperature before beginning an experiment (approximately 5 minutes for a plate at room temperature or

15 minutes for a plate at ambient + 4 °C).

IMPORTANT: To save the new default temperature value, you must restart the software.


Monitoring Experiments Remotely

page 45

MONITORING EXPERIMENTS REMOTELY

If the Octet system computer is connected to a local network, experiment progress can be monitored remotely from any networked computer, smartphone or mobile device using any web browser. In addition, instrument log files and previously run experiments can also be accessed remotely for review.

1.

From the

Main Menu

, click

File

>

Options

.

2.

In the

Options

dialog box (Figure 3-18), select the

Web Server

check box. Adjust the

Port

and

Refresh

settings and change the

Connect as

IP address if needed. The default

Refresh

rate of 10 will refresh the experiment view in the web browser every 10 seconds. Click

OK

.

NOTE: ForteBio recommends using the

Port

and

Connect as

(IP address) settings shown as default in the

Web Server

box, as they are unique to your particular Octet system.

Figure 3-17:

Selecting the Web Server in the Options Dialog Box

3.

Click

File

>

Options

to access the

Options

dialog box again. A

Web Server URL

will now be listed under the

Connect as

box (Figure 3-18). Note this URL as it will be

needed to access the experiment remotely.


page 46

Chapter 3:

Getting Started

Web Server URL

Figure 3-18:

Web Server URL

4.

Start the experiment in the Octet System Data Acquisition software as you normally would.

5.

Open a web browser on a remote computer or device that is on the same network as the Octet system.

NOTE: The remote computer or device must be on the same network as the

Octet system, or connected to the network the instrument is on via VPN.

6.

Enter the

Web Server URL

in the browser window or click the

Web Server URL

link in the

Options

dialog box. The experiment in progress will display (Figure 3-19).


Monitoring Experiments Remotely

page 47

Figure 3-19:

View of Quantitation Experiment (top) and Kinetics Experiment (bottom) via Web Browser

In the browser window, you can:

• Click the experiment name to view experiment details.

• Click

Log File

to display a log of current instrument activity.

• Click

Kinetics Data Repository

or

Quantitation Data Repository

to open and view previously run experiments.


page 48

Chapter 3:

Getting Started

MANAGING BIOSENSOR TYPES

The Octet System Data Acquisition software includes a factory set list of the types of biosensors available for quantitation or kinetic analysis. The available biosensor types display in the

Sensor Assignment

tab. Users can add custom biosensors as needed.

Viewing Available Biosensor Types

To view the available types of biosensors, from the

Main Menu,

click

Experiment

>

Edit

Sensor Types

.

The

Sensor Types

dialog box will display (Figure 3-20).

Figure 3-20:

Sensor Types Dialog Box


Managing Biosensor Types

page 49

Adding a Biosensor Type

To add a biosensor type:

1.

From the

Main Menu

, click

Experiment

>

Edit Sensor Types

.

2.

In the

Sensor Types

dialog box (Figure 3-21), click

Add

next to the

Quantitation Sensors

or

Kinetic Sensors

box (depending on the type of biosensor that will be added).

3.

In the

Add Sensor

dialog box, enter a name for the biosensor type and click

OK

.

Figure 3-21:

Adding a Biosensor Type

Removing a Biosensor Type

To remove a biosensor type, select the biosensor name in the

Quantitation Sensors

or

Kinetic Sensors

box and click

Delete

.

Factory-loaded biosensor types cannot be deleted. Only the biosensor types that users add to the system can be deleted.


page 50

Chapter 3:

Getting Started


page 51

CHAPTER 4:



21 CFR Part 11 Compliance

21 CFR Part 11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

ForteBio GxP Server Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Selecting a Server Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Starting a User Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Compliance Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

page 52

Chapter 4:


21 CFR PART 11 SOFTWARE

The Data Acquisition and Data Analysis software for Octet systems is available in an optional 21 CFR Part 11 version that enables users in GMP and GLP laboratories to comply with 21 CFR Part 11 regulations. This version of the software includes features such as user account management, audit trails and electronic signatures. In addition, the 21 CFR Part 11 version utilizes the ForteBio GxP Server module to manage the information recorded during user sessions.

This chapter explains how to use the ForteBio GxP Server module, compliance features and administrative functions specific to the 21 CFR Part 11 versions of the Data Acquisition and

Data Analysis software.

FORTEBIO GXP SERVER MODULE

When the Data Acquisition or Data Analysis 7.0 21 CFR Part 11 software is launched, users are prompted to log on to the ForteBio GxP Server module. This initiates a user session where all system, software and user events are recorded. During user sessions, the GxP

Server module manages and stores this recorded information. User sessions are closed when the user logs out or a set period of inactivity is reached. A new user session is initiated each time a user accesses the software.

SELECTING A SERVER LOCATION

NOTES:





Please contact your administrator to determine the GxP Server module host location that should be used.



Once the GxP Server module host location is selected, this location will be used as the default selection for the user account. It does not need to be reselected each time a new user session is initiated.

Users must select the host location of the GxP Server module during the login process. The

GxP server can be run on the local host computer where the Data Acquisition or Data Analysis software is installed or from a network location.


Selecting a Server Location

page 53

To select a server location:

1.

Launch the Data Acquisition or Data Analysis software by double-clicking on the desktop icon:

Figure 4-1:

Login Box

The

Login

dialog box will display:

Figure 4-2:

Login Dialog Box

2.

Select a

Server

location by clicking on

...

(

Browse

).

The

Authentication Server



page 54

Chapter 4:


Figure 4-3:

Authentication Server Dialog Box

Click

Default

to recall the default server settings of localhost and Port 2002.

• Local host—If the local computer is to be used as the GxP Server module host, select the

Localhost

check box. Change the Port number if needed.

• Remote host on same subnet—If the GxP Server module is hosted on the same subnet, deselect the

Localhost

check box and click

Find

. A list of potential GxP

Server module addresses will be listed. Choose the desired location from the list and click

OK

.

Figure 4-4:

GxP Server Address Search Results

• Remote host on another subnet—If the GxP Server module is hosted on a different subnet, deselect the

Localhost

check box. Enter the IP address of the computer hosting the GxP Server module.


Selecting a Server Location

page 55

Figure 4-5:

Manual Entry of Remote Host Address

When the GxP Server module host location has been selected or entered, click

OK

to save changes and exit the


dialog box. The GxP Server module location will now be listed as the

Server

in the

Login

box.

Figure 4-6:

Login Dialog Box—Displaying GxP Server Location


page 56

Chapter 4:


STARTING A USER SESSION

NOTE: Before starting your first user session, please contact your administrator to determine the GxP Server module host location that should be used.

To start a user session:

1.


Figure 4-7:

Data Acquisition and Data Analysis Desktop Icons

The

Login


Figure 4-8:

Login Dialog Box

2.

Confirm that the

Server

location is correct. If not, please see “Selecting a Server Location” on page 52.

3.

From the

User

drop-down list, select your login name.


Starting a User Session

page 57

NOTE: To start an administrator session, select

Administrator

in the

User

drop

down list.

Figure 4-9:

Username Selection

4.

Enter your password in the

Password

text box. Click

?

for a password reminder if needed.

Figure 4-10:

Password Reminder

5.

Select a project from the

Project

drop-down list, if required.


page 58

Chapter 4:


Figure 4-11:

Project Selection

6.

Click

OK.

The Data Acquisition or Data Analysis software will now launch and start the user session. During the session, the user account and project selected at login display in the software status bar:

Figure 4-12:

Status Bar

NOTES:





Software operation may be restricted based on your user privileges. For more information on user privileges, please contact your administrator.



User sessions are automatically locked after a period of inactivity which is set by the administrator. The

Login

dialog box will display and a message indicating the session has been locked will be shown. You can choose to log back into the session or log off at this time. User sessions will not be locked during experimental data acquisition.


Compliance Features

page 59

COMPLIANCE FEATURES

The 21 CFR Part 11-compliant features provided in the 21 CFR Part 11 versions of the Data

Acquisition and Data Analysis software can be accessed by clicking the

Security

menu from the software’s

Main Menu

:

Figure 4-13:

Security Menu

NOTES:





The

Server Administration

menu option in the

Security

menu can be accessed only if you have administrator or review privileges.



Security

menu options in the Data Acquisition and Data Analysis software applications are identical.

Experiment and Method File Compliance

When using the 21 CFR Part 11 version of the Octet System Data Acquisition software, only

21 CFR Part 11-compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened. Files generated using the non-compliant version of the software cannot be opened, and a message indicating this will be presented.


page 60

Chapter 4:


Verifying Digital Signatures

The electronic signature of method (.fmf ) and data (.frd) files can be verified to ensure they were generated using 21 CFR Part 11 compliant software.

To verify digital signatures:

1.

Click

Security

>

Verify Document

.

The

Verify Digital Signature


Figure 4-14:

Verify Digital Signature Dialog Box

2.

Click

...

to browse for the desired .fmf or .frd file.

NOTE: When verifying digital signatures, both method (.fmf) and data (.frd) files can be selected in the Data Acquisition and Data Analysis software.



page 61

Figure 4-15:

File Selection

To change the file type available for selection, click on the file type box and select a different format:

Figure 4-16:

File Type Selection

3.

Select the desired file and click

OK

.

A message will display in the

Verify Digital Signature

dialog box indicating file compliance status:


page 62

Chapter 4:


Figure 4-17:

File Compliant (top), File Not Compliant (bottom)

Viewing the Audit Trail

The Audit Trail displays a historical log of user, system and software events recorded during user sessions. To view the Audit Trail, click

Security

>

View Audit Trail

.

Figure 4-18:

Audit Trail



NOTE: Events shown in the Audit Trail are those associated with the user account that is currently logged in and active only.

Events in the Audit Trail can be sorted by clicking on any of the column headers: page 63

Figure 4-19:

Audit Trail Events Sorted by Date/Time

By default, the events initially displayed in the Audit Trail will be those associated with the project selected at login and the machine (computer) currently being used. To view events for a specific project or computer, click on the

Project

or

Machine

drop-down list and select an entry:

Figure 4-20:

Selecting a Project in the Audit Trail

NOTE: Selections can be made in either one or both of the

Project

or

Machine

drop-down lists.


page 64

Chapter 4:


The list with then only display events for the entries selected:

Figure 4-21:

Project-Based Audit Trail Events

In addition to the specific project and machine selections, the following list options are also available:

•

(any)

—Displays all project and/or machine events for the user account

•

(none)

—Displays all project or machine events not associated with a specific project

(

Project

list only)

Changing Projects During a User Session

During an active session, users can switch to another project in the Data Acquisition or Data

Analysis software without having to log out.

To change projects during a user session:

1.

Click

Security

>

Change Projects

.

A list of projects assigned to your user account will be shown with the active project highlighted:

Figure 4-22:

Changing Projects

2.

Select the desired project from the list.

The selected project will now become the active project for the user session.



Changing the User Password

To change the user password:

1.

Initiate a new user session with your existing password.

2.

When the software launches, click

Security

>

Change Password

=.

The

Change Password

dialog box will display: page 65

Figure 4-23:

Change Password Dialog Box

3.

Enter the

Current password

for your user account. Click

?

for a password reminder.

4.

Enter the

New Password

and

Password reminder

(optional).

5.

Click

OK

to save changes and exit.

Locking the Application

The Data Acquisition or Data Analysis software can be locked during a user session to prevent another user from interrupting a session or experiment. When the application is locked, any experiments started will continue to run.

To lock the application:

1.

Click

Security

>

Lock Application

.

The software will be placed in locked mode immediately and the

Application Locked



page 66

Chapter 4:


Figure 4-24:

Application Locked Dialog Box

2.

The application will remain locked until it is unlocked or the active user logs off.

• Unlock—To resume the user session, enter your password and click

Unlock

.

• Log off—To discontinue the user session, click

Logoff

.

Ending a User Session

To end a user session:

1.

Click

Security

>

Logoff

.

2.

In the displayed dialog box, click

OK

.


page 67

CHAPTER 5:



Quantitation Experiments:



Octet RED96, QK e

and QK

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Starting a Quantitation Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Defining the Sample Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Managing Sample Plate Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Managing Assay Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Assigning Biosensors to Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Reviewing Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Saving Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Running a Quantitation Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

Managing Runtime Binding Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Managing Experiment Method Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Custom Quantitation Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

page 68

Chapter 5:

Quantitation Experiments: Octet RED96, QK e

and QK

INTRODUCTION

A quantitation experiment enables you to determine analyte concentration within a sample using a reference set of standards. After starting the Octet system hardware and the

Octet System Data Acquisition software, follow the steps (in Table 5-1) to set up and analyze

a quantitation experiment.

Table 5-1:

Setting Up and Analyzing a Quantitative Experiment

Software

Data



Acquisition

Step

1.

Select a quantitation experiment in the

Experiment wizard

or open a method file (.fmf ).

See

“Starting a Quantitation

Experiment” on page 69

Data Analysis

2.

Define a sample plate or import a sample plate definition.

“Defining the Sample Plate” on page 70

3.

Confirm or edit the assay settings.

“Managing Assay Parameter

Settings” on page 91

4.

Assign biosensors to samples.

“Assigning Biosensors to

Samples” on page 96

5.

Run the experiment.

6.

7.

Analyze the binding data.

Generate a report.

“Running a Quantitation


Octet System Data Analysis

Software User Guide

For more details on how to prepare the biosensors, see the appropriate biosensor product insert.


Starting a Quantitation Experiment

page 69

STARTING A QUANTITATION EXPERIMENT

NOTE: Before starting an experiment, check the plate temperature displayed in the status bar. Confirm that the temperature is appropriate for your experiment and if not, set a new temperature. If the Octet System Data Acquisition software is closed, the plate temperature will reset to the default startup value specified in the

Options


You can start a quantitation experiment by one of the following methods:

• Launch the


.

• Open a method file (.fmf ) by clicking

File

>


. Method files may be saved and recalled using the

File

menu and are automatically saved when an experi-

ment is run. For more details on method files see, “Managing Experiment Method

Files” on page 128.

• On the menu bar, click

Experiment

>

Templates

>

Quantitation

.



Starting an Experiment Using the Experiment Wizard

To start an experiment using the


:

1.

If the


is not displayed when the software is launched, click the


toolbar button or click

Experiment

>


(

Ctrl

+

N

) from the

Main Menu

.

2.

In the


, select

New Quantitation Experiment

(see Figure 5-1 left).

3.

Select a type of quantitation experiment (see Table 5-2 for options).

Table 5-2:

Quantitation Experiment Selection

Quantitation Experiment Description

Basic Quantitation A standard quantitation assay.

Basic Quantitation with

Regeneration

A standard quantitation assay that enables regeneration of biosensors.


page 70

Chapter 5:


and QK

Table 5-2:



Advanced Quantitation A standard two- or three-step quantitation assay that enables signal amplification for higher detection sensitivity.

Figure 5-1:

Selecting an Experiment Type in the Experiment Wizard (for Octet RED96)

4.

Click the arrow.

The

Experiment

dialog box displays (Figure 5-1 right).

DEFINING THE SAMPLE PLATE

Table 5-3 lists the steps to define a sample plate.

Table 5-3:

Defining a Sample Plate

Step

1.

Designate the samples.

See Page

70

2.

Annotate the samples (optional).

82

3.

Save the sample plate definition (optional).

88


Defining the Sample Plate

page 71

Designating Samples

Each well may be designated as a

Standard

,

Unknown

,

Control

, or

Reference

. A well may also remain

Unassigned

or be designated as

Reserved

by the system for Basic Quantitation with Regeneration and Advanced Quantitation experiments.

NOTE: It is important to define all of the wells that will be used in the assay.

Only wells that are selected and defined using one of the sample types in

Table 5-4 will be included in the assay.

Table 5-4:

Types of Sample Wells

Icon Description

Contains an analyte of known concentration. Data from the well is used to generate a standard curve during analysis.

Contains an analyte of unknown concentration. The concentration of the analyte is calculated from the well data and the standard curve.

A control sample, either positive or negative, of known analyte composition. Data from the well is not used to generate a standard curve during analysis.

• Positive Control: A control sample that contains analyte of known concentration

• Negative Control: A control sample known not to contain

 analyte

Provides a baseline signal which serves as a reference signal for

Unknowns

,

Controls

, and

Standards

. The reference signal can be subtracted during data acquisition in the

Runtime Binding Chart

and during data analysis.

Not used during the experiment.

Used by the system during Basic Quantitation with Regeneration experiments and Advanced Quantitation multi-step experiments for

Regeneration

(R),

Neutralization

(N), or

Detection

(D). Reserved wells are not available for use as

Standards

,

Unknowns

, Controls, or

References

.


page 72

Chapter 5:


and QK

Reserved Wells

In a Basic Quantitation with Regeneration or an Advanced Quantitation experiment, the


includes gray wells. These wells are reserved by the system and specify the location of particular sample types.

Reserved samples cannot be removed from the sample plate, but you can change their column location. To change the location of a reserved column ( , , or ) right-click a column header in the


and select

Regeneration

,

Neutralization

, or

Detection

.

Table 5-5:

Reserved Well Requirements

Reserved Well

Regeneration

Neutralization

Detection

Must Contain

Regeneration buffer that is used to remove analyte from the biosensor (typically low pH, high pH, or high ionic strength).

Neutralization buffer that is used to neutralize the biosensor after the regeneration step.

Secondary antibody or precipitating substrate that is used with an enzyme-antibody conjugate to amplify the analyte signal.

Sample concentrations are computed using the binding data from the detection wells.

Basic Quantitation with Regeneration

Advanced Quantitation

Figure 5-2:

Default Locations for Reserved Wells in a 96-Well Sample Plate Map



page 73

Selecting Wells in the Sample Plate Map

There are several ways to select wells in the

Sample Plate Map:

• Click a column header or select adjacent column headers by click-hold-drag

(Figure 5-3 left). To select non-adjacent columns, hold the Ctrl key and click the col-

umn header.

•

Click a row header or select adjacent row headers by click-hold-drag (Figure 5-3, cen-

ter).

•

Click a well or draw a box around a group of wells (Figure 5-3, right).

Figure 5-3:


NOTE: Shift-clicking in the

Sample Plate Map

mimics the head of the instrument during the selection.

Designating Standards

To designate standards:

1.

In the


, select the wells to define as standards.

2.

Click the

Standard

button below the


(see Figure 5-3), or right-click

and select

Standard

.

The standards are marked in the plate map and the


is updated.

3.

Select the concentration units for the standards using the

Concentration Units

dropdown list above the


.


page 74

Chapter 5:


and QK

Concentration Units

Standard

Button

Figure 5-4:

Plate Definition Window—Designating Standards

To remove a well designation, select the well(s) and click

Unassigned

. Or, right-click the well(s) and select

Clear Data

.

Assigning Standard Concentrations Using a Dilution Series

To assign standard concentrations using a dilution series:

1.

In the


, select the standard wells, right-click and select

Set Well

Data.

The

Set Well Data

dialog box displays (see Figure 5-5).



page 75

Figure 5-5:

Sample Plate Map—Setting a Dilution Series

2.

Select the

Dilution Series

option and enter the starting concentration value.

3.

Select a series operator, enter an operand, and select the appropriate dilution orienta-

tion (see Figure 5-6).

Highest

Concentration

Lowest

Concentration

Figure 5-6:

Concentration Representation in Dilution Series

4.

Click

OK

.

The


will display the standard concentrations entered.


page 76

Chapter 5:


and QK

Assigning a User-Specified Concentration to Standards

To assign a user-specified concentration to standards:

1.

In the



Set Well

Data.

The

Set Well Data


Figure 5-7:

Sample Plate Map—Assigning a Standard Concentration

2.

Select the

By value


3.

Click

OK

. The



Editing an Individual Standard Concentration

To enter or edit an individual standard concentration, in the

Conc

column of the

Sample

Plate Table

, double-click the value and enter a new value (see Figure 5-8).



page 77

Figure 5-8:

Sample Plate Table—Shortcut Menu of Edit Commands

NOTE: Edit commands (

Cut, Copy, Paste, Delete

) and shortcut keys (Cut -

Ctrl+x, Copy - Ctrl+c, Paste - Ctrl+v, Undo - Ctrl+z) are available in the

Sample Plate Table

. To view edit commands, double-click the cell. This highlights the value and allows it to be edited. Next, right-click to view the edit menu.

NOTE: The right-click menu is context-dependant. Right-clicking on a cell where the value is not highlighted and in edit mode opens the

Sample Plate

Map

menu used to designate sample types.


page 78

Chapter 5:


and QK

Designating Unknowns

To designate unknowns in the


, select the wells to define as unknown, right-click and select

Unknown

. The unknown wells are marked in the plate map and the

sample plate table is updated (see Figure 5-9).

Figure 5-9:

Plate Definition Window—Designate Unknown Wells


Unassigned


Clear Data

.

Assigning a Dilution Factor or Serial Dilution to Unknowns

To assign a dilution factor or serial dilution to unknowns:

1.

In the


, select the unknown wells (see Figure 5-9).

2.

Right-click and select

Set Well Data

.

The

Set Well Data




page 79

Figure 5-10:

Sample Plate Map—Setting a Dilution Factor or a Serial Dilution

To assign a dilution factor to selected wells:

1.

In the

Set Well Data

dialog box (see Figure 5-10), select the

By Value

option.

2.

Enter the dilution factor value and click

OK

.

To assign a serial dilution to selected wells:

1.

In the

Set Well Data


Dilution series

option.

2.

Enter the starting dilution, select a series operator, and enter a series operand.

3.

Select the appropriate dilution orientation: (see Figure 5-11).

Highest

Concentration

Lowest

Concentration

Figure 5-11:


4.

Click

OK

.

The


will display the dilution factors entered.


page 80

Chapter 5:


and QK

Editing a Dilution Factor in the Sample Plate Table

To edit a dilution factor in the


:

1.

In the

Set Well Data

dialog box (see Figure 5-10), double-click a cell in the

Dilution

Factor

column for the desired unknown.

2.

Enter the new value (the default dilution factor is 1)

Figure 5-12:









Sample Plate

Map




page 81

Designating Controls or Reference Wells

Controls are samples of known concentration that are not used to generate a standard curve. A reference well contains sample matrix only, and is used to subtract non-specific binding of the sample matrix to the biosensor. During data analysis, data from reference wells can be subtracted from standards and unknowns to correct for background signal.

• To designate controls, select the control wells and click

Control

(below the

Sample

Plate Map),

or right-click and select

Control

. Positive and Negative Control types can also be assigned using this menu.

• To designate reference wells, select the reference wells and click the

Reference

button below the

Sample Plate Map,

or right-click the selection and choose

Reference

.

The wells are marked in the


and the


is updated

(see Figure 5-12).

Figure 5-13:

Designate Controls or Reference Wells





Unassigned


Clear Data

.


page 82

Chapter 5:


and QK

Annotating Samples

You can enter annotations (notes) for multiple samples in the


or enter information for an individual sample in the


. For greater clarity, annotation text may be displayed as the legend of the


during data acquisition, but annotations must be entered before the experiment is started. If the annotation is entered after the experiment is started, it will not be available for display as a legend.

Annotating Wells in the Sample Plate Map

To annotate one or more wells:

1.

In the


, select the samples to annotate, right-click and select

Set

Well Data

.

2.

In the

Set Well Data

dialog box (see Figure 5-14), enter the

Sample ID

and/or

Well

Information

and click

OK

.

Figure 5-14:

Adding Sample Annotations from the Sample Plate Map

Annotating Wells in the Sample Plate Table

To annotate an individual well in the


:

1.

Double-click the table cell for

Sample ID

or

Well Information

.

2.

Enter the desired information in the respective field (see Figure 5-15).



page 83

NOTE: A series of Sample IDs may also be assembled in Excel and pasted into the


.

Figure 5-15:

Adding Sample Annotations in the Sample Plate Table








Sample Plate

Map



page 84

Chapter 5:


and QK

Replicate Groups

When samples are assigned to a

Replicate Group

, the Octet System Data Analysis software will automatically calculate statistics for all samples in that group. The average binding rate, average concentration and corresponding standard deviation as well CV% are presented in the

Results

table for each group (see Figure 5-16).

Figure 5-16:

Replicate Group Result Table Statistics

NOTE: Replicate Group information can also be entered in the Results table in the Octet System Data Analysis software.

Assigning Replicate Groups in the Sample Plate Map

To assign

Replicate Groups

in the


:

1.

Select the samples to group, right-click and select

Set Well Data

.

2.

In the

Set Well Data

dialog box (see Figure 5-17), enter a name in the

Replicate Group

box and click

OK

.



page 85

Figure 5-17:

Add Replicate Group from the Sample Plate Map

3.

Repeat the previous steps to assign new samples to the existing

Replicate Group

, or to designate another set of samples to a new

Replicate Group

. Multiple groups can be used in an experiment.

IMPORTANT: The Octet System Data Analysis software will only recognize and calculate statistics for samples that use the same Replicate Group names, spacing and capitalization must be identical. For example, samples assigned to Group 2 and group2 are treated as two groups.

NOTE: When performing a Multiple Analyte experiment, if the same Replicate

Group name is used with different biosensor types, they will be treated as separate groups. Statistics for these groups will be calculated separately for each biosensor type.

Wells in the


will show color-coded outlines as a visual indication of

which wells are in the same group (see Figure 5-18).


page 86

Chapter 5:


and QK

Figure 5-18:

Replicate Groups Displayed in Sample Plate Map

The


will update with the

Replicate Group

names entered (see

Figure 5-19).

Figure 5-19:

Replicate Groups in Sample Plate Table



Assigning Replicate Groups in the Sample Plate Table

To assign


in the


:

1.

Double-click the desired cell in the

Replicate Group

table column.

2.

Enter a group name (see Figure 5-20).

page 87

Figure 5-20:

Add Replicate Group from the Sample Plate Table








Sample Plate

Map


3.


Replicate Group


Replicate Group




page 88

Chapter 5:


and QK



MANAGING SAMPLE PLATE DEFINITIONS

NOTE: After you define a sample plate, you can export and save the plate definition for future use.

Exporting a Plate Definition

To export a plate definition:

1.

In the


(see Figure 5-21), click

Export

.

Figure 5-21:

Export Button in Sample Plate Table

2.

In the

Export Plate Definition

window (see Figure 5-22), select a folder, enter a name

for the plate (.csv), and click

Save

.


Managing Sample Plate Definitions

page 89

Figure 5-22:

Export Plate Definition Window

Importing a Plate Definition

To import a plate definition:

1.

In the



Import

.

Figure 5-23:

Import Button in Sample Plate Table

2.

In the

Import Plate Definition

window (see Figure 5-24), select the plate definition

(.csv), and click

Open

.


page 90

Chapter 5:


and QK

Figure 5-24:

Import Plate Definition Window

NOTE: You can also create a .csv file for import. Figure 5-25 shows the appro-

priate column information layout.

Figure 5-25:

Example Sample Plate File (.csv)


Managing Assay Parameter Settings

page 91

MANAGING ASSAY PARAMETER SETTINGS

Modifying Assay Parameter Settings

You can modify the assay parameter settings during sample plate definition. However, the changes are only applied to the current experiment. To save modified parameter settings,

you must define a new assay. For details on creating a new assay, see “Custom Quantitation

Assays” on page 129.

Viewing User-Modifiable Assay Parameter Settings

To view the user-modifiable settings for an assay, click

Modify

in the

Assay Settings

box.

The

Assay Parameters

box will display (Figure 5-26). The settings available are experimentdependent.

Figure 5-26:

Modifying Assay Parameters


page 92

Chapter 5:


and QK

Basic Quantitation Assay Parameters

Figure 5-27:

Assay Parameters—Basic Quantitation Assay

Table 5-6:

Basic Quantitation Assay Parameters

Parameter

Single analyte

Description

For single-analyte experiments using only one biosensor type per sample well.

Multiple analyte and

Replicates per sensor type

For multi-analyte experiments using multiple biosensor types per sample well, and the number of replicate assays in each well per biosensor type.

Quantitation Time (s) The duration of data acquisition seconds while the biosensor is incubated in sample.

NOTE: A subset of data points may be selected for processing during data analysis.

Quantitation Shake speed (rpm)

The sample platform orbital shaking speed (rotations per minute).



Basic Quantitation with Regeneration Assay Parameters

page 93

Figure 5-28:

Assay Parameters—Basic Quantitation with Regeneration

Table 5-7:


Parameter

Single analyte

Multiple analyte and Replicates per sensor type

Quantitation

Time(s) and Shake speed (rpm)

Description



The duration of data acquisition in seconds while the biosensor is incubated in sample and the sample platform orbital shaking speed (rotations per minute).


Regeneration


Neutralization


The duration time and shaking speed of the regeneration step where the biosensor is incubated in regeneration buffer to remove bound analyte.

The duration time and shaking speed of the neutralization step where the biosensor is incubated in neutralization buffer after the regeneration step.


page 94

Chapter 5:


and QK

Table 5-7:


Parameter

Pre-condition

 sensors

Post-condition sensors

Regeneration cycles



Description

Performs a set of regeneration/neutralization steps prior to the start of the experiment. The pre-conditioning settings are equivalent to the time and rpm settings for the regeneration in the assay. For example, an acidic pre-conditioning buffer maximizes the binding competence of Pro-A biosensors.

Post-conditions biosensors after Basic Quantitation with Regeneration, allowing re-racked biosensors to be stored in a regenerated state.

The number of regeneration-neutralization cycles that a biosensor undergoes before reuse.

Advanced Quantitation Assay Parameters

Figure 5-29:

Assay Parameters—Advanced Quantitation

Table 5-8:

Advanced Quantitation Assay Parameters

Parameter

Single analyte


Description





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Table 5-8:

Advanced Quantitation Assay Parameters (Continued)

Parameter

Sample Time(s) and

Shake speed (rpm)

Description



Buffer Time(s) and

Shake speed (rpm)

Enzyme Time(s) and Shake speed

(rpm)

2nd Buffer Time(s) and Shake speed

(rpm)

Detection Time(s) &

Shake speed (rpm)

The duration of biosensor incubation in the first buffer in seconds and the sample platform orbital shaking speed (rotations per minute).

The duration of biosensor incubation in seconds in the enzyme solution and the sample platform orbital shaking speed (rotations per minute).

The duration of biosensor incubation in seconds in the second buffer solution and the sample platform orbital shaking speed

(rotations per minute).

The duration of data acquisition during the detection step in seconds in an advanced quantitation assay.


Offline

Reuse Buffer

Regeneration


Neutralization


Choose this option to incubate sample with biosensors outside the Octet system. Offline incubation is best performed on the

ForteBio Sidekick biosensor immobilization station.

Allows buffer wells to be reused. If unselected, the number of buffer columns must equal the number of sample columns. If selected, the number of buffer columns may be less than the number of sample columns as the buffer columns are reused.




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Table 5-8:

Advanced Quantitation Assay Parameters (Continued)

Parameter

Pre-condition

 sensors


Regeneration cycles



Description

Performs a set of regeneration/neutralization steps prior to the start of the experiment. The pre-conditioning settings are equivalent to the time and rpm settings for the regeneration in the assay. For example, an acidic pre-conditioning buffer maximizes the binding competence of Protein A biosensors.



NOTE: In an Advanced Quantitation experiment, this option is only available if the first step (biosensor incubation in sample) is performed online.

ASSIGNING BIOSENSORS TO SAMPLES

After the sample plate is defined, biosensors must be assigned to the samples.

Biosensor Assignment in Single-Analyte Experiments

In a single analyte experiment, only one biosensor type is assigned to each sample and only one analyte is analyzed per experiment.

NOTE: For single analyte experiments, the

Single Analyte

option must be selected in the

Assay Parameters

dialog box. For more information, please

see “Managing Assay Parameter Settings” on page 91.

Click the


tab, or click the arrow to access the Sensor Assignment window (see Figure 5-30).

The software generates a color-coded

Sensor Tray Map

and


that shows how the biosensors are assigned to the samples by default.


Assigning Biosensors to Samples

page 97

Figure 5-30:

Sensor Assignment Window for Basic Quantitation without Regeneration

1.

Assign biosensors in one of two ways:

• Select a column(s) in the

Sensor Tray Map

, right-click and select a biosensor type from the drop-down list (see Figure 5-30 left).

• Select a cell in the

Sensor Type

table column, click the down arrow and select a biosensor type from the drop-down list (see Figure 5-30 right).

All wells in the

Sensor Type

column will automatically populate with the biosensor type selected.


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Figure 5-31:

Changing Biosensor Types in the Sensor Tray Map (left) and Sensor Type Column (right)

2.

To designate reference biosensors, select the desired biosensors in the

Sensor Tray

Map

, right-click and select

Reference

. The reference biosensors are marked with an

R

.

NOTE: Reference biosensors may also be designated in the

Runtime Binding

Chart

during acquisition.

3.

Optional: Double-click in any cell in the

Lot Number

column to enter the biosensor lot number. All wells in the

Lot Number

column will automatically populate with the lot number entered.

4.

Optional: Double-click in a cell in the

Information

column to enter biosensor information for a particular cell.

NOTE: Edit commands (



Ctrl+x, Copy - Ctrl+c, Paste - Ctrl+v, Undo - Ctrl+z) are available in the table.

To view edit commands, double-click the cell. This highlights the value and allows it to be edited. Next, right-click to view the edit menu.



page 99

NOTE: For greater clarity, annotation text may be displayed as the legend of the

Runtime Binding Chart

during data acquisition but annotations must be entered before the experiment is started. If the annotation is entered after the experiment is started, it will not be available for display as a legend.

5.

Optional for the Octet RED96 instrument only: After an assay is completed, the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container. To return the biosensors to the tray, click the

Replace sensors in tray after use

check box (see Figure 5-32).

Figure 5-32:

Replace Sensors in Tray After Use Check Box

NOTE: Biosensors can be regenerated up to a max of 11 times per experiment.



Biosensor Assignment in Multiple Analyte Experiments

In a multiple analyte experiment, more than one biosensor type is assigned to the same sample, allowing multiple analytes to be analyzed in a single experiment.

NOTE: For multiple analyte experiments, the

Multiple Analyte






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Click the




Sensor Tray Map

and


that shows how the biosensors are assigned to the samples by default. In the example shown in

Figure 5-30, one replicate had been previously selected with the

Multiple Analyte

assay parameter option.

Figure 5-33:

Sensor Assignment Window for Basic Quantitation Using the Multiple Analyte Option

There are two ways to assign biosensors:

• Select a column in the

Sensor Tray Map



Sensor Type




page 101

Figure 5-34:


Biosensor Assignment Using Heterogeneous Biosensor Trays

The default

Tray Format

is

Heterogeneous

. Heterogeneous biosensor trays contain a mixture of biosensor types.

NOTE: When using this

Heterogeneous

option, the order of biosensor types in each tray must be identical.

1.

If Heterogeneous Trays is not displayed next to the

Tray Format

button, click the button.

The

Tray Format


2.

Select

Heterogeneous

and click

OK

.


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Figure 5-35:

Tray Format Dialog Box

The Tray 1

Sensor Tray Map

will be displayed by default.

3.

Select all columns with default biosensor assignments in the

Sensor Tray Map

, rightclick and select the first biosensor type to be used (see Figure 5-36).

The

Sensor Type

column will update accordingly.

Figure 5-36:

Populating the Sensor Tray Map with First Biosensor Type

4.

Select the columns in the

Sensor Tray Map

that should contain the second biosensor

type, right-click and select the second biosensor type (see Figure 5-38).

The

Sensor Type




page 103

Figure 5-37:

Populating the Sensor Tray Map with Second Biosensor Type

5.

Repeat this column selection and assignment process for all other biosensor types to be used in the experiment. The software will automatically update the number of biosensor trays needed and biosensor assignments in all trays according to the column assignments made in Tray 1.

In the example shown in Figure 5-38, Protein A and Protein G biosensor types are used

for a multiple analyte experiment using two replicates. Three heterogeneous biosensor trays will be needed for the experiment.


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Figure 5-38:

Biosensor Assignment using Heterogeneous Trays and Two Biosensor Types

6.

To view or change the biosensor assignments in another tray, click the

Sensor Tray

button and select a tray number from the drop down list.

The

Sensor Tray Map

and table for the tray selected will be shown and biosensor assignments can be changed as needed (see Figure 5-39).



page 105

Figure 5-39:

Tray Selection

7.


Sensor Tray

Map


Reference

.

The reference biosensors are marked with an

R

.



Chart


8.


Lot Number

column to enter a biosensor lot number. All wells in the

Lot Number

column for that biosensor type will automatically populate with the lot number entered.

9.


Information











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10. Optional: After an assay is completed, the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container. To return the biosensors to the tray, click the


check box

(see Figure 5-40).

Figure 5-40:





Biosensor Assignment Using Homogeneous Trays

Homogeneous biosensor trays contain only one biosensor type.

NOTE: Using the

Homogeneous

option will necessitate switching trays during the experiment.

1.

Click

Tray Format

.

The

Tray Format

dialog box displays (see Figure 5-41) and the

Sensors

box will be populated with the default biosensor type.



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Figure 5-41:


2.

Select

Homogeneous

. Click

Add

to select the first biosensor type (see Figure 5-42).

Figure 5-42:

Selecting a Biosensor Type in the Tray Format Dialog Box

3.

Repeat this step to add any additional biosensor types that will be used in the experiment. To remove a biosensor type, select a biosensor type in the

Sensor

box and click

Remove.

4.

Adjust the order of biosensor types as needed by selecting the biosensor type in the

Sensor

box and clicking

Move Up

or

Move Down

.


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The order of biosensor types listed in the

Sensor

box will be used as the default tray assignment (see Figure 5-43).

Figure 5-43:

Biosensor Types List Order in Sensor Box

5.

Click

OK

.

The software will automatically calculate the number of biosensor trays needed and assign biosensors types to each tray.

In the example shown in Figure 5-44, Protein A and Protein G biosensor types will be used for the multiple analyte experiment using two replicates. Four homogeneous biosensor trays (two for each biosensor type) will be needed for the experiment. The Tray 1

Sensor Tray Map




page 109

Figure 5-44:

Biosensor Assignment using Homogeneous Trays and Two Biosensor Types

6.

To view the biosensor assignments in another tray, click the

Sensor Tray


The

Sensor Tray Map

and table for the tray selected will be shown (see Figure 5-39).


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Figure 5-45:

Tray Selection

7.


Sensor Tray

Map


Reference

.


R

.



Chart


8.


Lot Number

column to enter a biosensor lot number.

All wells in the

Lot Number

column for the biosensor type selected will automatically populate with the lot number entered.

9.


Information









page 111






check box

(see Figure 5-46).

Figure 5-46:





Biosensor Regeneration

For Basic Quantitation with Regeneration experiments only, the Sensor Assignment tab includes the Regenerations parameter, which specifies the maximum number of regeneration cycles for each column of biosensors. The specified number of regeneration cycles determines the minimum number of cycles required for each column of sensors. This calculation may result in non-equal regeneration cycles for columns of biosensors. The fractional use of the regeneration and neutralization wells by each column of sensors is represented by a pie chart (Figure 5-47).


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Figure 5-47:

Fractional Use of Regeneration and Neutralization Wells

Using Partial Biosensor Trays

If you are using a partial tray of biosensors (some biosensors are missing), specify the missing columns in the

Sensor Tray Map

:

1.

Select the column(s) without biosensors and click

Remove

, or right-click the selection and select

Remove

.

If the number of specified biosensors in the


tab is less than the number required to perform the assay, the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay.

2.

To view the additional biosensor tray that is required for the assay, select Tray 2 from the

Sensor Tray

drop-down list (Figure 5-48). In the example shown, Tray 1 is a partial tray that does not contain enough biosensors for the assay. To designate a second tray, select Tray 2 from the

Sensor Tray

drop-down list (Figure 5-48 top). The

Sensor Tray

Map

will then display the additional biosensors required for the assay (Figure 5-48 bottom).



page 113

Sensor

Tray Drop-

Down



List

Figure 5-48:

Example Assay Using One Partial Biosensor Tray and Biosensors from a Second Tray

To restore biosensors that have been removed, select the columns to restore and click

Fill

. To restore all sensors on the plate, click

Fill Plate

.

NOTE: If multiple biosensor trays are used, only the first biosensor tray can be a partial tray. During the experiment, the software prompts you to insert the appropriate tray in the Octet instrument.


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REVIEWING EXPERIMENTS

Before running an experiment, you can review the sample plate layout and the biosensors assigned to each assay in the experiment.

In the

Review Experiment

window, move the slider left or right to highlight the biosensors and samples in an assay, or click the arrows to select an assay.

Slider

Figure 5-49:

Review Experiment Window

SAVING EXPERIMENTS

After a run, the software automatically saves the experiment information that you specified

(sample plate definition, biosensor assignment, assay settings) to an experiment method file (.fmf ). If you set up an experiment, but do not start the run, you can manually save the experiment method.

To manually save an experiment method:

1.

Click the


button , or on the main menu, click

File

>

Save Method

File

. To save more than one open experiment, click the

Save All Methods Files

button

.

2.

In the

Save

dialog box, enter a name and location for the file, and click

Save

.


Saving Experiments

page 115

NOTE: If you edit a saved experiment and want to save it without overwriting the original file, select

File

>

Save Method File As

and enter a new name for the experiment.

Saving an Experiment to the Template Folder

If you save an experiment to the factory-installed Template folder, the experiment will be available on the menu bar. To view templates click

Experiment

>

Templates

>

Quantitation

>

Experiment Name (

see Figure 5-50).

Follow the steps above to save an experiment to the Template folder located at C:\Program

Files\ForteBio\DataAcquisition\TemplateFiles.

IMPORTANT: Do not change the location of the Template folder. If the Template folder is not at the factory-set location, the software may not function properly.

Figure 5-50:

Experiments in the Template Folder


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RUNNING A QUANTITATION EXPERIMENT

IMPORTANT: Before starting an experiment, ensure that the biosensors are properly rehydrated. For details on how to prepare the biosensors, see the appropriate biosensor product insert.

Loading the Biosensor Tray and Sample Plate

To load the biosensor tray and sample plate:

1.

Open the Octet instrument door (lift the handle up).

2.

Place the biosensor tray on the biosensor stage (left side) so that well A1 is located at

the upper right corner (see Figure 5-51).

3.

Place the sample plate on the sample stage (right side) so that well A1 is located at the

upper right corner (see Figure 5-51).

Well A1 Position

Figure 5-51:

Biosensor Stage (left) and Sample Stage (right)

IMPORTANT: Ensure that the bottom of the sample plate and biosensor tray are flat on each stage.

4.

Close the Octet instrument door.

5.

Allow the plate to equilibrate.

The time required for temperature equilibration depends on the temperature that your application requires and the initial temperature of the sample plate. For specific biosensor rehydration times, see the appropriate biosensor product insert.


Running a Quantitation Experiment

page 117

Starting an Experiment

To start the experiment:

1.

Click the

Run Experiment

tab, or click the arrow to access the Run Experiment win-

dow (see Figure 5-52).

Figure 5-52:

Run Experiment Window—Octet RED96

2.

Confirm the defaults or enter new settings. See “Run Experiment Window Settings” on page 119 for more information on experimental settings.

NOTE: If you delay the experiment start, you have the option to shake the plate until the experiment starts.

3.

To start the experiment, click .

If you specified a delayed experiment start, a message box displays the remaining time until the experiment starts.

If you selected the

Open runtime charts automatically

option, the

Runtime Binding

Chart

window displays the binding data in real-time and the experiment progress (see

Figure 5-53).


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NOTE: For more details about the


, see “Managing

Runtime Binding Charts” on page 122.

Figure 5-53:

Runtime Binding Chart

4.

Optional: Click

View

>


to view the log file (see Figure 5-54).

The experiment temperature is recorded at the beginning of every experiment as well as each time the manifold picks up a new set of biosensors. Instrument events such biosensor pick up, manifold movement, integration time, biosensor ejection and sample plate temperature are recorded in the log file.

WARNING: Do not open the Octet instrument door when an experiment is in progress. If the door is opened the data from the active acquisition step is lost.

The data acquired in previous steps is saved, however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning.



page 119

Figure 5-54:

Instrument Status Log

Run Experiment Window Settings

The following

Data File Location and Name

settings are available on the

Run Experiment

Tab:

Table 5-9:

Data File Location and Name

Item

Assay type

Quantitation data repository

Description

The name of the selected assay.

The location where quantitation data files (.frd) are saved. Click

Browse

to select another data location.

NOTE: It is recommended that you save the data to the local machine first, then transfer to a network drive.

Experiment Run name

(sub-directory)

Plate name/barcode

(file prefix)

2nd Plate name/barcode

Specifies a subdirectory name for the data files (.frd) that are created. The software generates one data file for each biosensor.

A user-defined field where you can enter text or a barcode

(barcode reader required).

A user-defined field where you can enter text or a barcode

(barcode reader required) for a second plate.


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Table 5-9:

Data File Location and Name (Continued)

Item

Auto Increment File ID

Start

Description

Each file is saved with a number after the plate name. For example, if the Auto Increment File ID Start number is 1, the first file name is xxx_001.frd.

The following

Run Settings

are available on the

Run Experiment

Tab:

Table 5-10:

Run Settings

Item

Delayed experiment start

Start after

Shake sample plate while waiting

Open runtime charts automatically

Automatically save runtime chart

Set plate temperature

(°C)

Description

Specifies a time delay for the start of the experiment.Enter the number of seconds to wait before the experiment starts after you click

.

Enter the number of seconds to delay the start of the experiment.

If the experiment has a delayed start time, this setting shakes the plate until the experiment starts.

Displays the


for the current biosensor during data acquisition.

Saves an image (.jpg) of the


. The binding data (.frd) is saved as a text file, regardless of whether a chart image is created.

Specifies a plate temperature and enters the temperature in the dialog box. If not selected, the plate temperature is set to the default temperature specified in

File > Options

. The factory set default temperature is 30 °C.

NOTE: If the actual plate temperature is not equal to the set plate temperature, a warning displays and the Octet System Data Acquisition software provides the option to wait until the set temperature is reached before proceeding with the run, continue without waiting until the set temperature is reached, or cancel the run.

Advanced settings are available for the Octet QK e

, Octet RED and Octet RED96 systems. The signal to noise ratio of the assay can be optimized by selecting different acquisition rates.

The acquisition rate refers to the number of binding signal data points reported by the

Octet system per second and is reported in Hertz (per second). A higher acquisition rate



page 121 generates more data points per second and monitors faster binding events better than a slower acquisition rate. A lower acquisition rate allows the software enough time to perform more averages of the collected data. Typically, more averaging leads to reduced noise and thus, better signal-to-noise ratios. Therefore, the frequency setting should be determined based on consideration of the binding rate, the amount of signal generated in your assay and some experimentation with the settings.

Table 5-11:

Advanced Settings for Octet QK e

, Octet RED and Octet RED96

Item

Acquisition rate,

Octet QK e

Acquisition rate,

Octet RED and

Octet RED96

Description

• High sensitivity quantitation (0.3 Hz, averaging by 40)—

The average of 40 data frames is reported as one data point. One data point is reported every 3.3 seconds.

• Standard quantitation (0.6 Hz, averaging by 5)—The average of five data frames is reported as one data point. One data point is reported every 1.6 seconds.

• High sensitivity quantitation (2 Hz, averaging by 50)—The average of 50 data frames is reported as one data point.

Two data points are reported per second.

• Standard quantitation (5 Hz, averaging by 20)—The average of 20 data frames is reported as one data point. Five data points are reported per second.

Recommended sensor offset for quantitation—3 mm Sensor offset

(mm)—Octet QK e only

Default Sets acquisition rate and sensor offset to the defaults.

The following

General Settings


Run Experiment

Tab:

Table 5-12:

General Settings

Item Description

Machine name The computer name that controls the Octet instrument and acquires the data.

User name

Description

The user logon name.

A user-specified description of the assay or assay purpose. The description is saved with the method file (.fmf ).


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Stopping an Experiment

To stop an experiment in progress, click or click

Experiment

>

Stop

.

The experiment is aborted. The data for the active biosensor is lost, the biosensor is ejected into the waste tray, and the event is recorded in the experimental log.

NOTE: After the experiment is run, the software automatically saves the experiment method (.fmf).

MANAGING RUNTIME BINDING CHARTS

If the


check box is selected in the Run Experiment window, the Runtime Binding Charts are automatically displayed when data acquisition

starts (see Figure 5-55). The


window displays the current step number, time remaining for the current step, (total) elapsed experimental time, and total experiment time.

The


is updated at the start of each experimental step. The active biosensor column is color-coded (A=green, B=magenta, C=orange, D=purple, E=olive, F= black, G=red, H=blue) within the

Sensor Tray Map

. Used sensor columns that are inactive are colored black. Active sample columns are colored green. Each data acquisition step is represented by

Sample Column X

in the

Current Binding Charts

box.

To selectively display acquisition data for a particular acquisition step:

1.

Click the corresponding

Sample Column

number.

2.

Select a sub-set of sensors for a displayed column under

Sensors to Chart

box (see

Figure 5-55).

WARNING: Do not close the


window until the experiment is complete and all data is acquired. If the window is closed, the charts are not saved. To remove the chart from view, minimize the window. The Octet

System Data Acquisition software saves the


as displayed at the end of the experiment. For example, modifying a chart by hiding the data for a particular biosensor will cause this data not to be included in the bitmap image generated at the end of the run.


Managing Runtime Binding Charts

page 123

Figure 5-55:

Runtime Binding Chart Window

Opening a Runtime Binding Chart

After an experiment is run, you can open and review the


at any time:

1.

Click

File

>

Open Experiment

.

2.

In the dialog box that appears, select an experiment folder and click

Select

.

Viewing Reference-Subtracted Data

If the experiment includes reference biosensors, you can display reference-subtracted data during acquisition in the chart by clicking the

Subtract reference sensors

check box in the chart window. To view raw data, remove the check mark next to this option.

Reference biosensors can be designated:

• During experiment setup in the


tab

• During acquisition in the Runtime Binding Chart


box

• During analysis in the

Data Selection

tab


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Designating a Reference Biosensor During Acquisition

To designate a reference biosensor during acquisition:

1.

In the


list or the

Sensor Tray

, right-click a biosensor and select

Reference

(see Figure 5-57).

Figure 5-56:

Designating a Reference Biosensor in the Runtime Binding Chart

The selected biosensor will be shown with an

R

in the


list and

Sensor

Tray (

see

Figure 5-57).

2.

Click the


check box

(

see

Figure 5-57).

Figure 5-57:

Subtract Reference Sensors check box in the Runtime Binding Chart

NOTE: Subtracting reference data in the


only makes a visual change to the data on the screen. The actual raw data is unaffected and the reference subtraction must be re-done in data analysis if needed.



page 125

Viewing Inverted Data

The data displayed in the


can be inverted during real-time data acquisition or data analysis after the experiment has completed. To invert data, select the

Flip Data

check box (see Figure 5-58). Uncheck the box to return to the default data display.

Figure 5-58:

Data Inverted Using Flip Data Function

Magnifying the Runtime Binding Chart

To magnify the chart, press and hold the mouse button while you draw a box around the chart area to magnify.

To undo the magnification, right-click the chart and select

Undo Zoom

.


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Scaling a Runtime Binding Chart

To scale the


:

1.

Right-click the chart and select

Properties

.

2.

In the

Runtime Graph Properties

dialog box, select

Fullscale

or

Autoscale

.

Adding a Runtime Binding Chart Title

To add a


title:

1.


Properties

.

2.

In the


dialog box, enter a graph title or subtitle.

Selecting a Runtime Binding Chart Legend

To select a


legend:

1.


Properties

.

2.

In the


dialog box (see Figure 5-59), select one of the fol-

lowing legends:

• Sensor Location

• Sample ID

• Sensor Information

• Concentration/Dilution

Figure 5-59:


3.

Click

OK

.

NOTE: Text for

Sample ID

,

Sensor Information

, or

Concentration/Dilution

is taken from the

Plate Definition

and

Sensor Assignment

tabs, and must be entered before the experiment is started.



Viewing Multiple Runtime Binding Charts

To view multiple Runtime Binding Charts, click

Window

>

New Window

.

Exporting or Printing the Runtime Binding Chart

To export the


as a graphic or data file:

1.


Export Data

.

2.

In the

Exporting

dialog box (see Figure 5-60), select the export options and click

Export

.

page 127

Figure 5-60:

Exporting Dialog Box

Table 5-13:

Runtime Binding Chart Export Options

Task Export Option Export



Destination

Text/

Data

EMF, WMF,

BMP, JPG, or PNG

Save the binding data

Export the

Runtime

Binding

Chart to a graphic file

Click

File

>

Browse

to select a folder and enter a file name.

Click

File

>

Browse


Result

Creates a tab-delimited text file of the numerical raw data from each biosensor. Open the file with a text editor such as Notepad.

Creates a graphic image.


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Table 5-13:

Runtime Binding Chart Export Options (Continued)




Destination

Clipboard Copy the

Runtime

Binding

Chart

Print the

Runtime

Binding

Chart

Printer

Result

Copies the chart to the system clipboard

Opens the Print dialog box.

MANAGING EXPERIMENT METHOD FILES

After you run an experiment, the Octet System Data Acquisition software automatically saves the method file (.fmf ), which includes the sample plate definition, biosensor assignment, and the run parameters. An experiment method file provides a convenient initial template for subsequent experiments. Open a method (.fmf ) and edit it if necessary.



Table 5-14:

Managing Experiment Method Files

Menu Bar Command/

Toolbar Button

File

>

Open Method

File

File

>

Save Method

File

or

File

>

Save Method

File As

Description

Enables you to select and open a method file (.fmf )

Saves one method file or all method files. Saves a method file before the experiment is run.

Saves a method file to a new name so that the original file is not overwritten.


Custom Quantitation Assays

CUSTOM QUANTITATION ASSAYS

Defining a Custom Assay

To define a custom assay:

1.

Click

Experiment

>


.

The


dialog box appears; see Figure 5-61.

page 129

Figure 5-61:

Edit Assay Parameters Dialog Box

2.

In the directory tree of assays, select the type of standard assay to modify. For example, to define a new basic quantitation assay, in the Basic Quantitation folder, select

Standard Assay

.

3.

Click

Duplicate

.

4.

In the

New Assay

dialog box (see Figure 5-62 top), enter an

Assay name

.

5.

Optional: In the

Assay Description

, enter information about the assay.

6.

Click

Save

.

The new assay appears in the directory tree of available assays (see Figure 5-62 bottom).


page 130

Chapter 5:


and QK

Figure 5-62:

Defining a New Assay



page 131

Editing Assay Parameters

To edit assay parameters:

1.

In the


dialog box, confirm that the new assay is selected in

Available Assays

(see Figure 5-62 bottom).

2.

Modify the assay parameters as needed. A complete list of parameters for each type of quantitation experiment follows this procedure.

3.

Click

Save

to accept the new parameter values. The new assay is added to the system.

NOTE: Not all parameters are available for all of the assays.




Figure 5-63:


Table 5-15:


Parameter

Single analyte

Description



page 132

Chapter 5:


and QK

Table 5-15:

Basic Quantitation Assay Parameters (Continued)

Parameter Description











page 133

Figure 5-64:


Table 5-16:


Parameter

Single analyte


Quantitation


Description





Regeneration




page 134

Chapter 5:


and QK

Table 5-16:


Parameter

Neutralization


Pre-condition

 sensors


Regeneration cycles



Description








page 135

Figure 5-65:


Table 5-17:


Parameter

Single analyte


Sample Time(s) and

Shake speed (rpm)

Description





Buffer Time(s) and

Shake speed (rpm)



page 136

Chapter 5:


and QK

Table 5-17:


Parameter


(rpm)


(rpm)

Detection Time(s) &

Shake speed (rpm)

Description






Offline

Reuse Buffer

Regeneration


Neutralization


Pre-condition

 sensors













page 137

Table 5-17:


Parameter

Regeneration cycles

Description



Selecting a Custom Assay

You can select a custom assay when you define a sample plate.

To select a custom assay:

1.

In the


tab, click

Modify

in the

Assay Settings

box.

The



Figure 5-66:

Selecting a Custom Assay

2.

Select the custom assay from the directory tree and click

OK

.


page 138

Chapter 5:


and QK


page 139

CHAPTER 6:



Quantitation Experiments:



Octet RED384 and QK384

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140

Starting a Quantitation Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

Defining the Sample Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

Managing Sample Plate Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Working with a Reagent Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

Managing Assay Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

Assigning Biosensors to Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173



Running a Quantitation Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193

Managing Runtime Binding Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199


Custom Quantitation Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206

page 140

Chapter 6:

Quantitation Experiments: Octet RED384 and QK384

INTRODUCTION

A quantitation experiment enables you to determine analyte concentration within a sample using a reference set of standards. After starting the Octet system hardware and the

Octet System Data Acquisition software, follow the steps (in Table 6-1) to set up and analyze

a quantitation experiment.

Table 6-1:

Setting Up and Analyzing a Quantitative Experiment

Software

Data



Acquisition

Step

1.

Select a quantitation experiment in the



2.


3.

Define a or import a reagent plate

(optional) for a Basic Quantitation with Regeneration experiment or an

Advanced Quantitation experiment).

4.

Confirm or edit the assay settings.

See

“Starting a Quantitation



“Working with a Reagent

Plate” on page 165

5.


6.

Run the experiment.

Data Analysis 7.

Analyze the binding data.

8.

Generate a report.

“Modifying Assay Parameter Settings” on page 167



“Running a Quantitation





Starting a Quantitation Experiment

page 141

STARTING A QUANTITATION EXPERIMENT

NOTE: Before starting an experiment, check the plate temperature displayed in the status bar. Confirm that the temperature is appropriate for your experiment and if not, set a new temperature. If the Octet System Data Acquisition software is closed, the plate temperature will reset to the default startup value specified in the

Options


You can start a quantitation experiment using one of the following options:

• Launch the


.


File

>



File


ment is run. For more details on method files see “Managing Experiment Method



Experiment

>

Templates

>

Quantitation

.




To start an experiment using the


:

1.

If the




toolbar button or click

Experiment

>


(

Ctrl

+

N

) from the

Main Menu

.

2.

In the


, select

New Quantitation Experiment

(see Figure 6-1, left).

3.

Select a type of quantitation experiment (see Table 6-2 for options).

Table 6-2:



Basic Quantitation A standard quantitation assay.

Basic Quantitation with

Regeneration

A standard quantitation assay that enables regeneration of biosensors.


page 142

Chapter 6:


Table 6-2:



Advanced Quantitation A standard two-or three-step quantitation assay that enables signal amplification for higher detection sensitivity.

Read Head Setting

Figure 6-1:

Selecting an Experiment Type in the Experiment Wizard (for Octet RED384)

4.

Click the arrow.

The

Experiment

window displays (Figure 6-1, right).


Table 6-3 lists the steps to define a sample plate.

Table 6-3:

Defining a Sample Plate

Step See Page

1.

Select the instrument read head configuration (8 or 16 channels).

143

2.

Select the sample plate format (96 or 384 wells).

3.


144

144

4.

Annotate the samples (optional).

5.


157

163



page 143

Read Head Configuration and Plate Layout

The Octet read head contains the collection optics. If the read head is set to 8 channels, one column of 8 biosensors interrogate 8 plate wells. If the read head is set to 16 channels, two

columns of biosensors interrogate 16 wells (Figure 6-1).

The read head configuration and the plate format (96 or 384 wells) determine the plate lay-

out (Figure 6-2).

8 Channel Read Head


Biosensors interrogate 8 wells in a column, one column is interrogated at a time.

Biosensors interrogate 16 wells in two columns. Columns 1 & 2 are interrogated at the same time. Columns

3 & 4 are interrogated at the same time, and so on.

Figure 6-2:

Color-Coded Wells Display How Biosensors Interrogate a 96-well Plate, 8 Channel or 16-Channel Read Head






Figure 6-3:

Color-Coded Wells Display How Biosensors Interrogate a 384-well Plate, 8 Channel or



16 Channel Read Head


page 144

Chapter 6:


NOTE: Keep the read head configuration in mind when laying out the sample plate. While reading a 384-well sample plate, both the 8 channel and 16 channel read heads can freely step through the plate by either moving left or right to step across columns or step one row up or down.

Changing the Plate Format

To change the sample plate format:

1.

Click the

Modify

button above the plate map.

2.

In the

Modify Plates

box, select

96 Well

or

384 Well

format.

Figure 6-4:

Changing the Sample Plate Format

NOTE: In Basic Quantitation with Regeneration and Advanced Quantitation experiments, a reagent plate format option is also available. Please refer to

“Working with a Reagent Plate” on page 165 for more information.


Each well may be designated as a

Standard

,

Unknown

,

Control

, or

Reference

. A well may also remain

Unassigned

or be designated as

Reserved

by the system for Basic Quantitation with Regeneration and Advanced Quantitation experiments.



page 145




Table 6-4:



Contains an analyte of known concentration. Data from the well is used to generate a standard curve during analysis.

Contains an analyte of unknown concentration. The concentration of the analyte is calculated from the well data and the standard curve.




 analyte

Provides a baseline signal which serves as a reference signal for

Unknowns

,

Controls

, and

Standards

. The reference signal can be subtracted during data acquisition in the


and during data analysis.

Not used during the experiment.

Used by the system during Basic Quantitation with Regeneration experiments and Advanced Quantitation multi-step experiments for

Regeneration

(R),

Neutralization

(N), or

Detection

(D). Reserved wells are not available for use as

Standards

,

Unknowns

, Controls, or

References

.


page 146

Chapter 6:


Reserved Wells

In a Basic Quantitation with Regeneration or an Advanced Quantitation experiment, the


includes gray wells. These wells are reserved by the system and specify the location of particular sample types. The default location of the reserved wells depends on the sample plate format (96 or 384-wells) and the Octet instrument read head configuration (8 or 16 channels).

Reserved samples cannot be removed from the sample plate, but you can change their column location. To change the location of a reserved column ( , , or ) right-click a column header in the


and select

Regeneration

,

Neutralization

, or

Detection

.

Table 6-5:

Reserved Well Requirements

Reserved Well

Regeneration

Neutralization

Detection

Must Contain

Regeneration buffer that is used to remove analyte from the biosensor (typically low pH, high pH, or high ionic strength).

Neutralization buffer that is used to neutralize the biosensor after the regeneration step.

Secondary antibody or precipitating substrate that is used with an enzyme-antibody conjugate to amplify the analyte signal.

Sample concentrations are computed using the binding data from the detection wells.





page 147

16 Channel

Read Head

8 Channel

Read Head



16 Channel

Read Head

8 Channel

Read Head

Figure 6-5:

Default Locations for Reserved Wells in 96-well (top) and 384-well Sample Plate Maps (bottom)


page 148

Chapter 6:





:


(Figure 6-6 left). To select non-adjacent columns, hold the Ctrl key and click the col-

umn header.

•


ter).

•




Figure 6-6:





Designating Standards

To designate standards:

1.

In the


, select the wells to define as standards.

2.

Click the

Standard

button below the


(see Figure 6-7), or right-click

and select

Standard

.

The standards are marked in the plate map and the


is updated.

3.

Select the concentration units for the standards using the

Concentration Units

dropdown list above the


.



Concentration units page 149

Standard

Button

Figure 6-7:

Plate Definition Window—Designating Standards


Unassigned


Clear Data

.

Assigning Standard Concentrations Using a Dilution Series

To assign standard concentrations using a dilution series:

1.

In the



Set Well

Data.

The

Set Well Data



page 150

Chapter 6:


Figure 6-8:

Sample Plate Map—Setting a Dilution Series

2.

Select the

Dilution Series


3.



Highest

Concentration

Lowest

Concentration

Figure 6-9:


4.

Click

OK

.

The





page 151

Assigning a User-Specified Concentration to Standards

1.

To assign a user-specified concentration to standards:

1.

In the



Set Well

Data.

The

Set Well Data


Figure 6-10:

Sample Plate Map—Assigning a Standard Concentration

2.

Select the

By value


3.

Click

OK

. The



Editing an Individual Standard Concentration

To enter or edit an individual standard concentration, in the

Conc

column of the

Sample

Plate Table

, double-click the value and enter a new value (see Figure 6-11).


page 152

Chapter 6:


Figure 6-11:









Sample Plate

Map




page 153

Designating Unknowns

To designate unknowns in the


, select the wells to define as unknown, right-click and select

Unknown

. The unknown wells are marked in the plate map and the


is updated (see Figure 6-12).

Figure 6-12:

Plate Definition Window—Designate Unknown Wells


Unassigned


Clear Data

.

Assigning a Dilution Factor or Serial Dilution to Unknowns

To assign a dilution factor or serial dilution to unknowns:

1.

In the


, select the unknown wells (see Figure 6-12).

2.

Right-click and select

Set Well Data

.

The

Set Well Data



page 154

Chapter 6:


Figure 6-13:

Sample Plate Map—Setting a Dilution Factor or a Serial Dilution

To assign a dilution factor to selected wells:

1.

In the

Set Well Data


By Value

option.

2.

Enter the dilution factor value and click

OK

.

To assign a serial dilution to selected wells:

1.

In the

Set Well Data


Dilution series

option.

2.

Enter the starting dilution, select a series operator, and enter a series operand.

3.

Select the appropriate dilution orientation (see Figure 6-14).

Highest

Concentration

Lowest

Concentration

Figure 6-14:


4.

Click

OK

.

The


will display the dilution factors entered.



page 155

Editing a Dilution Factor in the Sample Plate Table

To edit a dilution factor in the


:

1.

In the


(see Figure 6-15), double-click a cell in the

Dilution Factor

column for the desired unknown.

2.

Enter the new value (the default dilution factor is 1).

Figure 6-15:









Sample Plate

Map



page 156

Chapter 6:


Designating Controls or Reference Wells

Controls are samples of known concentration that are not used to generate a standard curve. A reference well contains sample matrix only, and is used to subtract non-specific binding of the sample matrix to the biosensor. During data analysis, data from reference wells can be subtracted from standards and unknowns to correct for background signal.

• To designate controls, select the control wells and click

Control

(below the

Sample

Plate Map),

or right-click and select

Control

. Positive and Negative Control types can also be assigned using this menu.

• To designate reference wells, select the reference wells and click the

Reference

button below the

Sample Plate Map,

or right-click the selection and choose

Reference

.

The wells are marked in the


and the


is updated

(see Figure 6-15).

Figure 6-16:

Designate Controls or Reference Wells






page 157


Unassigned


Clear Data

.











1.

In the



Set

Well Data

.

2.

In the

Set Well Data

dialog box (see Figure 6-17), enter

Sample ID

and/or


and click

OK

.

Figure 6-17:

Adding Sample Annotations from the Sample Plate Map




:

1.


Sample ID

or


.

2.



page 158

Chapter 6:




.

Figure 6-18:

Adding Sample Annotations in the Sample Plate Table








Sample Plate

Map




page 159


When samples are assigned to a

Replicate Group

, the Octet System Data Analysis software will automatically calculate statistics for all samples in that group. The average binding rate, average concentration and corresponding standard deviation as well CV% are presented in the

Results

table for each group (see Figure 6-19).

Figure 6-19:

Replicate Group Result Table Statistics

NOTE: Replicate Group information can also be entered in the Results table in the Octet System Data Analysis software.


To assign


in the


:

1.

Select the samples to group, right-click and select

Set Well Data

.

2.

In the

Set Well Data


Replicate Group

box and click

OK

.


page 160

Chapter 6:


Figure 6-20:


3.


Replicate Group


Replicate Group





Wells in the






page 161

Figure 6-21:


The



Replicate Group

names entered (see

Figure 6-22).

Figure 6-22:



page 162

Chapter 6:



To assign


in the


:

1.


Replicate Group

table column.

2.


Figure 6-23:









Sample Plate

Map


3.


Replicate Group


Replicate Group





page 163







1.

In the



Export

.

Figure 6-24:

Export Button in Sample Plate Table

2.

In the


window (see Figure 6-24), select a folder, enter a name for the plate (.csv), and click

Save

.


page 164

Chapter 6:


Figure 6-25:




1.

In the



Import

.

Figure 6-26:

Import Button in Sample Plate Table

2.

In the



(.csv), and click

Open

.


Working with a Reagent Plate

page 165

Figure 6-27:


NOTE: You can also create a .csv file for import. Figure 6-28 shows the appropriate column information layout.

Figure 6-28:

Example Sample Plate Definition File (.csv)

WORKING WITH A REAGENT PLATE

You can include an optional reagent plate in a Basic Quantitation with Regeneration or

Advanced Quantitation experiment. Using a reagent plate enables higher sample throughput since no reagents are included in the sample plate. A reagent plate can contain:

• Regeneration and neutralization reagents for Basic Quantitation with Regeneration experiments

• Buffers, enzyme solutions, and detection reagents for Advanced Quantitation experiments


page 166

Chapter 6:


An experiment can include any combination of sample and reagent plate formats (96- or

384-well). However, a reagent plate can include only reagent wells (regeneration, neutralization, detection). Wells for standards, unknowns, controls and references can not be assigned to the reagent plate.

NOTE: The reagent plate format (96- or 384-well) and the read head configuration (8 or 16 channels) determine the reagent plate layout. For more details,

see “Read Head Configuration and Plate Layout” on page 143.

To define a reagent plate:

1.

Select the

Reagent Plate

radio button above the plate map to display the

Reagent

Plate Map

(Figure 6-29).

2.

Click

Modify

to display the

Modify Plates

dialog box.

Figure 6-29:

Modifying the Reagent Plate

3.

Select a reagent plate format (

96 Well

or

384 Well

) and click

OK

.

4.

In the

Reagent Plate Map

, right-click a column to use and make a selection on the shortcut menu that appears:

• Advanced Quantitation—Select

Detection

.

• Basic Quantitation with Regeneration—Select

Regeneration

or

Neutralization

. Repeat this step to set both the regeneration and neutralization reagent columns.

The


then shows where to dispense the reagents in the plate

(Figure 6-30).



page 167

96-well Format Reagent Plate

384-well Format Reagent Plate

Figure 6-30:

Example Reagent Plate Layouts for an Advanced Quantitation Experiment—16 Channel

Read Head

To remove well designations, select the column(s) and click

Unassigned

, or right-click and choose

Clear Data

.

Saving a Reagent Plate Definition

Exporting and saving a reagent plate definition is done in the same manner as you would

for sample plates. For details “Managing Sample Plate Definitions” on page 163.

MANAGING ASSAY PARAMETER SETTINGS

Modifying Assay Parameter Settings

You can modify the assay parameter settings during sample plate definition. However, the changes are only applied to the current experiment. To save modified parameter settings,

you must define a new assay. For details on creating a new assay, see “Custom Quantitation

Assays” on page 206.

Viewing User-Modifiable Assay Parameter Settings

To view the user-modifiable settings for an assay, click

Modify

in the

Assay Settings

box.

The

Assay Parameters

box will display (Figure 6-31). The settings available are experiment-

dependent.


page 168

Chapter 6:


Figure 6-31:

Modifying Assay Parameters




page 169

Figure 6-32:


Table 6-6:


Parameter

Single analyte

Description










page 170

Chapter 6:



Figure 6-33:


Table 6-7:


Parameter

Single analyte


Quantitation


Description





Regeneration


Neutralization






page 171

Table 6-7:


Parameter

Pre-condition

 sensors


Regeneration cycles



Description





Figure 6-34:


Table 6-8:


Parameter

Single analyte


Description




page 172

Chapter 6:


Table 6-8:


Parameter

Sample Time(s) and

Shake speed (rpm)

Description



Buffer Time(s) and

Shake speed (rpm)


(rpm)


(rpm)

Detection Time(s) &

Shake speed (rpm)







Offline

Reuse Buffer

Regeneration


Neutralization









page 173

Table 6-8:


Parameter

Pre-condition

 sensors


Regeneration cycles



Description






After the sample plate is defined, biosensors must be assigned to the samples.

NOTE: When using a 96-well plate with the 8 channel read head, do not put biosensors in columns 2, 4, 6, 8, 10, and 12 if the biosensors will be returned to the biosensor tray and not discarded. If the biosensors will be ejected, biosensors can be placed in all columns.

Biosensor Assignment in Single-Analyte Experiments

In a single analyte experiment, only one biosensor type is assigned to each sample and only one analyte is analyzed per experiment.

NOTE: For single analyte experiments, the

Single Analyte





Click the




page 174

Chapter 6:



Sensor Tray Map

and


that shows how the biosensors are assigned to the samples by default.

Figure 6-35:

Sensor Assignment Window for Basic Quantitation without Regeneration

1.

Assign biosensors in one of two ways:

• Select column(s) in the

Sensor Tray Map



Sensor Type


All wells in the

Sensor Type




page 175

Figure 6-36:


2.


Sensor Tray

Map


Reference


R

.



Chart


3.


Lot Number


Lot Number

column will automatically populate with the lot number entered.

4.


Information








page 176

Chapter 6:





5.

Optional: After an assay is completed, the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container. To return the biosensors to the tray, click the


check box

(see Figure 6-37).

Figure 6-37:







page 177

Biosensor Assignment in Multiple Analyte Experiments

In a multiple analyte experiment, more than one biosensor type is assigned to the same sample, allowing multiple analytes to be analyzed in a single experiment.

NOTE: For multiple analyte experiments, the

Multiple Analyte





Click the




Sensor Tray Map

and


that shows how the biosensors are assigned to the samples by default. In the example shown in

Figure 6-35, one replicate had been previously selected with the

Multiple Analyte

assay parameter option.

Figure 6-38:

Sensor Assignment Window for Basic Quantitation Using the Multiple Analyte Option


page 178

Chapter 6:


There are two ways to assign biosensors:


Sensor Tray Map

, right-click and select a biosensor type from

the drop-down list (see Figure 6-39 left).


Sensor Type

table column, click the down arrow and select a bio-

sensor type from the drop-down list (see Figure 6-39 right).

Figure 6-39:


Biosensor Assignment Using Heterogeneous Biosensor Trays

The default

Tray Format

is

Heterogeneous

. Heterogeneous biosensor trays contain a mixture of biosensor types.

NOTE: When using this

Heterogeneous

option, the order of biosensor types in each tray must be identical.

1.

If Heterogeneous Trays is not displayed next to the

Tray Format

button, click the button.

The

Tray Format


2.

Select

Heterogeneous

and click

OK.



page 179

Figure 6-40:


The Tray 1

Sensor Tray Map


3.

Select all columns with default biosensor assignments in the

Sensor Tray Map

, right-

click and select the first biosensor type to be used (see Figure 6-41).

The

Sensor Type


Figure 6-41:

Populating the Sensor Tray Map with First Biosensor Type

4.

Select the columns in the

Sensor Tray Map

that should contain the second biosensor

type, right-click and select the second biosensor type (see Figure 6-43).

The

Sensor Type



page 180

Chapter 6:


Figure 6-42:

Populating the Sensor Tray Map with Second Biosensor Type

5.

Repeat this column selection and assignment process for all other biosensor types to be used in the experiment. The software will automatically update the number of biosensor trays needed and biosensor assignments in all trays according to the column assignments made in Tray 1.

In the example shown in Figure 6-43, Protein A and Protein G biosensor types are used

for a multiple analyte experiment using two replicates. Three heterogeneous biosensor trays will be needed for the experiment.



page 181

Figure 6-43:

Biosensor Assignment using Heterogeneous Trays and Two Biosensor Types

6.

To view or change the biosensor assignments in another tray, click the

Sensor Tray


The

Sensor Tray Map

and table for the tray selected will be shown and biosensor

assignments can be changed as needed (see Figure 6-44).


page 182

Chapter 6:


Figure 6-44:

Tray Selection

7.


Sensor Tray

Map


Reference

.


R

.



Chart


8.


Lot Number


Lot Number

column for that biosensor type will automatically populate with the lot number entered.

9.


Information












page 183



check box

(see Figure 6-37).

Figure 6-45:





Biosensor Assignment Using Homogeneous Trays

Homogeneous biosensor trays contain only one biosensor type.

NOTE: Using the

Homogeneous

option will necessitate switching trays during the experiment.

1.

Click

Tray Format

.

The

Tray Format

dialog box displays (see Figure 6-46) and the

Sensors

box will be populated with the default biosensor type.


page 184

Chapter 6:


Figure 6-46:


2.

Select

Homogeneous

. Click

Add

to select the first biosensor type (see Figure 6-47).

Figure 6-47:

Selecting a Biosensor Type in the Tray Format Dialog Box

3.

Repeat this step to add any additional biosensor types that will be used in the experiment. To remove a biosensor type, select a biosensor type in the

Sensor

box and click

Remove.

4.

Adjust the order of biosensor types as needed by selecting the biosensor type in the

Sensor

box and clicking

Move Up

or

Move Down

.



page 185

The order of biosensor types listed in the

Sensor

box will be used as the default tray

assignment (see Figure 6-48).

Figure 6-48:

Biosensor Types List Order in Sensor Box

5.

Click

OK

.

The software will automatically calculate the number of biosensor trays needed and assign biosensors types to each tray.

In the example shown in Figure 6-49, Protein A and Protein G biosensor types will be

used for the multiple analyte experiment using two replicates. Four homogeneous biosensor trays (two for each biosensor type) will be needed for the experiment. The Tray 1

Sensor Tray Map



page 186

Chapter 6:


Figure 6-49:

Biosensor Assignment using Homogeneous Trays and Two Biosensor Types

6.

To view the biosensor assignments in another tray, click the

Sensor Tray


The

Sensor Tray Map

and table for the tray selected will be shown (see Figure 6-44).



page 187

Figure 6-50:

Tray Selection

7.


Sensor Tray

Map


Reference

.


R

.



Chart


8.


Lot Number


Lot Number

column for the biosensor type selected will automatically populate with the lot number entered.

9.


Information

column to enter biosensor information for particular cell.










page 188

Chapter 6:




check box

(see Figure 6-37).

Figure 6-51:





Biosensor Regeneration

For Basic Quantitation with Regeneration experiments only, the Sensor Assignment tab includes the Regenerations parameter, which specifies the maximum number of regeneration cycles for each column of biosensors. The specified number of regeneration cycles determines the minimum number of cycles required for each column of sensors. This calculation may result in non-equal regeneration cycles for columns of biosensors. The fractional use of the regeneration and neutralization wells by each column of sensors is represented by a pie chart (Figure 6-52).



page 189

Figure 6-52:

Fractional Use of Regeneration and Neutralization Wells


If you are using a partial tray of biosensors (some biosensors are missing), specify the missing columns in the

Sensor Tray Map

:

1.

Select the column(s) without biosensors and click

Remove

, or right-click the selection and select

Remove

.

If the number of specified biosensors in the


tab is less than the number required to perform the assay, the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay.

2.

To view the additional biosensor tray that is required for the assay, select Tray 2 from the

Sensor Tray

drop-down list (Figure 6-53). In the example shown, Tray 1 is a partial tray that does not contain enough biosensors for the assay. To designate a second tray, select Tray 2 from the

Sensor Tray

drop-down list (Figure 6-53 top). The

Sensor Tray

Map

will then display the additional biosensors required for the assay (Figure 6-53 bottom).


page 190

Chapter 6:


Sensor

Tray Drop-

Down



List

Figure 6-53:

Example Assay Using One Partial Biosensor Tray and Biosensors from a Second Tray

To restore biosensors that have been removed, select the columns to restore and click

Fill

. To restore all sensors on the plate, click

Fill Plate

.

NOTE: If multiple biosensor trays are used, only the first biosensor tray can be a partial tray. During the experiment, the software prompts you to insert the appropriate tray in the Octet instrument.


Reviewing Experiments

page 191


Before running an experiment, you can review the sample plate layout and the biosensors assigned to each assay in the experiment.

In the


window, move the slider left or right to highlight the biosensors and samples in an assay, or click the arrows to select an assay.

Slider

Figure 6-54:


SAVING EXPERIMENTS

After a run, the software automatically saves the experiment information that you specified

(sample plate definition, biosensor assignment, assay settings) to an experiment method file (.fmf ). If you set up an experiment, but do not start the run, you can manually save the experiment method.

To manually save an experiment method:

1.

Click the


button , or on the main menu, click

File

>

Save Method

File

. To save more than one open experiment, click the

Save All Methods Files

button

.

2.

In the

Save


Save

.


page 192

Chapter 6:


NOTE: If you edit a saved experiment and want to save it without overwriting the original file, select

File

>

Save Method File As



If you save an experiment to the factory-installed Template folder, the experiment will be available for selection. To view templates, click

Experiment

>

Templates

>

Quantitation

>

Experiment Name

(see Figure 6-55).

Follow the steps above to save an experiment to the Template folder located at C:\Program

Files\ForteBio\DataAcquisition\TemplateFiles.

IMPORTANT: Do not change the location of the Template folder. If the Template folder is not at the factory-set location, the software may not function properly.

Figure 6-55:

Experiments in the Template Folder



page 193

RUNNING A QUANTITATION EXPERIMENT

IMPORTANT: Before starting an experiment, ensure that the biosensors are properly rehydrated. For details on how to prepare the biosensors, see the appropriate biosensor product insert.

Loading the Biosensor Tray, Sample and Reagent Plates

To load the biosensor tray, sample plate, and reagent plate:

1.

Open the Octet instrument door (lift the handle up) and present the instrument stage

(click the

Present Stage

button ).

2.

Place the biosensor tray, sample plate, and reagent plate on the appropriate stage so

that well A1 is located at the upper right corner (see Figure 6-56):

a. Place the rehydration plate and biosensor tray on the biosensor stage (left platform). b. Place the sample plate on the sample stage (middle platform).

c. Optional: Place the reagent plate on the reagent stage (right platform) if you are using a reagent plate.

Well A1 Position

Biosensor Tray & Rehydration Plate Stage

Sample Plate

Stage

Reagent Plate

Stage

Figure 6-56:

Octet Instrument t Stage Platform

IMPORTANT: Ensure that the bottom of the sample plate, reagent plate, biosensor tray and rehydration plate are flat on each stage.

3.

Click to close the Octet instrument door.

4.



page 194

Chapter 6:



Starting an Experiment


1.

Click the

Run Experiment

tab, or click the arrow to access the Run Experiment win-

dow (see Figure 6-57).

Figure 6-57:


2.

Confirm the defaults or enter new settings. See “Run Experiment Window Settings” on page 196 for more information on experimental settings.


3.





page 195

If you selected the


option, the

Runtime Binding

Chart

window displays the binding data in real-time and the experiment progress (see

Figure 6-58).



, see “Managing

Runtime Binding Charts” on page 199.

Figure 6-58:


4.

Optional: Click

View

>




WARNING: Do not open the Octet instrument door when an experiment is in progress. If the door is opened the data from the active acquisition step is lost.

The data acquired in previous steps is saved, however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning.


page 196

Chapter 6:


Figure 6-59:



The following



Run Experiment

Tab:

Table 6-9:


Item

Assay type

Quantitation data repository

Description


The location where quantitation data files (.frd) are saved. Click

Browse



Experiment

Run Name

(sub-directory)

Plate name/ barcode (file prefix)


Specifies a subdirectory name for the data files (.frd) that are created.

The software generates one data file for each biosensor.

A user-defined field where you can enter text or a barcode (barcode reader required).

A user-defined field where you can enter text or a barcode (barcode reader required) for a second plate.



page 197

Table 6-9:

Data File Location and Name (Continued)

Item


Start

Description


The following

Run Settings


Run Experiment

Tab:

Table 6-10:

Run Settings

Item


Start after




Set plate temperature (°C)

Description

Specifies a time delay for the start of the experiment. Enter the number of seconds to wait before the experiment starts after you click

.



Displays the







File > Options


NOTE: If the actual plate temperature is not equal to the set plate temperature, a warning displays and the

Octet System Data Acquisition software provides the option to wait until the set temperature is reached before proceeding with the run, continue without waiting until the set temperature is reached, or cancel the run.

Advanced settings are available for Octet RED384 and Octet QK384 systems. The signal to noise ratio of the assay can be optimized by selecting different acquisition rates. The acquisition rate refers to the number of binding signal data points reported by the Octet system per second and is reported in Hertz (per second). A higher acquisition rate generates more


page 198

Chapter 6:

Quantitation Experiments: Octet RED384 and QK384 data points per second and monitors faster binding events better than a slower acquisition rate. A lower acquisition rate allows the software enough time to perform more averages of the collected data. Typically, more averaging leads to reduced noise and thus, better signalto-noise ratios. Therefore, the frequency setting should be determined based on consideration of the binding rate, the amount of signal generated in your assay and some experimentation with the settings.

The following

Advanced Settings

are available for the Octet384 system:

Table 6-11:

Advanced Settings Octet RED384


Acquisition rate • High sensitivity quantitation (2.0 Hz, averaging by 50)—The average of 50 data frames is reported as one data point. Two data points are reported per second.

• Standard quantitation (5.0 Hz, averaging by 20)—The average of 50 data frames is reported as one data point. Five data points are reported per second.

• High concentration quantitation (10.0 Hz, averaging by 5)—

The average of 5 data frames is reported as one data point. Ten data points are reported per second.

Recommended sensor offset: Quantitation—3 mm Sensor off set

(mm)

Default Sets the acquisition speed and sensor offset at the default settings.

The following


are available for the OctetQK384 system:

Table 6-12:

Advanced Settings Octet QK384


Acquisition rate • High sensitivity quantitation (0.3 Hz, averaging by 40)—The average of 40 data frames is reported as one data point. One data point is reported every 3.3 seconds.

• Standard quantitation (0.6 Hz, averaging by 5)—The average of 5 data frames is reported as one data point. One data point is reported every 1.6 seconds.

Recommended sensor offset: Quantitation—3 mm Sensor off set

(mm)




page 199

The following



Run Experiment

Tab:

Table 6-13:

General Settings

Item


User name

Description

Description

The user logon name.




Experiment

>

Stop

.



MANAGING RUNTIME BINDING CHARTS

If the





window displays the current step number, time remaining for the current step, (total) elapsed experimental time, and total experiment time.

The



Sensor Tray Map

. Used sensor columns that are inactive are colored black. Active sample columns are colored green. Each data acquisition step is represented by

Sample Column X

in the


box.

To selectively display acquisition data for a particular acquisition step:

1.


Sample Column

number.

2.

Select a sub-set of sensors for a displayed column in the


box (see

Figure 6-60).


page 200

Chapter 6:








Figure 6-60:


Opening a Runtime Binding Chart



at any time:

1.

Click

File

>

Open Experiment

.

2.


Select

.



page 201


If the experiment includes reference biosensors, you can display reference-subtracted data during acquisition in the chart by clicking the


check box in the chart window. To view raw data, remove the check mark next to this option.




tab



box


Data Selection

tab



1.

In the


list or the

Sensor Tray


Reference

(see Figure 6-61).

Figure 6-61:



R

in the


list and

Sensor

Tray (

see

Figure 6-64).

2.

Click the


check box

(

see

Figure 6-64).

Figure 6-62:



page 202

Chapter 6:




only makes a visual change to the data on the screen. The actual raw data is unaffected and the reference subtraction must be re-done in data analysis if needed.





Flip Data


Figure 6-63:





Undo Zoom

.


To scale the


:

1.


Properties

.

2.

In the


dialog box, select

Fullscale

or

Autoscale

.



page 203


To add a


title:

1.


Properties

.

2.

In the




To select a


legend:

1.


Properties

.

2.

In the



lowing legends:

• Sensor Location

• Sample ID



Figure 6-64:


3.

Click

OK

.

NOTE: Text for

Sample ID

,


, or


is taken from the


and




page 204

Chapter 6:




Window

>

New Window

.


To export the



1.


Export Data

.

2.

In the

Exporting


Export

.

Figure 6-65:


Table 6-14:





Destination

Text/

Data

EMF, WMF,

BMP, JPG, or PNG


Export the

Runtime

Binding


Click

File

>

Browse


Click

File

>

Browse


Result




Managing Experiment Method Files

page 205

Table 6-14:





Destination

Clipboard Copy the

Runtime

Binding

Chart

Print the

Runtime

Binding

Chart

Printer

Result







Table 6-15:




File

>

Open Method

File

File

>

Save Method

File

or

File

>

Save Method

File As

Description





page 206

Chapter 6:


CUSTOM QUANTITATION ASSAYS

Defining a Custom Assay

To define a custom assay:

1.

Click

Experiment

>


.

The


dialog box appears (see Figure 6-66).

Figure 6-66:

Edit Assay Parameters Dialog Box

2.

In the directory tree of assays, select the type of standard assay to modify. For example, to define a new basic quantitation assay, in the Basic Quantitation folder, select

Standard Assay

.

3.

Click

Duplicate

.

4.

In the

New Assay

dialog box (see Figure 6-67 top), enter an

Assay name

.

5.

Optional: In the

Assay Description

, enter information about the assay.

6.

Click

Save

.

The new assay appears in the directory tree of available assays (see Figure 6-67 bottom).



page 207

Figure 6-67:

Defining a New Assay


page 208

Chapter 6:


Editing Assay Parameters

To edit assay parameters:

1.

In the


dialog box, confirm that the new assay is selected in

Available Assays

(see Figure 6-67 bottom).

2.

Modify the assay parameters as needed. A complete list of parameters for each type of quantitation experiment follows this procedure.

3.

Click

Save

to accept the new parameter values. The new assay is added to the system.

NOTE: Not all parameters are available for all of the assays.




Figure 6-68:


Table 6-16:


Parameter

Single analyte

Description




page 209

Table 6-16:

Basic Quantitation Assay Parameters (Continued)

Parameter Description









page 210

Chapter 6:



Figure 6-69:


Table 6-17:


Parameter

Single analyte


Quantitation


Description





Regeneration





page 211

Table 6-17:


Parameter

Neutralization


Pre-condition

 sensors


Regeneration cycles



Description






page 212

Chapter 6:



Figure 6-70:


Table 6-18:


Parameter

Single analyte


Sample Time(s) and

Shake speed (rpm)

Description





Buffer Time(s) and

Shake speed (rpm)




page 213

Table 6-18:


Parameter


(rpm)


(rpm)

Detection Time(s) &

Shake speed (rpm)

Description






Offline

Reuse Buffer

Regeneration


Neutralization


Pre-condition

 sensors












page 214

Chapter 6:


Table 6-18:


Parameter

Regeneration cycles

Description



Selecting a Custom Assay

You can select a custom assay when you define a sample plate.

To select a custom assay:

1.

In the


tab, click

Modify

in the

Assay Settings

box.

The



Figure 6-71:

Selecting a Custom Assay

2.

Select the custom assay from the directory tree and click

OK

.


page 215

CHAPTER 7:



Kinetics Experiments:



Octet RED96, QK e

and QK

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Starting a Basic Kinetics Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217



Defining a Kinetic Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236




Running a Kinetics Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260

Managing the Runtime Binding Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267



page 216

Chapter 7:

Kinetics Experiments: Octet RED96, QK e

and QK

INTRODUCTION

A basic kinetics experiment enables you to determine the association and dissociation rate of a molecular interaction. After starting the Octet system hardware and the Octet System

Data Acquisition software, follow the steps (in Table 7-1) to set up and analyze a quantitation experiment.

Table 7-1:

Setting Up and Analyzing a Kinetic Experiment

Software

Data



Acquisition

Step

1.

Select a kinetics experiment in the



2.


3.

Specify assay steps.

Data Analysis

4.

5.

6.

7.


Run the experiment.

View and process the raw data.

Analyze the data.

See

“Starting a Basic Kinetics



“Defining a Kinetic Assay” on page 236



“Running a Kinetics Experiment” on page 260



NOTE: Before starting an experiment, check the sample plate temperature displayed in the status bar. Confirm that the temperature is appropriate for your experiment and if not set a new temperature. If the Octet System Data Acquisition software is closed, the plate temperature will reset to the default startup value specified in the

Options

window when the software is relaunched.


Starting a Basic Kinetics Experiment

page 217

STARTING A BASIC KINETICS EXPERIMENT

You can start a kinetics experiment using one of the following options:

• Launch the


.


File

>



File





Experiment > Templates > Kinetics

.




1.

If the




toolbar button , or click

Experiment > New Experiment Wizard

(

Ctrl

+

N

) from the

Main Menu

.

2.

In the


, click

New Kinetics Experiment


3.

Click the arrow button( ). The

Basic Kinetics Experiment

window displays

(Figure 7-1, right).

Figure 7-1:

Starting a Kinetics Experiment with the Experiment Wizard


page 218

Chapter 7:


and QK


The steps to define a sample plate include:

Step

4.


5.



See Page

218

232




Table 7-2 displays the well types that can be assigned to a plate map.

Table 7-2:



Any type of sample. For example, an analyte.

Reference sample. For example, a buffer-only control biosensor that is used to correct for system drift.

A control sample, either positive or negative, of known analyte composition.



 analyte

Any type of buffer. For example, the buffer in a baseline, association, or dissociation step.

Activation reagent. Makes the biosensor competent for binding.

Quenching reagent. Blocks unreacted immobilization sites on the biosensor surface.

Ligand to be immobilized (loaded) on the biosensor surface.

Wash buffer.

Regeneration reagents dissociate the analyte from the ligand.



page 219




:

• Click a column header or select adjacent column headers by click-hold-drag. To select non-adjacent columns, hold the Ctrl key and click the column header

(Figure 7-2 left).

•


ter).

•


Figure 7-2:





Designating Well Types

In the


, select the wells, right-click and select a sample type (see

Figure 7-24).


page 220

Chapter 7:


and QK

Figure 7-3:

Designating a Well Type in the Plate Definition Window

To remove a well designation, in the


, select the well(s) and click

Remove


Clear Data

(see Figure 7-4).

Figure 7-4:

Clearing Sample Data from a Sample Plate



page 221

Entering Sample Information

NOTE: You must specify sample (analyte) concentration and molecular weight, otherwise the Octet System Data Acquisition software cannot compute a K

D

value. If the sample concentration is not specified, only k d

and k obs are calculated. You can also annotate any well with

Sample ID

or

Well Information,

and assign


.

Assigning Molecular Weight and Molar Concentration

1.

In the


, select the sample wells, right-click and select

Set Well Data

.

2.

In the

Set Well Data

dialog box, enter the analyte molecular and molar concentration

(Figure 7-5).

Molecular Weight and

Molar Concentration

Figure 7-5:

Entering Molecular Weight and Molar Concentration from the Sample Plate Map

The information displays in the


(see Figure 7-6).


page 222

Chapter 7:


and QK

3.

In the


, select the sample concentration units and the molar concentration units.

Concentration units

Figure 7-6:

Entering Molecular Weight and Molar Concentration from the Plate Table

Assigning User Specified Sample Concentrations

To assign sample concentrations using a dilution series:

1.

In the


, select the desired wells, right-click and select

Set Well

Data.

The

Set Well Data


2.

Select the

By value




page 223

Figure 7-7:

Sample Plate Map—Assigning Sample Concentrations by Value

3.

Click

OK

. The


will display the entered concentration.

Assigning Concentrations Using a Dilution Series


1.

In the


, select the wells, right-click, and select

Set Well Data

.

The

Set Well Data

dialog box displays (see Figure 7-8)

2.

Select the

Dilution Series



page 224

Chapter 7:


and QK

Figure 7-8:

Sample Plate Map—Assigning Sample Concentrations Using Dilution Series

3.



Highest

Concentration

Lowest

Concentration

Figure 7-9:


4.

Click

OK

.

The


displays the standard concentrations.



page 225











1.

In the



Set

Well Data

.

2.

In the

Set Well Data


Sample ID

and/or

Well

Information

and click

OK

.

Figure 7-10:

Add Sample Annotations from the Sample Plate Map


page 226

Chapter 7:


and QK




:

1.


Sample ID

or


.

2.




.

Figure 7-11:

Add Sample Annotations in the Sample Plate Table








Sample Plate

Map




enable data to be organized into custom groups during data analysis

(see Figure 7-12).



page 227

Figure 7-12:

Replicate Group Color-Coding

NOTE: Replicate Group information can also be entered in the Octet System

Data Analysis software.


To assign


in the


:

1.

Select the samples you wish to group, right-click and select

Set Well Data

.

2.

In the

Set Well Data


Replicate Group

box and click

OK

.


page 228

Chapter 7:


and QK

Figure 7-13:


3.


Replicate Group


Replicate Group


IMPORTANT: The Octet System Data Analysis software will only recognize and group samples that use the same Replicate Group names, spacing and capitalization must be identical. For example, samples assigned to Group 2 and group2 are treated as two groups.

Wells in the






page 229

Figure 7-14:


The



Replicate Group

names entered (see

Figure 7-15)

Figure 7-15:



To assign


in the


:

1.


Replicate Group

table column.

2.



page 230

Chapter 7:


and QK

Figure 7-16:


Edit commands (

Cut, Copy, Paste, Delete

) and shortcut keys (Cut - Ctrl+x, Copy - Ctrl+c,

Paste - Ctrl+v, Undo - Ctrl+z) are available in the


. To view edit commands, double-click the cell. This highlights the value and allows it to be edited. Next, rightclick to view the edit menu.


Sample Plate

Map


3.


Replicate Group


Replicate Group





page 231

Editing the Sample Table

Changing Sample Well Designations

To change a well designation, right-click the well in the


and make a

new selection (see Figure 7-17).

Figure 7-17:

Sample Plate Table—Well Designation

Editing Sample Information

To edit sample data in the


, double-click a value and enter a new value

(see Figure 7-18).


page 232

Chapter 7:


and QK

Figure 7-18:

Sample Plate Table—Editing Sample Data

Edit commands (






NOTE: The right-click menu is context-dependant. Right-clicking on a cell where the value is not highlighted and in edit mode opens the right-click menu used to designate sample types.







1.

In the


, click

Export

(see Figure 7-19).

page 233

Figure 7-19:

Sample Plate Map— Export Button

2.

In the


window (see Figure 7-20), select a folder, enter a name for the plate (.csv), and click

Save

.

Figure 7-20:



page 234

Chapter 7:


and QK



1.

In the Sample Plate Definition window (see Figure 7-19: on page 233), click

Import

.

Figure 7-21:

Sample Plate Map— Import Button

2.

In the



(.csv), and click

Open

.

Figure 7-22:


NOTE: You can also create a .csv file for import. Figure 7-23 shows the appropriate column information layout.



Figure 7-23:

Example Plate Definition File (.csv)

page 235


page 236

Chapter 7:


and QK

DEFINING A KINETIC ASSAY

After the sample plate is defined, the assay must be defined. The steps to define a kinetic assay include:

Step

1.

Define the step types.

2.

Build the assay by assigning a step type to a column(s) in the sample plate.

3.


See Page

236

241

232

Defining Step Types

Table 7-3 lists the example step types to define a kinetic assay. Use these examples as a

starting point to create your own step types.

Table 7-3:

Sample Step Types for Kinetic Assays

Step Type

Association

Step Description

Calculates the k obs

. Select this step type when binding the second protein of interest (analyte) to the biosensor. This step should be performed at 1,000 rpm.

Dissociation Calculates the k d

. Select this step type when monitoring the dissociation of the protein complex. This step should be performed at 1,000 rpm.

Baseline Can be used to align the data. Select this step type when establishing the biosensor baseline in the presence of buffer. This step can be performed with no flow (0 rpm). However, if the baseline step directly precedes an association step, perform the baseline step at 1,000 rpm.

Loading

IMPORTANT: An assay must include a baseline step followed by a set of association/dissociation steps to be analyzed. The Octet System Data Analysis software recognizes the baseline/association/dissociation step series during processing. Data cannot be processed if this sequence is not included in the assay setup.

Not used in data analysis. Select this step type when binding the first protein of interest (ligand) to the biosensor.

NOTE: This step may be performed offline (outside the

Octet instrument).


Defining a Kinetic Assay

page 237

Table 7-3:

Sample Step Types for Kinetic Assays (Continued)

Step Type

Custom

Activation

Quenching


Can be used for an activity not included in any of the above step types.

Used when employing a reagent to chemically prepare the biosensor for loading.

Used to render unreacted immobilization sites on the biosensor inactive.

Creating Step Types

Click the


tab, or click the arrow to access the Assay Definition window

(see Figure 7-24). The

Step Data List

shows the types of assay steps that are available to build an assay. By default, the list includes a baseline step.

To create different types of assay steps:

1.

Click

Add

.

2.

In

Assay Step Definition

dialog box (Figure 7-24), specify the step information:

a. Choose a step type.

b. Optional: Edit the step name.

c. Set the step time and shake speed (

Time

range: 2 to 48,000 seconds,

Shake speed

range: 100 to 1,500 rpm or 0).


page 238

Chapter 7:


and QK

Figure 7-24:

Creating an Assay Step Type

3.

Apply a threshold to the step: a. In the

Step Data List

, click the

Threshold

check box.

The

Threshold Parameters


b. Set the threshold parameters (refer to Table 7-4 for the parameter definitions).



page 239

Figure 7-25:

Setting Assay Step Threshold Parameters

NOTE: If thresholds are applied, the step is terminated when either the step time elapses or the threshold termination criteria is reached.

Table 7-4:

Threshold Parameters


Active Channels Specifies the instrument channels that monitor the threshold criteria for the assay step. Select an option for terminating the step:

• The threshold is achieved on ALL channels

• The threshold is achieved on ANY ONE channel

Signal Change

Gradient

The threshold is a user-specified amount of ascending or descending signal change (nm).

The threshold is a binding gradient (nm/min) for a user-specified time (min).

Filtering The amount of data (seconds) to average when computing the signal change or gradient threshold.


page 240

Chapter 7:


and QK

4.

Click

OK

to save the newly-defined step. The new step type appears in the

Step Data

List

.

5.

Repeat the previous steps for each step type to create until all the desired steps are

added (see Figure 7-26).

Figure 7-26:

Step Data List—Displaying Step Types

6.

To delete a step type from the list, click the corresponding row in the

Step Data List

and click

Remove

, or press the

Delete

key.

Copying and Editing Step Types

To define a step type by copying an existing one, click the step type (row) in the

Step Data

List

and click

Copy

. The copied step type appears at the end of the

Step Data List.

To define a step type by editing an existing one:

1.

Double-click the cell in the step’s

Name, Time

or

Shake speed

column and then enter a new value. Or, right-click the cell to display a shortcut menu of editing commands


NOTE: Keyboard commands can also be used (

Ctrl

+

x

=cut,

Ctrl

+

c

=copy,

Ctrl

+

v

=paste,

Ctrl

+

z

=undo).

2.

Click the cell in the step’s

Type

column, then select another name from the drop-down

list (see Figure 7-27, right).



page 241

Figure 7-27:

Editing a Step Value (left) or Step Type (right)

Building an Assay

After creating the different step types that the assay will use, step types are assigned to columns in the Sample Plate or Reagent Plate maps.

To build an assay:

1.

Select a step type in the

Step Data List

.

2.

In the


, double-click the column that is associated with the selected step type. For information about sample plate wells, mouse over a well to view a tool

tip (see Figure 7-28).

Figure 7-28:

Tool Tip of Well Information

The selected wells are marked with hatching (for example, ) and the step appears in the

Assay Steps List

(see Figure 7-29) with an associated

Assay Time

.


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2

1

New Assay Step

Figure 7-29:

Assigning a Step Type to a Column in the Sample Plate

3.

Repeat the previous steps to define each step in the assay. As each step is added, the total

Experiment

and

Assay Time

update (see Figure 7-30).

Total Experiment

Time

Figure 7-30:

Experiment and Assay Time Updates as Steps Are Added to the Assay

Total Assay Time



page 243

IMPORTANT: If you intend to analyze the data from a sample using the I

nterstep correction

feature in the Octet System Data Acquisition software, the assay must use the same well to perform baseline and dissociation for the sample.

Replicating Steps within an Assay

To copy steps and add them to an assay:

1.

In the


, select the step(s) to copy and click

Replicate

(for example, in

Figure 7-31, step rows 1–4 are selected).

• To select adjacent steps, press and hold the

Shift

key while you click the first and last step in the selection.

• To select non-adjacent steps, press and hold the

Ctrl

key while you click the desired steps.

2.

In the

Replicate Steps

dialog box (see Figure 7-31), click the

Append to current assay

option.

3.

Click the

Offset steps

check box and set the options, as appropriate. (For more details on offset options, see Table 7-5.)

Figure 7-31:

Replicating Assay Steps by Appending


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4.

Click

OK

. The step(s) appear at the end of the assay in the


.

Table 7-5:

Replicate Steps Options .

Item

Add as a new assay

Append to current assay

Offset steps

Sample steps only

All steps

Description

Adds the replicate step(s) as a new assay to the

Assay

Steps List

.

Adds the replicate step(s) to the end of the current assay.

Assigns the replicate steps to different columns in the sample plate.

Applies the offset to the sample plate only.

Applies the offset to the sample plate and reagent plate.

NOTE: Reagent plates are only available when using an Octet384 or Octet QK384 instrument.

Sample steps will be adjusted horizontally by X columns

Specifies the column in which to add the new step(s). For example, if a step in column 11 is copied and the replicate step should begin in column 12, enter

1

. Enter

0

to apply the step(s) to the same columns.

Applies only to the Octet384 or Octet QK384 instruments.

Sample steps will be adjusted vertically by one row

Starting a New Assay

A new assay will utilize a new set of biosensors. To start a new assay using the next available sensor column:

1.

Select a column in the


.

2.

Right-click to view the shortcut menu and select

Start New Assay

(see Figure 7-32).

3.

Add steps to the assay as described earlier.



page 245

Figure 7-32:

Start New Assay

Inserting or Adding an Assay Step

To insert an assay step:

1.

Select a step in the

Step Data List

.

2.

In the


, select the row above where you want to insert the step.

3.

In the


, right-click the column to which the step will be applied and select

Insert Assay Step

.

The step is inserted into the


.

To add an assay step:

1.


Step Data List

.

2.

In the


, right-click the column to which the step will be applied, and select

Add Assay Step

.

The step is added to the end of the


.


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Selecting a Biosensor for the Assay

To select the biosensor type associated with the assay, click the

Sensor Type

arrow ( ) for

any step in the assay and select a sensor type from the drop-down list (Figure 7-33). The

biosensor type will automatically update for every assay step.

Figure 7-33:

Selecting an Assay Sensor Type

NOTE: The

Sensor Type

for the assay must be selected or changed from the

Assay Steps List

. Changing the

Sensor Type

from the


Tab

will not update the assay.

Editing an Assay

To edit the step type or the biosensor type:

1.

In the


:

• To change the step type, click the

Step Name

arrow ( ) and select a step name from the drop-down list (Figure 7-34, top).

• To change the biosensor type, click the

Sensor Type

arrow ( ) for any step in the assay and select a sensor type from the drop-down list (Figure 7-34, bottom).

The biosensor type will automatically update for every assay step.

NOTE: The

Step Name

drop-down list includes only the step types defined in the

Step Data List

.



page 247

Figure 7-34:

Editing an Assay Step Name (top) or Sensor Type (bottom) in the Assay Steps List

To reorder or remove an assay step:

1.

Select a step (row) in the


.

2.

Click the

Move Up

,

Move Down

, or

Remove

button located above the list.

IMPORTANT: An assay must have a baseline step followed by a set of association/dissociation steps to be analyzed. The Octet System Data Acquisition software recognizes the baseline/association/dissociation set of steps.

Adding an Assay Through Replication

A sample plate can include multiple assays that are the same (replicates) or different. Each assay utilizes a new set of biosensors. Replicates within a single assay will therefore use the same biosensor and replicates in different assays will use different biosensors.

To add a replicate assay to a plate:

1.

In the


, select the steps to copy and click

Replicate

.


Shift



Ctrl

key while you click the steps.

2.

In the

Replicate Steps

dialog box, click the

Add as a new assay

option (Figure 7-35).


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Figure 7-35:

Adding a Replicate Assay to a Plate

3.

Click the

Offset steps

check box and set the options as appropriate (see Table 7-5 on page 244 for more information). If the replicate assay uses the same sample columns as the original assay, do not choose the

Offset steps

option. If the replicate assay uses a different sample column, select

Offset steps

and the appropriate options.

•

Sample steps only

offsets the sample wells by the value specified under

Sample steps will be adjusted

. The offset will not be applied to reagent wells such as buffer, loading, regeneration, neutralization and detection.

•

All Steps

offsets all wells in the assay, including sample and reagent wells, by the value specified under


.

4.

Click

OK

. The new assay appears in the


.

5.

Continue to add assay steps as needed.



page 249


After you define the sample plate and assay(s), click the


tab, or click the arrow to access the Sensor Assignment window. The color-coded

Sensor Tray

and


show the locations of the biosensors associated with the samples

Figure 7-36).

NOTE: If an experiment includes more than one type of biosensor, the software automatically creates a separate sensor tray for each type of biosensor. If the different types of biosensors are in the same tray, change the biosensor type as appropriate.

The biosensor types shown in the

Sensor Type

table column are those designated during

the kinetics assay definition. In the example shown in Figure 7-36, the experiment includes

three assays in the same wells. The use of those wells by three different biosensors is indicated by the pie chart colors.

NOTE: The

Sensor Type

for the assay must be first be defined in the

Assay

Steps List

on the

Assay Definition Tab

. Changing the

Sensor Type

from the

Sensor Assignment Tab



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Figure 7-36:

Sensor Assignment Window

Hover the cursor over a well in the

Sensor Tray Map

or


to display a tool tip with sample or biosensor information (see Figure 7-37).



page 251

Figure 7-37:


Replacing the Biosensors in the Biosensor Tray

After an assay is completed, the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container. To return the biosensors to the tray, click the



Figure 7-38:






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and QK

Entering Biosensor Information

To enter information about a biosensor:

1.


Lot Number


Lot Number

column for that biosensor type will automatically

populate with the lot number entered (see Figure 7-39).

2.

Optional: Double-click a cell in the

Information

table column. Enter or edit the biosen-

sor information as appropriate (see Figure 7-39).






Figure 7-39:

Entering or Editing Biosensor Information

Changing the Biosensor Location

If you prefer to not use the default biosensor columns, you can select other column(s) to use. There are two ways to do this:

• Method 1—In the

Sensor Tray Map

,

Remove

the columns you do not want to use.

The software automatically selects the next available column(s).

• Method 2—Remove all columns from the

Sensor Tray Map

, then select the columns you want to use.

Method 1

1.

In the

Sensor Tray Map

(see Figure 7-40), select the columns to not use and click

Remove

. Or, right-click the selection and select

Remove

(Figure 7-40 left). The software automatically selects the next available biosensor columns in the tray (Figure 7-40

right).



2.

Click

Fill Plate

to return the

Sensor Tray Map

to the default layout.

page 253

Figure 7-40:

Changing Biosensor Location (Method 1)

Method 2

1.

In the

Sensor Tray Map

, select all of the columns and click

Remove

(Figure 7-41 top

left). Or, right-click the selection and select

Remove

. All columns will be shown as

Missing

(Figure 7-41 top right).

2.

Select the column(s) to use and click

Fill


Fill

(Figure 7-41 bottom left). The software fills the selected columns in the tray

(Figure 7-41 bottom right).


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Chapter 7:


and QK

Figure 7-41:


Click

Fill Plate

to return the

Sensor Tray Map


Using Heterogenous Trays

If heterogenous biosensor trays will be used, the column location of each biosensor type in the tray can be identified in the

Sensor Assignment Tab

. Assignment of biosensors that will not be used in the assay enables the software to auto-assign the biosensors that will be used in the assay by biosensor type.

There are two ways to change the biosensor type:


Sensor Tray Map


the drop-down list (Figure 7-42 left). The associated wells in the

Sensor Type



Sensor Type


sensor type from the drop-down list (Figure 7-42 right). All other wells in the same

column of the

Sensor Tray Map

as the selected cell will automatically populate with the biosensor type selected.



page 255

Figure 7-42:

Sensor Assignment Window—Changing the Biosensor Type



window were specified previously in the


window, and default locations are assigned automatically. To assign biosensor types for heterogenous trays:

1.

Select the column location of the biosensor type (see Figure 7-43).

Figure 7-43:

Selecting a Sensor Tray Column

2.

Right-click in the

Sensor Tray Map

or click in a cell in the

Sensor Type

table column and select a biosensor type from the drop-down list. The biosensor type associated

with the assay will shift location accordingly (see Figure 7-44). In the example shown,

Streptavidin is the

Sensor Type

used for the current assay. Column 1 was reassigned as

AHC according to the heterogeneous tray being used.


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and QK

Figure 7-44:

Assay Sensor Type Reassignment

3.

Repeat the previous steps to assign locations for the remaining biosensor types in the tray.

IMPORTANT: Ensure that the biosensor types selected in the

Assay Definition

window have assigned column(s) in the


window or the experiment cannot be run.


If you remove biosensors from the

Sensor Tray Map

and there are not enough remaining biosensors for the experiment, the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay(s).

The experiment in the example shown in (Figure 7-45) includes three assays, and Tray 1

does not include enough biosensors for the experiment. To view the additional biosensor tray that is required for the assay, select Tray 2 from the

Sensor Tray

drop-down list

(Figure 7-45 top). The

Sensor Tray Map

will then display the additional biosensors required

for the assay (Figure 7-45 bottom). If necessary, change the location of these biosensors.



page 257

Figure 7-45:

Example Experiment Using Two Biosensor Trays

NOTE: Up to two trays may be used per assay, but only the first biosensor tray can be a partial tray. During the experiment run, the software prompts you to insert the appropriate tray in the Octet instrument.

Reference Biosensors


Sensor Tray Map


Reference


R

.



Chart



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and QK

Changing the Biosensor Type

The biosensor type used in the assay must be selected in the


window. To change the biosensor type:

1.

Click the

Assay Definition Tab.

2.

In the


, click the cell in the

Sensor Type

column to change.

3.

Select from the drop-down list (see Figure 7-46).

IMPORTANT: Ensure that the same biosensor types are selected in both the

Assay Definition and the Sensor Assignment windows or the experiment cannot be run.

Figure 7-46:

Assay Definition Window—Changing the Biosensor Type


Before running an experiment, you can review the sample plate layout, assays and assay steps as well as the biosensors assigned to each assay in the experiment.

In the


window (Figure 7-47), move the slider left or right to highlight

the biosensors and samples associated with an assay step, or click the arrows. Alternatively, select an assay step to view the biosensors and samples associated with it.



Slider page 259

Figure 7-47:


SAVING EXPERIMENTS

After an experiment is run, the software automatically saves the experiment information that you specified (sample plate definition, biosensor assignment, assay settings) to an experiment method file (.fmf ). If you set up an experiment, but do not start the run, you can manually save the experiment method.

To manually save an experiment:

1.

Click


( ), or on the main menu, click

File > Save Method File

.

If there is more than one open experiment and you want to save all of them, click

Save

All Methods Files

.

2.

In the

Save


Save

.

NOTE: If you edit a saved experiment and want to save it without overwriting the original file, click

File > Save Method File As



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If you save an experiment to the factory-installed Template folder, the experiment will be available for selection. To view templates, select

Experiment > Templates > Kinetics >

Experiment Name

(Figure 7-48).

Follow the steps above to save an experiment to the Template folder located at



C:\Program Files\ForteBio\DataAcquisition\TemplateFiles.

IMPORTANT: Do not change the location of the Template folder. If the Template folder is moved from the factory-set location, the software may not function properly.

Figure 7-48:

Saved Experiments in the Template Folder

RUNNING A KINETICS EXPERIMENT

IMPORTANT: Before starting an experiment, ensure that the biosensors are properly rehydrated. For details on how to prepare biosensors, see the appropriate biosensor product insert.

Loading the Biosensor Tray and Sample Plate

To load the biosensor tray and sample plate:

1.

Open the Octet instrument door (lift the handle up).

2.

Place the biosensor tray on the biosensor stage (left side) so that well A1 is located at

the upper right corner (see Figure 7-49).

3.

Place the sample plate on the sample stage (right side) so that well A1 is located at the

upper right corner (see Figure 7-49).


Running a Kinetics Experiment

page 261

Well A1 Position

Figure 7-49:

Biosensor Stage (left) and Sample Stage (right)

IMPORTANT: Make sure that the bottom of the sample plate and biosensor tray are flat on the stages.

4.

Close the Octet instrument door.

5.



Starting the Experiment


1.

Click the

Run Experiment

tab, or click the arrow ( ) to access the Run Experiment

window (see Figure 7-50).


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Chapter 7:


and QK

Figure 7-50:


2.

Confirm the default settings or enter new settings. See “Run Experiment Window Settings” on page 264 for more information on experimental settings.


3.



If you select the


option, the

Runtime Binding

Chart

window displays the binding data in real-time, as well as the experiment prog-

ress (Figure 7-51).



, see “Managing the Runtime Binding Chart” on page 267.



page 263

Figure 7-51:


4.

Optional: Click

View

>




Figure 7-52:



page 264

Chapter 7:


and QK

WARNING: Do not open the Octet instrument door when an experiment is in progress. If the door is opened, the data from the active biosensors is lost. The data already acquired is saved, however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning.


The following



Run Experiment

Tab:

Table 7-6:


Item

Assay type


Description


The location where the subdirectory will be created. The subdirectory contains the data (.frd) files. Click

Browse



Experiment

Run Name

(sub-directory)




Start

Specifies a subdirectory name for the data files (.frd). The software generates one data file for each biosensor that includes the data from all steps the biosensor performs.


A user-defined field where you can enter text or a barcode (barcode reader required) for a second plate. This field is also used to generate the path of the saved directory.




page 265

The following

Run Settings


Run Experiment

Tab:

Table 7-7:

Run Settings

Item


Start after





Description


.



Displays the







File > Options




Advanced settings are available for the Octet QK e

, Octet RED and Octet RED96 systems. The signal to noise ratio of the assay can be optimized by selecting different acquisition rates.

The acquisition rate refers to the number of binding signal data points reported by the

Octet system per minute and is reported in Hertz (per second). A higher acquisition rate generates more data points per second and monitors faster binding events better than a slower acquisition rate. A lower acquisition rate allows the software enough time to perform more averages of the collected data. Typically, more averaging leads to reduced noise


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Chapter 7:


and QK and thus, better signal-to-noise ratios. The choice of a setting should be determined based upon consideration of the binding rate and the amount of signal generated in your assay, and some experimentation with the settings.

Table 7-8:

Advanced Settings Octet QK e

, Octet RED and Octet RED96

Item

Acquisition rate



Octet QK e

Acquisition rate

Octet RED96

Sensor offset (mm) -

Octet QK e

Default

only



Description

• High sensitivity kinetics (0.3 Hz, averaging by 40) - The average of 40 data frames is reported as one data point. One data point is reported every 3.3 seconds.

• Standard kinetics (0.6 Hz, averaging by 5) - The average of five data frames is reported as one data point.

One data point is reported every 1.6 seconds.

• High sensitivity kinetics (2 Hz, averaging by 50): - The average of 50 data frames is reported as one data point. Two data points are reported per second.

• Standard kinetics (5 Hz, averaging by 20 - The average of 20 data frames is reported as one data point.

Recommended sensor offset: Large molecule kinetics—4 mm

Sets acquisition rate and sensor offset to the defaults.



Experiment

>

Stop

.




Managing the Runtime Binding Chart

page 267

MANAGING THE RUNTIME BINDING CHART

If the


check box is selected in the Run Experiment

window (Figure 7-53), the Runtime Binding Charts are automatically displayed when data

acquisition starts. The


window displays the assay step status, experiment progress, and the elapsed experiment time.

The



Sensor Tray Map

. Used sensor columns that are inactive are colored black. Active sample columns are colored green. Each assay in the experiment is represented by

Assay X

in the


box.

To selectively display data for particular assay:

1.


Assay

number.

2.

Select a subset of sensors for a displayed column under


box (see

Figure 7-53).







Figure 7-53:



page 268

Chapter 7:


and QK

Opening the Runtime Binding Chart



at any time:

1.

Click

File > Open Experiment

.

2.


Select

.


If the experiment includes reference biosensors, you can display reference-subtracted data in the chart by clicking the

Subtract Reference Biosensor

check box in the chart window.

To view raw data, remove the check mark next to this option.




tab



box


Data Selection

tab



1.

In the


list or the

Sensor Tray


Reference

(see Figure 7-54).

Figure 7-54:



R

in the


list and

Sensor

Tray (

see

Figure 7-55).

2.

Click the


check box

(

see

Figure 7-55).



page 269

Figure 7-55:




only makes a visual change to the data on the screen. The actual raw data is unaffected and the reference subtraction must be repeated during data analysis if needed.





Flip Data


Figure 7-56:



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Chapter 7:


and QK

Aligning Data by a Selected Step

To align the binding data to the beginning of a user-selected step, in the

Runtime Binding

Chart

(see Figure 7-57), right-click a step and select

Align to Step <number>.

To remove the step alignment, right-click the step and select

Unaligned

.

Figure 7-57:

Runtime Binding Chart—Aligning the Data to a User-Selected Step

Extending or Skipping an Assay Step

During acquisition, the duration of the active step may be extended. You can also terminate the active step and begin the next step in the assay.

NOTE: If the step you want to extend or terminate includes biosensors used in

Parallel Reference, Double Reference, or Average Reference subtraction methods, the data will not be analyzed.

To extend the duration of the active step:

1.

In the chart window, click the

Extend Current Step

button.

2.

In the


dialog box (see Figure 7-58), enter the number of seconds

to extend the step and click

OK

.



page 271

Figure 7-58:

Extend Current Step Dialog Box

Terminating a Step to Begin the Next Step

To terminate a step and begin the next step in the assay:

1.


Go to Next Step

button.

2.

In the

Data Acquisition

dialog box, click

OK

.




Undo Zoom

.


To scale the


:

1.


Properties

.

2.

In the


dialog box, select

Fullscale

or

Autoscale

.


To add a


title:

1.


Properties

.

2.

In the




To select a


legend:

1.


Properties

.

2.

In the



lowing legends:

• Sensor Location

• Sample ID




page 272

Chapter 7:


and QK

Figure 7-59:


NOTE: Text for

Sample ID

,


, or


is taken from the


and



3.

Click

OK

.



Window

>

New Window

.


To export the



1.


Export Data

.

2.

In the

Exporting


Export

.



page 273

Figure 7-60:


Export the

Runtime

Binding


Copy the

Runtime

Binding

Chart

Print the

Runtime

Binding

Chart

Table 7-9:





Destination

Text/

Data

EMF, WMF,

BMP, JPG, or PNG


Click

File

>

Browse


Click

File

>

Browse


Clipboard

Printer

Result






page 274

Chapter 7:


and QK





Table 7-10:




File

>

Open Method

File

File

>

Save Method

File

or

File

>

Save Method

File As

Description





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CHAPTER 8:



Kinetics Experiments:



Octet RED384 and QK384

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276

Starting a Basic Kinetics Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277



Working with a Reagent Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299

Defining a Kinetic Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302




Running a Kinetics Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324

Managing the Runtime Binding Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331



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Chapter 8:

Kinetics Experiments: Octet RED384 and QK384

INTRODUCTION

A basic kinetics experiment enables you to determine the association and dissociation rate of a molecular interaction. After starting the Octet system hardware and the Octet System

Data Acquisition software, follow the steps (in Table 8-1) to set up and analyze a quantitation experiment.

Table 8-1:

Setting Up and Analyzing a Kinetic Experiment

Software

Data



Acquisition

Step

1.

Select a kinetics experiment in the



2.


3.

Define a or import a reagent plate

(optional).

4.

Specify assay steps.

5.


6.

Run the experiment.

Data Analysis 7.

View and process the raw data.

8.

Analyze the data.

See

“Starting a Basic Kinetics



“Working with a Reagent

Plate” on page 299

“Defining a Kinetic Assay” on page 302



“Running a Kinetics Experiment” on page 324



NOTE: Before starting an experiment, check the sample plate temperature displayed in the status bar. Confirm that the temperature is appropriate for your experiment and if not set a new temperature. If the Octet System Data Acquisition software is closed, the plate temperature will reset to the default startup value specified in the

Options

window when the software is relaunched.


Starting a Basic Kinetics Experiment

page 277

STARTING A BASIC KINETICS EXPERIMENT

You can start a kinetics experiment using one of the following options:

• Launch the


.


File

>



File





Experiment > Templates > Kinetics

.




To start an experiment from the

Experiment Wizard:

1.

If the




toolbar button , or click

Experiment > New Experiment Wizard

(

Ctrl

+

N

) from the

Main Menu

.

2.

In the


, click

New Kinetics Experiment


3.

Click the arrow button( ).

The

Basic Kinetics Experiment

window displays (Figure 8-1, right).


page 278

Read Head Setting

Chapter 8:


Figure 8-1:

Starting a Kinetics Experiment with the Experiment Wizard


The steps to define a sample plate include:

Step See Page

1.

Select the instrument read head configuration (8 or 16 channels).

278

2.

Select the sample plate format (96 or 384 wells).

3.


4.


280

280

296

Read Head Configuration and Plate Layout

The Octet read head contains the collection optics. If the read head is set to 8 channels, one column of 8 biosensors interrogate 8 plate wells. If the read head is set to 16 channels, two

columns of biosensors interrogate 16 wells (see Figure 8-2). The read head configuration and the plate format (96 or 384 wells) determine the plate layout (see example Figure 8-2).





page 279




Figure 8-2:

Color-Coded Wells Display How Biosensors Interrogate a 96-well Plate, 8 Channel or 16-Channel Read Head






Figure 8-3:

Color-Coded Wells Display How Biosensors Interrogate a 384-well Plate, 8 Channel or 16

Channel Read Head

NOTE: Keep the read head configuration in mind when laying out the sample plate.While reading a 384-well sample plate, both the 8 channel and 16 channel read heads can freely step through the plate by either moving left or right to step across columns or step one row up or down.


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Chapter 8:


Changing the Sample Plate Format

To change the sample plate format:

1.

Click

Modify

(above the plate map).

2.

In the

Modify Plates

dialog box, select

96 Well

or

384 Well

format.

Figure 8-4:

Changing the Sample Plate Format





Table 8-2 displays the well types that can be assigned to a plate map.

Table 8-2:



Any type of sample. For example, an analyte.

Reference sample. For example, a buffer-only control biosensor that is used to correct for system drift.




 analyte

Any type of buffer. For example, the buffer in a baseline, association, or dissociation step.



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Table 8-2:



Activation reagent. Makes the biosensor competent for binding.

Quenching reagent. Blocks unreacted immobilization sites on the biosensor surface.

Ligand to be immobilized (loaded) on the biosensor surface.

Wash buffer.

Regeneration reagents dissociate the analyte from the ligand.




:


(Figure 8-5 left). To select non-adjacent columns, hold the Ctrl key and click the column header.

• Click a row header or select adjacent row headers by click-hold-drag (Figure 8-5, center).

• Click a well or draw a box around a group of wells(Figure 8-5, right).

Figure 8-5:






page 282

Chapter 8:


Designating Well Types

In the


, select the wells, right-click and select a sample type. (Figure 8-6).

Figure 8-6:

Designating a Well Type in the Plate Definition Window

To remove a well designation, in the


, select the well(s) and click

Remove


Clear Data

(see Figure 8-7).

Figure 8-7:

Clearing Sample Data from a Sample Plate



page 283

Entering Sample Information

NOTE: You must specify sample (analyte) concentration and molecular weight; otherwise, the Octet System Data Acquisition software cannot compute a K

D value. If the sample concentration is not specified, only k d

and k obs are calculated. You can also annotate any well with

Sample ID

or

Well Information,

and assign


.

Assigning Molecular Weight and Molar Concentration

1.

In the


, select the sample wells, right-click and select

Set Well Data

.

2.

In the

Set Well Data

dialog box, enter the analyte molecular and molar concentration

(Figure 8-8).


page 284

Chapter 8:


Molecular Weight and

Molar Concentration

Figure 8-8:

Entering Molecular Weight and Molar Concentration from the Sample Plate Map

The information displays in the


(see Figure 8-9).

3.

In the


, select the sample concentration units and the molar concentration units.



Figure 8-9:

Entering Molecular Weight and Molar Concentration from the Plate Table

Assigning User Specified Sample Concentrations


1.

In the


, select the desired wells, right-click and select

Set Well

Data.

The

Set Well Data


2.

Select the

By value


page 285

Concentration units


page 286

Chapter 8:


Figure 8-10:

Sample Plate Map—Assigning Sample Concentrations by Value

3.

Click

OK

. The


will display the entered concentration.

Assigning Concentrations Using a Dilution Series


1.

In the


, select the wells, right-click, and select

Set Well Data

.

The

Set Well Data

dialog box displays (see Figure 8-11)

2.

Select the

Dilution Series




page 287

Figure 8-11:

Sample Plate Map—Assigning Sample Concentrations Using Dilution Series

3.



Highest

Concentration

Lowest

Concentration

Figure 8-12:

Concentration Representation in Dilution Series:

4.

Click

OK

.

The


displays the standard concentrations.


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Chapter 8:












1.

In the



Set

Well Data

.

2.

In the

Set Well Data


Sample ID

and/or

Well

Information

and click

OK

.

Figure 8-13:

Add Sample Annotations from the Sample Plate Map



page 289




:

1.


Sample ID

or


.

2.




.

Figure 8-14:

Add Sample Annotations in the Sample Plate Table

Edit commands (







Sample Plate

Map




enable data to be organized into custom groups during data analysis

(see Figure 8-15).


page 290

Chapter 8:


Figure 8-15:

Replicate Group Color-Coding

NOTE: Replicate Group information can also be entered in the Octet System

Data Analysis software.


To assign


in the


:

1.

Select the samples you wish to group, right-click and select

Set Well Data

.

2.

In the

Set Well Data


Replicate Group

box and click

OK

.



page 291

Figure 8-16:


3.


Replicate Group


Replicate Group



Wells in the


will show color-coded outlines as a visual indication of which wells are in the same group (see Figure 8-17).


page 292

Chapter 8:


Figure 8-17:


The



Replicate Group

names entered (see

Figure 8-18)



page 293

Figure 8-18:



To assign


in the


:

1.


Replicate Group

table column.

2.



page 294

Chapter 8:


Figure 8-19:


Edit commands (







Sample Plate

Map


3.


Replicate Group


Replicate Group





page 295

Editing the Sample Table

Changing Sample Well Designations

To change a well designation, right-click the well in the


and make a

new selection (see Figure 8-20).

Figure 8-20:

Sample Plate Table—Well Designation

Editing Sample Information

To edit sample data in the


, double-click a value and enter a new value

(see Figure 8-21).


page 296

Chapter 8:


Figure 8-21:

Sample Plate Table—Editing Sample Data

Edit commands (






NOTE: The right-click menu is context-dependant. Right-clicking on a cell where the value is not highlighted and in edit mode opens the right-click menu used to designate sample types.







1.

In the


, click

Export

(see Figure 8-22).

page 297

Figure 8-22:

Sample Plate Map — Export Button

2.

In the


window (see Figure 8-23), select a folder, enter a name

for the plate (.csv), and click

Save

.

Figure 8-23:



page 298

Chapter 8:




1.

In the Plate Definition window (see Figure 8-22: on page 297), click

Import

.

Figure 8-24:

Sample Plate Map—

Import

Button

2.

In the



(.csv), and click

Open

.

Figure 8-25:


NOTE: You can also create a .csv file for import. Figure 8-26 shows the appro-

priate column information layout.



page 299

Figure 8-26:

Example Plate Definition File (.csv)

WORKING WITH A REAGENT PLATE

You can include an optional reagent plate in a Basic Kinetics experiment. Using a reagent plate enables higher sample throughput since no reagents are included in the sample plate. An experiment can include any combination of sample and reagent plate formats

(96- or 384-well). The reagent plate can be used for reagents but not samples, references or controls.

NOTE: The reagent plate format (96- or 384-well) and the read head configuration (8 or 16 channels) determine the reagent plate layout. For more details,

see “Read Head Configuration and Plate Layout” on page 278.

To modify a reagent plate:

3.

Click

Modify Plates

above the


. The

Modify Plates



page 300

Chapter 8:


Figure 8-27:

Modifying the Reagent Plate

4.

Select a reagent plate format (

96 Well

or

384 Well

) and click

OK

.

5.

Select the

Reagent Plate

radio button above the plate table. This will display the

Reagent Plate Table

.

6.

In the


, right-click a column to use and select

Buffer

,

Activation

,

Quench

,

Load

,

Wash

, or

Regeneration

from the shortcut menu (see Figure 8-28). The

well designations appear in the


. Repeat this step to define other wells in the reagent plate.



page 301

Figure 8-28:

Defining Wells in the Reagent Plate

7.

Optional: Enter well data or reagent information in the


.

To remove well designations, select the column(s) and click

Remove

, or right-click and choose

Clear Data

.

Saving a Reagent Plate Definition

Exporting and saving reagent plate definition is done in the same manner as you would for

sample plates. For details “Managing Sample Plate Definitions” on page 296.


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Chapter 8:


DEFINING A KINETIC ASSAY

After the sample plate is defined, the assay must be defined. The steps to define a kinetic assay include:

Step

1.

Define the step types.

2.

Build the assay by assigning a step type to a column(s) in the sample plate.

3.


See Page

302

306

296

Defining Step Types

Table 8-3 lists the example step types to define a kinetic assay. Use these examples as a

starting point to create your own step types.

Table 8-3:

Sample Step Types for Kinetic Assays .

Step Type

Association


Calculates the k obs

. Select this step type when binding the second protein of interest (analyte) to the biosensor. This step should be performed at 1,000 rpm.

Dissociation Calculates the k d

. Select this step type when monitoring the dissociation of the protein complex. This step should be performed at 1,000 rpm.

Baseline Can be used to align the data. Select this step type when establishing the biosensor baseline in the presence of buffer. This step can be performed with no flow (0 rpm). However, if the baseline step directly precedes an association step, perform the baseline step at 1,000 rpm.

Loading

IMPORTANT: An assay must include a baseline step followed by a set of association/dissociation steps to be analyzed. The Octet System Data Analysis software recognizes the baseline/association/dissociation step series during processing. Data cannot be processed if this sequence is not included in the assay setup.

Not used in data analysis. Select this step type when binding the first protein of interest (ligand) to the biosensor.

NOTE: This step may be performed offline (outside the

Octet instrument).



page 303

Table 8-3:

Sample Step Types for Kinetic Assays (Continued).

Step Type

Custom

Activation

Quenching


Can be used for an activity not included in any of the above step types.

Used when employing a reagent to chemically prepare the biosensor for loading.

Used to render unreacted immobilization sites on the biosensor inactive.

Creating Step Types

Click the


tab, or click the arrow to access the Assay Definition window

(see Figure 8-29). The

Step Data List

shows the types of assay steps that are available to build an assay. By default, the list includes a baseline step.

To create different types of assay steps:

1.

Click

Add

.

2.

In

Assay Step Definition

dialog box (Figure 8-29), specify the step information:

a. Choose a step type.

b. Optional: Edit the step name.

c. Set the step time and shake speed (

Time

range: 2 to 48,000 seconds,

Shake speed

range: 100 to 1,500 rpm or 0).

Figure 8-29:

Creating an Assay Step Type


page 304

Chapter 8:


3.

Apply a threshold to the step: a. In the

Step Data List

, click the

Threshold

check box.

The

Threshold Parameters

dialog box displays (see Figure 8-30). b. Set the threshold parameters (refer to Table 8-4 for the parameter definitions).

Figure 8-30:

Setting Assay Step Threshold Parameters

NOTE: If thresholds are applied, the step is terminated when either the step time elapses or the threshold termination criteria is reached.

Table 8-4:

Threshold Parameters


Active Channels Specifies the instrument channels that monitor the threshold criteria for the assay step. Select an option for terminating the step:

• The threshold is achieved on ALL channels

• The threshold is achieved on ANY ONE channel

Signal Change The threshold is a user-specified amount of ascending or descending signal change (nm).



page 305

Table 8-4:

Threshold Parameters (Continued)

Item

Gradient

Filtering

Description

The threshold is a binding gradient (nm/min) for a user-specified time (min).

The amount of data (seconds) to average when computing the signal change or gradient threshold.

4.

Click

OK

to save the newly-defined step. The new step type appears in the

Step Data

List

.

5.

Repeat the previous steps for each step type to create until all the desired steps are

added (see Figure 8-31).

Figure 8-31:

Step Data List—Displaying Step Types

6.

To delete a step type from the list, click the corresponding row in the

Step Data List

and click

Remove

, or press the

Delete

key.

Copying and Editing Step Types

To define a step type by copying an existing one, click the step type (row) in the

Step Data

List

and click

Copy

. The copied step type appears at the end of the

Step Data List.

To define a step type by editing an existing one:

1.

Double-click the cell in the step’s

Name

,

Time

, or

Shake speed

column and then enter a new value. Or, right-click the cell to display a shortcut menu of editing commands


NOTE: Keyboard commands can also be used (

Ctrl

+

x

=cut,

Ctrl

+

c

=copy,

Ctrl

+

v

=paste,

Ctrl

+

z

=undo).

2.

Click the cell in the step’s

Type

column, then select another name from the drop-down

list (see Figure 8-32, right).


page 306

Chapter 8:


Figure 8-32:

Editing a Step Value (left) or Step Type (right)

Building an Assay

After creating the different step types that the assay will use, step types are assigned to columns in the Sample Plate or Reagent Plate maps.

To build an assay:

1.


Step Data List

.

2.

In the

Sample Plate

or


, double-click the column that is associated with the selected step type. For information about sample or reagent plate wells,

mouse over a well to view a tool tip (see Figure 8-33).

Figure 8-33:


The selected wells are marked with hatching (for example, ) and the step appears in the


(see Figure 8-34) with an associated

Assay Time

.



NOTE: In the


, Plate 1 is the Sample Plate and Plate 2 is the

Reagent Plate.

page 307

1

New Assay Step

2

Figure 8-34:

Assigning a Step Type to a Column in the Sample Plate

3.

Repeat the previous steps to define each step in the assay. As each step is added, the total

Experiment

and

Assay Time

update (see Figure 8-35).

Total Experiment

Time

Figure 8-35:

Experiment and Assay Time Updates as Steps Are Added to the Assay

Total Assay Time


page 308

Chapter 8:


IMPORTANT: If you intend to analyze the data from a sample using the I

nterstep correction

feature in the Octet System Data Acquisition software, the assay must use the same well to perform baseline and dissociation for the sample.

Replicating Steps Within an Assay

To copy steps and add them to an assay:

1.

In the


, select the step(s) to copy and click

Replicate

(for example, in

Figure 8-36, step rows 1–4 are selected).


Shift



Ctrl

key while you click the desired steps.

2.

In the

Replicate Steps

dialog box (see Figure 8-36), click the

Append to current assay

option.

3.

Click the

Offset steps

check box and set the options, as appropriate. (For more details on offset options, see Table 8-5.)

Figure 8-36:

Replicating Assay Steps by Appending



page 309

4.

Click

OK

. The step(s) appear at the end of the assay in the


.

Table 8-5:

Replicate Steps Options .

Item

Add as a new assay

Append to current assay

Offset steps

Sample steps only

All steps

Sample steps will be adjusted horizontally by X columns

Sample steps will be adjusted vertically by one row

Description

Adds the replicate step(s) as a new assay to the

Assay

Steps List.

Adds the replicate step(s) to the end of the current assay.

Assigns the replicate steps to different columns in the sample plate.

Applies the offset to the sample plate only.

Applies the offset to the sample plate and reagent plate.

Specifies the column in which to add the new step(s). For example, if a step in column 11 is copied and the replicate step should begin in column 12, enter

1

. Enter

0

to apply the step(s) to the same columns.

Choose this option to put the replicate step in the same column, but the next row.

Starting a New Assay

A new assay will utilize a new set of biosensors. To start a new assay using the next available sensor column:

1.

Select a column in the


.

2.

Right-click to view the shortcut menu and select

Start New Assay

(see Figure 8-37).

3.

Add steps to the assay as described earlier.

Figure 8-37:

Start New Assay


page 310

Chapter 8:


Inserting or Adding an Assay Step

To insert an assay step:

1.

Select a step in the

Step Data List

.

2.

In the


, select the row above where you want to insert the step.

3.

In the



Insert Assay Step

.

The step is inserted into the


.

To add an assay step:

1.


Step Data List

.

2.

In the



Add Assay Step

.

The step is added to the end of the


.

Selecting a Biosensor for the Assay

To select the biosensor type associated with the assay, click the

Sensor Type

arrow ( ) for any step in the assay and select a sensor type from the drop-down list (Figure 8-38). The biosensor type will automatically update for every assay step.

Figure 8-38:

Selecting an Assay Sensor Type

NOTE: The

Sensor Type



. Changing the

Sensor Type

from the


Tab




page 311

Editing an Assay

To edit the step type or the biosensor type:

In the


:

• To change the step type, click the

Step Name

arrow ( ) and select a step name

from the drop-down list (Figure 8-39, top).

• To change the biosensor type, click the

Sensor Type

arrow ( ) for any step in

the assay and select a sensor type from the drop-down list (Figure 8-39, bottom).

The biosensor type will automatically update for every assay step.

NOTE: The

Step Name

drop-down list includes only the step types defined in the

Step Data List

.

Figure 8-39:

Editing an Assay Step Name (top) or Sensor Type (bottom) in the Assay Steps List

To reorder or remove an assay step:

1.

Select a step (row) in the


.

2.

Click the

Move Up

,

Move Down

, or

Remove

button located above the list.

IMPORTANT: An assay must have a baseline step followed by a set of association/dissociation steps to be analyzed. The Octet System Data Acquisition software recognizes the baseline/association/dissociation set of steps.


page 312

Chapter 8:


Adding an Assay Through Replication

A sample plate can include multiple assays that are the same (replicates) or different. Each assay utilizes a new set of biosensors. Replicates within a single assay will therefore use the same biosensor and replicates in different assays will use different biosensors.

To add a replicate assay to a plate:

1.

In the


, select the steps to copy and click

Replicate

.


Shift



Ctrl

key while you click the steps.

2.

In the

Replicate Steps

dialog box, click the

Add as a new assay

option (Figure 8-40).

Figure 8-40:

Adding a Replicate Assay to a Plate

3.

Click the

Offset steps

check box and set the options as appropriate (see Table 8-5 on page 309 for more information). If the replicate assay uses the same sample columns as the original assay, do not choose the

Offset steps

option. If the replicate assay uses a different sample column, select

Offset steps

and the appropriate options.

•

Sample steps only

offsets the sample wells by the value specified under


. The offset will not be applied to reagent wells such as buffer, loading, regeneration, neutralization and detection.



page 313

•

All Steps

offsets all wells in the assay, including sample and reagent wells, by the value specified under


.

4.

Click

OK

. The new assay appears in the


.

5.

Continue to add assay steps as needed.


After you define the sample plate and assay(s), click the


tab or click the arrow to access the Sensor Assignment window. The color-coded

Sensor Tray

and


show the locations of the biosensors associated with the samples

Figure 8-41).

NOTE: When using a 96-well plate with the 8 channel read head, do not put biosensors in columns 2, 4, 6, 8, 10, and 12 if the biosensors will be returned to the biosensor tray and not discarded. If the biosensors will be ejected, biosensors can be placed in all columns.

NOTE: If an experiment includes more than one type of biosensor, the software automatically creates a separate sensor tray for each type of biosensor. If the different types of biosensors are in the same tray, change the biosensor type as appropriate.


Sensor Type

table column are those designated during

the kinetics assay definition. In the example shown in Figure 8-41, the experiment includes

two assays in the same wells. The use of those wells by two different biosensors is indicated by the pie chart colors.

NOTE: The

Sensor Type



in the

Assay Definition Tab

. Changing the

Sensor Type

from the

Sensor Assignment Tab



page 314

Chapter 8:


Figure 8-41:

Sensor Assignment Window

Hover the cursor over a well in the

Sensor Tray Map

or


to display a tool

tip with sample or biosensor information (see Figure 8-42).

Figure 8-42:




page 315

Replacing the Biosensors in the Biosensor Tray

After an assay is completed, the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container. To return the biosensors to the tray, click the



Figure 8-43:





Entering Biosensor Information

To enter information about a biosensor:

1.


Lot Number


Lot Number

column for that biosensor type will automatically

populate with the lot number entered (see Figure 8-44).

2.

Optional: Double-click a cell in the

Information

table column. Enter or edit the biosen-

sor information as appropriate (see Figure 8-44).







page 316

Chapter 8:


Figure 8-44:

Entering or Editing Biosensor Information

Changing the Biosensor Location

If you prefer to not use the default biosensor columns, you can select other column(s) to use. There are two ways to do this:

• Method 1—In the

Sensor Tray Map

,

Remove

the columns you do not want to use.

The software automatically selects the next available column(s).

•

Method 2— Remove

all columns from the

Sensor Tray Map

, then select the columns you want to use.

Method 1

In the

Sensor Tray Map

, select the columns to not use and click

Remove


Remove

(Figure 8-45 left).The software automatically selects the next available biosensor columns in the tray (Figure 8-45 right).

Click

Fill Plate

to return the

Sensor Tray Map


Figure 8-45:




page 317

Method 2

1.

In the

Sensor Tray Map

, select all of the columns and click

Remove

(Figure 8-46 top

left). Or, right-click the selection and select

Remove

. All columns will be shown as

Missing

(Figure 8-46 top right).

2.

Select the column(s) to use and click

Fill


Fill

(Figure 8-46 bottom left). The software fills the selected columns in the tray

(Figure 8-46 bottom right).

Figure 8-46:


Click

Fill Plate

to return the

Sensor Tray Map


Using Heterogenous Trays

If heterogenous biosensor trays will be used, the column location of each biosensor type in the tray can be identified in the

Sensor Assignment Tab

. Assignment of biosensors that will not be used in the assay enables the software to auto-assign the biosensors that will be used in the assay by biosensor type.


page 318

Chapter 8:


There are two ways to change the biosensor type:


Sensor Tray Map


the drop-down list (Figure 8-47 left). The associated wells in the

Sensor Type



Sensor Type


sensor type from the drop-down list (Figure 8-47 right). All other wells in the same

column of the

Sensor Tray Map

as the selected cell will automatically populate with the biosensor type selected.

Figure 8-47:

Sensor Assignment Window—Changing the Biosensor Type



window were specified previously in the


window, and default locations are assigned automatically. To assign biosensor types for heterogenous trays:

1.

Select the column location of the biosensor type (see Figure 8-48).



page 319

Figure 8-48:

Selecting a Sensor Tray Column

2.

Right-click in the

Sensor Tray Map

or click in a cell in the

Sensor Type

table column and select a biosensor type from the drop-down list. The biosensor type associated

with the assay will shift location accordingly (see Figure 8-49). In the example shown,

AHC is the

Sensor Type

used for the current assay. Columns 1 and 2 were reassigned as

Streptavidin according to the heterogeneous tray being used.


page 320

Chapter 8:


Figure 8-49:

Assay Sensor Type Reassignment

3.

Repeat the previous steps to assign locations for the remaining biosensor types in the tray.

IMPORTANT: Ensure that the biosensor types selected in the

Assay Definition

window have assigned column(s) in the


window or the experiment cannot be run.


If you remove biosensors from the

Sensor Tray Map

and there are not enough remaining biosensors for the experiment, the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay(s).

The experiment in the example shown in (Figure 8-50) includes two assays, and Tray 1 does

not include enough biosensors for the experiment. To view the additional biosensor tray that is required for the assay, select Tray 2 from the

Sensor Tray

drop-down list (Figure 8-50

top). The

Sensor Tray Map

will then display the additional biosensors required for the

assay (Figure 8-50 bottom). If necessary, change the location of these biosensors.



page 321

Figure 8-50:

Example Experiment Using Two Biosensor Trays

NOTE: Up to two trays may be used per assay, but only the first biosensor tray can be a partial tray. During the experiment run, the software prompts you to insert the appropriate tray in the Octet instrument.

Reference Biosensors


Sensor Tray Map


Reference


R

.



Chart



page 322

Chapter 8:


Changing the Biosensor Type

The biosensor type used in the assay must be selected in the


window. To change the biosensor type:

1.

Click the

Assay Definition Tab.

2.

In the


, click the cell in the

Sensor Type

column to change.

3.

Select from the drop-down list (see Figure 8-51).

IMPORTANT: Ensure that the same biosensor types are selected in both the

Assay Definition and the Sensor Assignment windows or the experiment cannot be run.

Figure 8-51:

Assay Definition Window—Changing the Biosensor Type


Before running an experiment, you can review the sample plate layout, assays and assay steps as well as the biosensors assigned to each assay in the experiment.

In the


window (Figure 8-52), move the slider left or right to highlight

the biosensors and samples associated with an assay step, or click the arrows. Alternatively, select an assay step to view the biosensors and samples associated with it.



Slider page 323

Figure 8-52:


SAVING EXPERIMENTS

After an experiment is run, the software automatically saves the experiment information that you specified (sample plate definition, biosensor assignment, assay settings) to an experiment method file (.fmf ). If you set up an experiment, but do not start the run, you can manually save the experiment method.

To manually save an experiment:

1.

Click


( ), or on the main menu, click

File > Save Method File

.

If there is more than one open experiment and you want to save all of them, click

Save

All Methods Files

.

2.

In the

Save


Save

.


page 324

Chapter 8:


NOTE: If you edit a saved experiment and want to save it without overwriting the original file, click

File > Save Method File As



If you save an experiment to the factory-installed Template folder, the experiment will be available for selection. To view templates, select

Experiment > Templates > Kinetics >

Experiment Name

(see Figure 8-53).

Follow the steps above to save an experiment to the Template folder located at



C:\Program Files\ForteBio\DataAcquisition\TemplateFiles.

IMPORTANT: Do not change the location of the Template folder. If the Template folder is moved from the factory-set location, the software may not function properly.

Figure 8-53:

Saved Experiments in the Template Folder

RUNNING A KINETICS EXPERIMENT

IMPORTANT: Before starting an experiment, ensure that the biosensors are properly rehydrated. For details on how to prepare biosensors, see the appropriate biosensor product insert.

Loading the Biosensor Tray, Sample, and Reagent Plates

To load the biosensor tray, sample plate, and reagent plate:

1.

Open the Octet instrument door (lift the handle up) and present the instrument stage

(click the

Present Stage

button ).

2.

Place the biosensor tray, sample plate, and reagent plate on the appropriate stage so

that well A1 is located at the upper right corner (see Figure 8-54):

a. Place the rehydration plate and biosensor tray on the biosensor stage (left plat-



form). b. Place the sample plate on the sample stage (middle platform).

c. Place the reagent plate on the reagent stage (right platform).

Well A1 Position

Biosensor Tray & Rehydration Plate Stage

Sample Plate

Stage

Reagent Plate

Stage

page 325

Figure 8-54:

Octet Instrument Stage Platform

IMPORTANT: Ensure that the bottom of the sample plate, reagent plate and biosensor tray are flat on the stages.

3.

Click to close the Octet instrument door.

4.





1.

Click the

Run Experiment

tab, or click the arrow ( ) to access the Run Experiment

window (see Figure 8-55).


page 326

Chapter 8:


Figure 8-55:

Run Experiment Tab—Octet RED384

2.

Confirm the default settings or enter new settings. See “Run Experiment Window Settings” on page 328 for more information on experimental settings.


3.



If you select the


option, the

Runtime Binding

Chart

window displays the binding data in real-time, as well as the experiment prog-

ress (Figure 8-56).



, see “Managing the Runtime Binding Chart” on page 331.



page 327

Figure 8-56:


4.

Optional: Click

View

>




Figure 8-57:



page 328

Chapter 8:


WARNING: Do not open the Octet instrument door when an experiment is in progress. If the door is opened, the data from the active biosensors is lost. The data already acquired is saved, however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning.


The following



Run Experiment

Tab:

Table 8-6:


Item

Assay type


Description


The location where the subdirectory will be created. The subdirectory contains the data (.frd) files. Click

Browse



Experiment

Run Name

(sub-directory)




Start

Specifies a subdirectory name for the data files (.frd). The software generates one data file for each biosensor that includes the data from all steps the biosensor performs.


A user-defined field where you can enter text or a barcode (barcode reader required) for a second plate. This field is also used to generate the path of the saved directory.




page 329

The following

Run Settings


Run Experiment

Tab:

Table 8-7:

Run Settings

Item


Start after





Description


.



Displays the







File > Options




Advanced settings are available for Octet RED384 and Octet QK384 systems. The signal to noise ratio of the assay can be optimized by selecting different acquisition rates. The acquisition rate refers to the number of binding signal data points reported by the Octet system per second and is reported in Hertz (per second). A higher acquisition rate generates more data points per second and monitors faster binding events better than a slower acquisition rate. A lower acquisition rate allows the software enough time to perform more averages of the collected data. Typically, more averaging leads to reduced noise and thus, better signalto-noise ratios. Therefore, the frequency setting should be determined based on consideration of the binding rate, the amount of signal generated in your assay and some experimentation with the settings.


page 330

Chapter 8:


The following


are available for the Octet384 system:

Table 8-8:

Advanced Settings Octet RED384


Acquisition rate • High sensitivity kinetics (2.0 Hz, averaging by 50)—The average of 50 data frames is reported as one data point. Two data points are reported per second.

• Standard kinetics (5.0 Hz, averaging by 20)—The average of 50 data frames is reported as one data point. Five data points are reported per second.

• Fast kinetics (10.0 Hz, averaging by 5)- The average of 5 data frames is reported as one data point. Ten data points are reported per second.

Recommended sensor offset: Large molecule kinetics—4 mm Sensor off set

(mm)


The following


are available for the OctetQK384 system:

Table 8-9:

Advanced Settings Octet QK384


Acquisition rate • High sensitivity kinetics (0.3 Hz, averaging by 40) - The average of 40 data frames is reported as one data point. One data point is reported every 3.3 seconds.

• Standard kinetics (0.6 Hz, averaging by 5) - The average of 5 data frames is reported as one data point. One data point is reported every 1.6 seconds.

Recommended sensor offset: Large molecule kinetics—4 mm Sensor off set

(mm)


The following



Run Experiment

Tab:

Table 8-10:

General Settings



User name The user logon name.



page 331

Table 8-10:

General Settings (Continued)

Item

Description

Description




Experiment

>

Stop

.



MANAGING THE RUNTIME BINDING CHART

If the





window displays the assay step status, experiment progress, and the elapsed experiment time.

The



Sensor Tray Map

. Used sensor columns that are inactive are colored black. Active sample columns are colored green. Each assay in the experiment is represented by

Assay X

in the


box.

To selectively display data for particular assay:

1.


Assay

number.

2.

Select a subset of sensors for a displayed column under


box (see

Figure 8-58).








page 332

Chapter 8:


Figure 8-58:


Opening the Runtime Binding Chart



at any time:

1.

Click

File > Open Experiment

.

2.


Select

.


If the experiment includes reference biosensors, you can display reference-subtracted data in the chart by clicking the

Subtract Reference Biosensor

check box in the chart window.

To view raw data, remove the check mark next to this option.




tab



box


Data Selection

tab



page 333



1.

In the


list or the

Sensor Tray


Reference

(see Figure 8-59).

Figure 8-59:



R

in the


list and

Sensor

Tray (

see

Figure 8-60).

2.

Click the


check box

(

see

Figure 8-60).

Figure 8-60:




only makes a visual change to the data on the screen. The actual raw data is unaffected and the reference subtraction must be repeated during data analysis if needed.


page 334

Chapter 8:






Flip Data


Figure 8-61:


Aligning Data by a Selected Step

To align the binding data to the beginning of a user-selected step, in the

Runtime Binding

Chart

(see Figure 8-62), right-click a step and select

Align to Step <number>

.

To remove the step alignment, right-click the step and select

Unaligned

.

Figure 8-62:

Runtime Binding Chart—Aligning the Data to a User-Selected Step



page 335

Extending or Skipping an Assay Step

During acquisition, the duration of the active step may be extended. You can also terminate the active step and begin the next step in the assay.

NOTE: If the step you want to extend or terminate includes biosensors used in

Parallel Reference, Double Reference, or Average Reference subtraction methods, the data will not be analyzed.

To extend the duration of the active step:

1.



button.

2.

In the


dialog box (see Figure 8-63), enter the number of seconds to extend the step and click

OK

.

Figure 8-63:

Extend Current Step Dialog Box

To terminate a step and begin the next step in the assay:

1.


Go to Next Step

button.

2.

In the

Data Acquisition

dialog box, click

OK

.




Undo Zoom

.


To scale the Runtime Binding Chart:

1.

Right-click the Runtime Binding Chart and select

Properties

.

2.

In the


dialog box, select

Fullscale

or

Autoscale

.


page 336

Chapter 8:



To add a


title:

1.


Properties

.

2.

In the




To select a


legend:

1.


Properties

.

2.

In the


dialog box, select one of the following legends:

• Sensor Location

• Sample ID



Figure 8-64:


NOTE: Text for

Sample ID

,


, or


is taken from the


and



3.

Click

OK

.



Window

>

New Window

.




To export the



1.


Export Data

.

2.

In the

Exporting


Export

.

page 337

Figure 8-65:


Table 8-11:





Destination

Text/

Data

EMF, WMF,

BMP, JPG, or PNG


Export the

Runtime

Binding


Click

File

>

Browse


Click

File

>

Browse


Result




page 338

Chapter 8:


Table 8-11:





Destination

Clipboard Copy the

Runtime

Binding

Chart

Print the

Runtime

Binding

Chart

Printer

Result







Table 8-12:




File

>

Open Method

File

File

>

Save Method

File

or

File

>

Save Method

File As

Description





page 339

CHAPTER 9:



Maintenance

Octet RED96 and Octet QK Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340

Octet RED384 and Octet QK384 Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342

page 340

Chapter 9:

Maintenance

OCTET RED96 AND OCTET QK SYSTEMS

Cleaning the Octet Instrument

NOTE: If you use the Octet instrument regularly, clean the interior horizontal surfaces daily with a Kimwipe® tissue moistened with a 30–60% isopropyl alcohol solution. Otherwise, clean once a week or as needed.

To clean the Octet instrument:

1.

Turn off the power to the instrument

2.

Open the system door.

3.

Wipe the biosensor and sample platform (Figure 9-1).

4.

Carefully wipe the eight biosensor pickup tips.

5.

Allow the surfaces to dry for at least one minute with the door open.

Biosensor Pickup Tips

Sample Platform

Biosensor Platform

Figure 9-1:

Octet Instrument

Emptying the Waste Container

To empty the waste container:

1.

Press on the container to open it (Figure 9-2).

2.

Pull the container out and completely remove it from the instrument.

3.

Remove the container insert with the biosensor tips and dispose of both in a biohazard container suitable for sharp objects.

NOTE: ForteBio recommends that the waste container be emptied after every run of a 96-biosensor tray.


Octet RED96 and Octet QK Systems

page 341

Figure 9-2:

Waste Container for the Octet Instrument

Replacing Fuses (Octet RED96 and Octet QK

e

Systems only)

Two replaceable fuses are located on the left back panel of the Octet instrument power

supply (Figure 9-3).

WARNING: Turn off and unplug the instrument before replacing the fuses.



Fuses

Figure 9-3:

Octet Instrument Power Supply Back Panel

To replace the fuses:

1.

Using a small screwdriver, gently pop the fuse drawer out.

2.

Remove the expired fuse and place a new one in the holder.


page 342

Chapter 9:

Maintenance

WARNING: Only use 5 amp slow-blow fuses.



3.

Reinstall the fuse drawer.

OCTET RED384 AND OCTET QK384 SYSTEMS

Cleaning the Octet Instrument

NOTE: If you use the Octet instrument regularly, clean the interior horizontal surfaces daily with a Kimwipe moistened with a 30–60% isopropyl alcohol solution. Otherwise, clean once a week or as needed.

To clean the Octet instrument:

1.

Present the sample plate stage (Figure 9-4).

2.

Turn off the power to the instrument.

3.

Open the system door.

4.

Wipe the biosensor and sample platform.

5.

Allow the surfaces to dry for at least one minute with the door open.

Position for well A1

Biosensor tray and

 rehydration plate

Sample plate stage Reagent plate stage

Figure 9-4:

Octet RED384 and QK384 Stage Platform


Octet RED384 and Octet QK384 Systems

Cleaning the Biosensor Pickup Tips

The biosensor pickup tips hold the biosensors during an assay.

NOTE: The biosensor pickup tips should be cleaned weekly, or as needed.



To clean the biosensor pickup tips:

1.

Present the sample plate stage.

2.

Turn off the power to the instrument.

3.

Remove the side panel of the instrument (Figure 9-5).

page 343

Biosensor pickup tips

Figure 9-5:

Octet Instrument Side Panel Removed

4.

Gently clean the biosensor pickup tips with a Kimwipe moistened with a 30-60% isopropyl alcohol solution. Remove any debris left from the biosensor hub.

5.

Allow the biosensor pickup tips to dry for at least one minute.

6.

Replace the side cover, and then turn on the instrument.

Replacing Fuses

Two replaceable fuses are located on the left back panel of the Octet instrument power supply (Figure 9-6).

WARNING: Turn off and unplug the instrument before replacing the fuses.




page 344

Fuses

Figure 9-6:

Octet Instrument Power Supply Back Panel

To replace the fuses:

1.

Using a small screwdriver, gently pop the fuse drawer out.

2.

Remove the expired fuse and place a new one in the holder.

WARNING: Only use 5 amp slow-blow fuses.



3.

Reinstall the fuse drawer.

Chapter 9:

Maintenance


page 345

APPENDIX A:



Using Octet384 Systems with an Automation Interface

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346

Design of the Automation Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346

Automation Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349


page 346

Chapter A:


OVERVIEW

The Octet Data Acquisition software provides support for an automation interface using a

COM port (RS-232) or a Transmission Control Protocol/Internet Protocol (TCP/IP) socket/ port.

An example application for testing the automation interface, called

AutomationClient.exe

, is included in the applications and Dynamic Link Libraries (DLLs) installed with the

Octet Data Acquisition software. The file is located in the C:\Program Files\ForteBio\DataAcquisition directory.



NOTES:



The automation interface can be used with Octet384 systems only.



The examples that follow are illustrated using a TCP/IP connection, but the serial port connection behaves identically.

DESIGN OF THE AUTOMATION INTERFACE

The automation interface is designed to be as universal as possible, making no assumptions about the communication medium or the language of the client application connecting to the Octet System Data Acquisition software.

The following guidelines apply:

• All commands and responses are ASCII strings, one per line.

• All lines are terminated with both carriage-return and line-feed characters ("\r\n").

• Each command starts with the name of the command and may then be followed by required and optional parameters.

• Each parameter starts with a switch definition (a la dos/unix command line) followed by the parameter itself, which allows parameters to be sent in any order.

• The command or response is terminated with a new line (CR/LF) sequence.

• Parameters containing embedded spaces need to be enclosed in double quotes.

Automation Interface Control Setup

Before the Octet System Data Acquisition software can be controlled using an automation interface, the correct automation options must be set. To do this, go to

File

>

Options

(

Figure A-1) and select the appropriate port in the

Automation

box.

NOTE: The Octet System Data Acquisition software can be controlled via automation interface through a serial port (RS-232) or a TCP/IP socket.


Design of the Automation Interface

page 347

Figure A-1:

Options Dialog Box—Automation Interface Selection

NOTE: The

Localhost

option can be useful in developing the automation client on the same computer that runs the Octet System Data Acquisition software.

NOTE: ForteBio recommends that the

Data File

repositories be set using shared folders addressed by “UNC” folder names so that the internal path used by the Data Acquisition application corresponds to the external path used to access/retrieve the data files recorded during the experiment. Alternatively, the path returned by the

GetRunInfo

command to access the data files from another computer on the LAN.


page 348

Chapter A:


Automation Client Example Application

The

Automation Client

example application can connect to the Octet System Data Acquisition software via serial port (RS-232) port or TCP/IP socket.

To connect the Automation Client example application:

1.

In the Octet System Data Acquisition software, go to

File > Options

(see

Figure A-1).

2.

In the

Automation

box, select the communication port to be used (either TCP/IP or

RS232, see Figure A-1).

3.

Launch

AutomationClient.exe

located in the C:\Program Files\ForteBio\DataAcquisition directory to display the


dialog box (Figure A-2).

Figure A-2:

Automation Client Window

4.

Select the TCP/IP or RS-232 port selected previously in the Octet Data Acquisition software

Options

dialog box (Figure A-1). To connect locally using

Localhost

, leave the

Machine

field blank.

5.

Click

Connect

.

If the port is successfully opened, the automation client dialog will be minimized and remain minimized, indicating that the connection succeeded and the port is open. Otherwise, the automation client dialog will minimize and come back again, indicating that the connection attempt failed.


Automation Commands

page 349

6.

After a successful connection is established, send the default

Version

command (in the

Send Commands

—

Command

field) and then click

Send

!.

A response similar to the following should appear in the

Response

box:

Figure A-3:

Send Commands—Command Field

The response indicates that the


has connected to the Octet System

Data Acquisition software. This example indicates that version 6.1.0.75 of the Data

Acquisition software is controlling an Octet instrument using version 1.0 of the automation interface.

AUTOMATION COMMANDS

Table A-1 summarizes the commands supported by the Octet System Data Acquisition soft-

ware automation interface.

NOTE: The symbolic names are provided for C++ clients who connect using the interface as defined in the AutomationAPI.h header file.

Table A-1:

Commands Supported by the Automation Interface

Command

Version

Reset

GetMethodInfo

Run

GetRunInfo

Symbolic Name

AUT_CMD_VERSION Returns the version of the application being automated, the type of instrument it is controlling, and the automation API version.

AUT_CMD_RESET Stops any running experiment and resets the instrument.

AUT_CMD_GETMETHODINFO Returns information about the resources required by given method file.

AUT_CMD_RUN

AUT_CMD_GETRUNINFO

Purpose

Runs an experiment using a given method file.

Returns information about the experiment currently running.


page 350

Chapter A:


Table A-1:

Commands Supported by the Automation Interface (Continued)

Command

Stop

Status

Present

Resume

Close

Cleanup

Symbolic Name

AUT_CMD_STOP

AUT_CMD_STATUS

AUT_CMD_PRESENT

AUT_CMD_RESUME

AUT_CMD_CLOSE

AUT_CMD_CLEANUP

Purpose

Stops a running experiment, ejecting the sensors if necessary.

Returns status during a running experiment:

OK

= ready

Busy

=running

Waiting

= waiting for a condition to be resolved

Error

= experiment was terminated by an error

Busy

is followed by descriptive information on the progress of the experiment (% complete)

(Octet 384 only)

Open the door and move the stage to the presentation position.

Indicates that the “Waiting” condition has been resolved (new sensor tray installed). Continues the experiment.

Closes the door if it is open.

Homes the read head on an

Octet 384 instrument.

Closes open MDI windows. Only valid when not busy. Useful when using the

Run

command without the

-s

option.



page 351

Typical Automation Session

The following example is a typical automation session that illustrates the use of the automation commands to run an experiment.

NOTE: Commands sent from the client application are designated as

SEND:

.

Responses received from the Octet System Data Acquisition software are designated as

RECV:

.

Connecting to the Data Acquisition Software

SEND: Version\r\n

RECV: 6.1.0.30 Pegasys 1.0

SEND: Status\r\n

RECV: OK

Preparing for an Experiment

SEND: Cleanup

RECV: OK

SEND: GetMethodInfo -mC:\MethodFiles\Q001.fmf\r\n

RECV: OK -p96,0 -t1 -s"Anti-Human IgG Fc"


SEND: Version\r\n


SEND: Status\r\n

RECV: OK

Getting Information about the Experiment

SEND: Version\r\n


SEND: Status\r\n

RECV: OK

Monitoring the Experiment

bool bBusy = true; while (bBusy)

{

Send("Status\r\n");

response = Recv();

if (response==OK)


page 352

Chapter A:


bBusy = false;

else

Sleep(1000); // sleep for a second

}

SEND: Status\r\n

RECV: Running (5%)

SEND: Status\r\n

RECV: Running (25%)

SEND: Status\r\n

RECV: Running (45%)

SEND: Status\r\n

RECV: Running (75%)

SEND: Status\r\n

RECV: Running (95%)

SEND: Status\r\n

RECV: OK

Stopping the Experiment and Presenting the Plate for Unloading

Both the

Stop

and the

Present

commands are asynchronous—they initially return

OK

to indicate that the command was accepted and started OK, but status must be polled until

OK

is returned to indicate completion.

SEND: Stop\r\n

RECV: OK

SEND: Status\r\n

RECV: Busy

SEND: Status\r\n

RECV: Busy

SEND: Status\r\n

RECV: OK

SEND: Present\r\n

RECV: OK



page 353

SEND: Status\r\n

RECV: Busy

SEND: Status\r\n

RECV: Busy

SEND: Status\r\n

RECV: OK

Advanced Automation Session

If an experiment is sufficiently complex it may require more than one tray of sensors to complete the experiment. This can be detected at the start of the experiment by checking the

-tN

response from the

GetMethodInfo

command. If N is greater than

1

, then the experiment requires more than one tray of sensors to complete.

If this is the case, initially the experiment will start as before, but halfway through the experiment the

Status

command will return

LoadSensors

indicating that the first tray of sensors has been exhausted and another tray of sensors needs to be loaded. At this point, you must issue the

Present

command to allow access to the sensor plate (polled for completion) and then once the new sensor tray is in place, the

Resume

command must be sent to resume the experiment.

Connecting to Data Acquisition

SEND: Version\r\n


SEND: Status\r\n

RECV: OK

Preparing for an Experiment

SEND: Cleanup

RECV: OK

SEND: GetMethodInfo -mC:\MethodFiles\Q002.fmf\r\n

RECV: OK -p96,0 -t2 -s"Anti-Human IgG Fc"


SEND: Run -mC:\MethodFiles\Q002.fmf -bP0001 -s\r\n

RECV: OK

Getting Information about the Experiment

SEND: GetRunInfo\r\n

RECV: OK -n"Experiment 2" -p"\\fbdata\Quantitation\Experiment 2"\r\n


page 354

Chapter A:


Monitoring the Experiment

bool MonitorExperiment(CCmdTransport *pPort)

{

// Poll the experiment until it is done.

for (;;)

{

Sleep(200); if (!SendRecv(pPort, AUT_CMD_STATUS + AUT_EOL, csResp)) return false; int nStart = 0;

CString csStatus = csResp.Tokenize(" ", nStart); if (csStatus == AUT_OK) break ; // SUCCESS else if (csStatus == AUT_STOPPED) break ; // SUCCESS else if (csStatus == AUT_RUNNING)

; else if (csStatus == AUT_WAITING)

; else if (csStatus == AUT_LOADSENSORS)

{

if (!LoadSensors(pPort)) return false ;

} else if (csStatus == AUT_BUSY)

; else if (csStatus == AUT_ERROR) return false ;

}

} bool LoadSensors(CCmdTransport *pPort)

{ if (!SendRecv(pPort, AUT_CMD_PRESENT + AUT_EOL, csResp)) return false ; if (csResp != AUT_OK) return false ;



page 355 if (!WaitNotBusy(pPort)) return false ;

// At this point the robot replaces the sensor tray.

AfxMessageBox( "Robot changes sensor tray..." ); if (!SendRecv(pPort, AUT_CMD_RESUME + AUT_EOL, csResp)) return false ; if (csResp != AUT_OK) return false ; return WaitNotBusy(pPort);

} bool WaitNotBusy(CClientResponder *pPort)

{

CCountdownTimer Timer(c_uBusyTimeoutMS);

CString csResp; while (!Timer.IsDone())

{

Sleep(200); if (!SendRecv(pPort, AUT_CMD_STATUS + AUT_EOL, csResp)) return false ; int nStart = 0;

CString csStatus = csResp.Tokenize(" ", nStart); if (csStatus == AUT_OK) return true ; else if (csStatus == AUT_STOPPED) return false ; else if (csStatus == AUT_RUNNING) return true ; else if (csStatus == AUT_WAITING) return true ; else if (csStatus == AUT_LOADSENSORS) return true ;


page 356

Chapter A:

Using Octet384 Systems with an Automation Interface else if (csStatus == AUT_BUSY)

; else if (csStatus == AUT_ERROR) return false ;

}

TRACE1( "Timeout waiting for not busy after %d ms\n" ,

Timer.GetElapsed()); return false ;

}

Automation API.H

//

**********************************************************************

***

//

// Copyright (c) 2011 ForteBio.

// All rights reserved.

//

//

**********************************************************************

***

// HEADER: AutomationAPI.h

// PURPOSE: Defines the commands supported by the automation API.

// AUTHOR: BHI Nov 2008

//

#ifndef INC_ACQUISITION_AUTOMATIONAPI_H

#define INC_ACQUISITION_AUTOMATIONAPI_H

// NOTES:

// Do not position the Octet instrument such that it is difficult to disconnect the power.

// The automation interface is string based. Commands and responses are strings, one per line.

// Each command starts with the name of the command and may then be followed by required and optional parameters.

// Each parameter starts with a switch definition (a la dos/unix command line) followed by the parameter itself. This allows parameters to be sent in any order.

// The command or response is terminated with a new line (CR/LF) sequence.

// Parameters containing embedded spaces must be enclosed in double quotes.

// Response items containing embedded spaces will be enclosed in double quotes.



page 357

// REVISIONS:

// 1.0 First release

// 1.1 Added (-p) plate file parameter to "Run" and "GetMethod-

Info"

// commands

// Added (-u) use-last-sensor-tray option to the "Run" command.

// Added "SetValue" command to set the temperature target.

// Version of the API described in this header file.

const char AUT_API_VERSION[] = "1.1" ;

// Status return values const char AUT_OK[] = "OK" ; const char AUT_STOPPED[] = "Stopped" ; const char AUT_RUNNING[] = "Running" ; const char AUT_WAITING[] = "Waiting" ; const char AUT_LOADSENSORS[] = "LoadSensors" ; const char AUT_BUSY[] = "Busy" ; // Resetting, Presenting const char AUT_ERROR[] = "ERROR" ; const char AUT_EOL[] = "\r\n" ;

// Parameter switches for the Run command const char AUT_SWITCH_METHOD = 'm' ; // Method file to load

(required) const char AUT_SWITCH_FOLDER = 'f' ; // Root folder for experiment data (optional) const char AUT_SWITCH_EXPERIMENT = 'e' ; // Overide for the experiment name in the FMF file (optional) const char AUT_SWITCH_PLATEFILE = 'p' ; // Plate file to import after method file is loaded (optional) const char AUT_SWITCH_BARCODE = 'b' ; // Bar code of Sample plate (optional) const char AUT_SWITCH_BARCODE1 = '1' ; // Alias for

AUT_SWITCH_BARCODE (optional) const char AUT_SWITCH_BARCODE2 = '2' ; // Bar code of Reagent plate (optional) const char AUT_SWITCH_LOTNUMBER = 'l' ; // Lot number of sensors

(optional) const char AUT_SWITCH_SILENT = 's' ; // Don't open the runtime window (optional) const char AUT_SWITCH_USELAST = 'u' ; // Reuse the sensor tray as it was left after last run (optional) const char AUT_SWITCH_VERBOSE = 'v' ; // Send back verbose status information


page 358

Chapter A:


// Parameter switches for the SetValue command const char AUT_SWITCH_TEMPERATURE = 't' ;

// Response parameter switches for the GetMethodInfo command const char AUT_RESPONSE_PLATEWELLS = 'p' ; const char AUT_RESPONSE_SENSORTRAYS = 't' ; const char AUT_RESPONSE_SENSORTYPE = 's' ; const char AUT_RESPONSE_EXPTYPE = 'e' ; const char AUT_RESPONSE_RERACKING = 'r' ;

// Response parameter switches for the GetRunInfo command const char AUT_RESPONSE_EXPNAME = 'n' ; const char AUT_RESPONSE_EXPPATH = 'p' ; const char AUT_CMD_VERSION[] = "Version" ;

// Returns the version of the app being automated, the hardware platform it controls, and the API version.

// Args: (none)

// Response: App product version (e.g. "6.0.0.120 Pegasys 1.0\r\n") const char AUT_CMD_RESET[] = "Reset" ;

// Stops any running experiment and resets the instrument.

// Args: (none)

// Response:

// "OK\r\n"

// "Error: <reason>\r\n" const char AUT_CMD_GETMETHODINFO[] = "GetMethodInfo" ;

// Returns info about a method file

// Args:

// -m <path> Method file name (required)

// Response:

// "OK -r<bool> -t<int> -s<name>\r\n"

// e.g. OK -p96,0 -t2 -s"SA (Streptavidin)\r\n"

// Response params:

// -p<int>,<int> Sizes of the plates in use e.g. p384,96

// -t<int> Number of sensor trays required (0 .. 5) e.g. -t2

// -s<name> Name of first sensor in the tray e.g. s"SA (Streptavidin)"

// "Error: load method\r\n"



page 359

// "Error: bad method\r\n" const char AUT_CMD_RUN[] = "Run" ;

// Runs an experiment

// Args:

// -m <path> Method file name (required)

// -p <path> Plate file to update sample plate in method settings (optional)

// -b <barcode> Sample plate bar code (optional)

// -1 <barcode> Sample plate bar code (optional)

// -2 <barcode> Reagent plate bar code (optional)

// -l <lotnumber> Sensor tray lot number (optional)

// -s Silent - does not open the runtime view (optional)

// -u Use the state of the sensor tray as it was left after last run

// Response:

// "OK\r\n"

// "Error: not ready\r\n"

// "Error: bad method\r\n"

// "Error: bad barcode\r\n" const char AUT_CMD_GETRUNINFO[] = "GetRunInfo" ;

// Returns information about an experiment that is currently running

// Args: (none)

// Response:

// "OK -n"Experiment 1" -p" \\ fbdata\Quantitation\Experiment 1 "\r\n"

// "Error: <reason>\r\n"

// Response params:

// -n<experiment name> Name of the experiment (folder name in repository) e.g. -n"Experiment 1"

// -p<experiment path> Full path to experiment folder in repository e.g. -p" \\fbdata\Quantitation\Experiment 1 " const char AUT_CMD_STOP[] = "Stop" ;

// Stops a running experiment

// Args: (none)

// Response:

// "OK\r\n"

// "Error: <reason>\r\n" const char AUT_CMD_SETVALUE[] = "SetValue" ;

// Sets a value


page 360

Chapter A:


// Args:

// -t <temp> Sets heater target temperature (DegC)

// Response:

// "OK\r\n"

// "Error: <reason>\r\n" const char AUT_CMD_STATUS[] = "Status" ;

// Returns status: OK=ready, Busy=running, Error=Experiment was terminated by an error.

// Busy is followed by descriptive information on the progress of the experiment (% complete)

// Args: (none)

// Response:

// "OK\r\n"

// "Waiting\r\n"

// "Busy\r\n"

// "Running (nn%)\r\n"

// "LoadSensors\r\n"

// "Error: <reason>\r\n" const char AUT_CMD_PRESENT[] = "Present" ; // Pegasys only

// Open the door and move the stage to the presentation position.

// Args: (none)

// Response:

// "OK\r\n"


// N.B.: Poll status waiting for "Waiting" condition to reappear const char AUT_CMD_RESUME[] = "Resume" ;

// Indicates that the "Waiting" condition has been resolved (new sensor tray installed). Continues the experiment.

// Args: (none)

// Response:

// "OK\r\n"


// Status will indicate busy until door is closed, then will return to

Running state.

const char AUT_CMD_CLOSE[] = "Close" ;

// Closes the stage if it is open.

// Args: (none)

// Response:



page 361

// "OK\r\n"


// Status will indicate busy until door is closed.

const char AUT_CMD_CLEANUP[] = "Cleanup" ;

// Closes open MDI windows. Only valid when not busy.

// Args: (none)

// Response:

// "OK\r\n"

// "Error: busy\r\n";

#endif // INC_ACQUISITION_AUTOMATIONAPI_H

Analysis Automation API

//

**********************************************************************

***

//

// Copyright (c) 2011 ForteBio.

// All rights reserved.

//

//

**********************************************************************

***

// HEADER: AutomationAPI.h

// PURPOSE: Defines the commands supported by the automation API.

// AUTHOR: BHI Nov 2008

//

#ifndef INC_ANALYSIS_AUTOMATIONAPI_H

#define INC_ANALYSIS_AUTOMATIONAPI_H

// NOTES:

// * The automation interface is string based. Commands and responses are

// strings, one per line.

// * Each command starts with the name of the command and may then be

// followed by required and

// optional parameters.

// * Each parameter starts with a switch definition (a la dos/unix command

// line) followed by the

// parameter itself. This allows parameters to be sent in any order.


page 362

Chapter A:


// * The command or response is terminated with a new line (CR/LF) sequence.

// * Parameters containing embedded spaces must be enclosed in double

// quotes.

// * Response items containing embedded spaces will be enclosed in double

// quotes.

// Version of thew API described in this header file.

const char AUT_API_VERSION[] = "1.0" ;

// Status return values const char AUT_OK[] = "OK" ; const char AUT_RUNNING[] = "Running" ; const char AUT_ERROR[] = "ERROR" ; const char AUT_BUSY[] = "Busy" ; const char AUT_STOPPED[] = "Stopped" ; // Stopped by user .

const char AUT_EOL[] = "\r\n" ;

// Parameter switches for the LOAD command const char AUT_SWITCH_DATASET = 'd' ;

// Parameter switches for the ANALYZE command const char AUT_SWITCH_PARAMS = 'p' ; const char AUT_SWITCH_XMLINFO = 'x' ;

// COMMAND API

// =========== const char AUT_CMD_VERSION[] = "Version" ;

// Returns the version of the app being automated, and the API version.

// Args: (none)

// Response: App product version (e.g. "6.3.1.12 1.0\r\n") const char AUT_CMD_LOAD[] = "Load" ;

// Loads an experiment

// Args:

// -d <path> Path to experiment data files

// Response:

// "OK\r\n"




page 363 const char AUT_CMD_ANALYZE[] = "Analyze" ;

// Runs an analysis

// Args:

// -p <path> Path to parameters (INI file)

// -x <path> Path to XML information file (optional, can be multiple XML info files)

// Response:

// "OK\r\n"

// "Error: <reason>\r\n" const char AUT_CMD_STATUS[] = "Status" ;

// Returns status: OK=ready, Busy=running, Error=Action was terminated by an error.

// Busy is followed by descriptive information on the progress of the experiment (% complete)

// Args: (none)

// Response:

// "OK\r\n"

// "Busy\r\n"

// "Running (nn%)\r\n"


#endif // INC_ANALYSIS_AUTOMATIONAPI_H


page 364

Chapter A:



page 365

APPENDIX B:



21 CFR Part 11 Software

Administrator Options

Installing the Data Acquisition 7.0 21 CFR Part 11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366

Installing the Data Analysis 7.0 21 CFR Part 11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369

Installing the ForteBio GxP Server Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371

Administrator Account Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374

Starting an Administrator User Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378

Accessing Administrator Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381

Accessing the GxP Server Module Directly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396

Restarting the GxP Server Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398


page 366

Chapter B:

21 CFR Part 11 Software Administrator Options

INSTALLING THE DATA ACQUISITION 7.0 21 CFR PART 11 SOFTWARE

To install the Data Acquisition 7.0 21 CFR Part 11 software:

1.

Insert the software

V7.0 CFR CD (7.00.35/7.0.0.9)

into your CD drive.

• If the Autoplay dialog box displays, choose to open the CD to view files.

• If the Autoplay dialog box does not display, navigate to the CD using Windows

Explorer.

Optical drives are typically found under the

D:\

or

E:\

drive.

2.

Double-click

DataAcquisition-CFR-7_0_0_x.exe

to launch the installation wizard (see

Figure B-1).

Figure B-1:

Data Acquisition 7.0 (for 21 CFR Part 11) Software Setup Wizard

3.

Click

Next

to display the Choose Install Location dialog box (Figure B-2).


Installing the Data Acquisition 7.0 21 CFR Part 11 Software

page 367

Figure B-2:

Choose Install Location Dialog Box

The default location for the software on the local machine is

C:\Program Files\Forte-

Bio\DataAcquisition7

.

4.

Click

Next

to accept this path location.

The Choose Start Menu Folder dialog box displays (Figure B-3).

Figure B-3:

Choose Start Menu Folder Dialog Box

The default Start Menu folder is

ForteBio

.

5.

Click

Install

.

The installation wizard takes a few seconds to install (Figure B-4).


page 368

Chapter B:


Figure B-4:

Installation Progress

The installation wizard displays the Completing the Data Acquisition 7.0 Setup Wizard

dialog box (Figure B-5).

Figure B-5:

Completing the Data Analysis 7.0 Setup

6.

Click

Finish

to complete the installation.


Installing the Data Analysis 7.0 21 CFR Part 11 Software

page 369

INSTALLING THE DATA ANALYSIS 7.0 21 CFR PART 11 SOFTWARE

To install the Data Analysis 7.0 21 CFR Part 11 software:

1.

Insert the software CD into your CD drive.

2.

Navigate to the window listing the files located on the installation CD.

3.

Double-click

DataAnalysis-CFR-7_0_0_x.exe

to launch the installation wizard (see

Figure B-6).

Figure B-6:

Data Analysis 7.0 (for 21 CFR Part 11) Software Setup Wizard

4.

Click

Next


Figure B-7:

Choose Install Location Dialog Box


page 370

Chapter B:




Bio\DataAnalysis7

.

5.

Click

Next



Figure B-8:



ForteBio

.

6.

Click

Install

.


Figure B-9:



Installing the ForteBio GxP Server Module

page 371

The installation wizard displays the Completing the Data Analysis 7.0 Setup Wizard dialog box (Figure B-10).

Figure B-10:

Completing the Data Analysis 7.0 Setup

7.

Click

Finish


INSTALLING THE FORTEBIO GXP SERVER MODULE

The ForteBio GxP Server module can be installed and run from the following locations:

• A local host computer where the ForteBio Data Acquisition or Data Analysis 7.0 21

CFR Part 11 software is installed

• A remote host computer networked to a machine where the ForteBio Data Acquisition or Data Analysis 7.0 21 CFR Part 11 software is installed

Upon launching the Octet System Data Acquisition or Data Analysis 7.0 CFR 11 software, you are required to select the GxP Server module host location. If the GxP Server module is installed in multiple locations, you can select any host server. The user session event record will be saved only to the host location selected, making it possible to have records for the same user in multiple locations.

NOTE: For administrators only. To ensure that all records are saved to one location, ForteBio recommends that administrators install a single copy of the

ForteBio GxP Server module on the network that can then be accessed by all users.


page 372

Chapter B:


To install the ForteBio GxP Server software:

1.

Navigate to the window listing the files located on the installation CD.

2.

Double-click

ForteBio GxP Server 7.0.exe

to launch the installer.

3.

If prompted with the Do you want the following program from an unknown publisher to

make changes to this computer? message, reply

Yes

.

The installation wizard should display (Figure B-11).

Figure B-11:

ForteBio GxP Server 7.0 Software Setup Wizard

4.

Click

Next


Figure B-12:

Choose Install Location


Installing the ForteBio GxP Server Module

page 373



Bio\DataAnalysis7

.

5.

Click

Next



Figure B-13:



ForteBio

.

6.

Click

Install

.


Figure B-14:



page 374

Chapter B:


The installation wizard displays the Completing the ForteBio GxP Server 7.0 Setup Wizard dialog box (Figure B-15).

Figure B-15:

Completing the ForteBio GxP Server Software 7.0 Setup

7.

Click

Finish


ADMINISTRATOR ACCOUNT SETUP

To set up the administrator account:

1.


Figure B-16:


The

Login



Administrator Account Setup

page 375

Figure B-17:

Login Dialog Box

2.

Select a

Server

location by clicking

...

(

Browse

).

The



Figure B-18:

Authentication Server Dialog Box

Click

Default

to recall the default server settings of localhost and Port 2002.

• Local host—If the local computer is to be used as the GxP Server module host, select the

Localhost

check box. Change the Port number if needed.

• Remote host on same subnet—If the GxP Server module is hosted on the same subnet, deselect the

Localhost

check box and click

Find

. A list of potential GxP

Server module addresses will be listed. Choose the desired location from the list and click

O

K.


page 376

Chapter B:


Figure B-19:

GxP Server Address Search Results

• Remote host on another subnet—If the GxP Server module is hosted on a different subnet, deselect the

Localhost

check box. Enter the IP address of the computer hosting the GxP Server module.

Figure B-20:

Manual Entry of Remote Host Address

When the GxP Server module host location has been selected or entered, click

OK

to save changes and exit the


dialog box. The GxP Server module location will now be listed as the

Server

in the

Login

box.

NOTE: Once the GxP Server module host location is selected, this location will be used as the default selection for the administrator account. It does not need to be re-selected each time a new session is initiated.


Administrator Account Setup

page 377

Figure B-21:

Login Dialog Box—DisplayingGxP Server Location

3.

From the

User

drop-down list, select

Administrator

.

4.

Leave the Password blank and the

Project

set to

(none)

and click

OK.

Figure B-22:

Administrator User Selection

The

Change Password

dialog box will display (Figure B-23).


page 378

Chapter B:


Figure B-23:


5.

Enter a

New password

and


(optional) and click

OK

.

The Data Acquisition or Data Analysis software will now launch and initiate an administrator user session which will allow access to administration options.

STARTING AN ADMINISTRATOR USER SESSION

Administrators initiate new user sessions the same way non-administrative users do.

To start an administrator user session:

1.


Figure B-24:


The

Login



Starting an Administrator User Session

page 379

Figure B-25:

Login Dialog Box

2.

Confirm that the

Server

location is correct. If not, please see “Administrator Account

Setup” on page 374.

3.

Select

Administrator

from the

User

drop-down list.

Figure B-26:

Administrator User Name Selection

4.

Enter your password in the

Password

text box. Click

?

for a password reminder if needed.


page 380

Chapter B:


Figure B-27:

Password Reminder

5.

Select a project from the

Project

drop-down list, if required.

Figure B-28:

Project Selection

6.

Click

OK.

The Data Acquisition or Data Analysis software will now launch and start the administrator session. During the session, the administrator account and project selected at login display in the software status bar:

Figure B-29:

Status Bar


Accessing Administrator Options

page 381

NOTE: Administrator and user sessions are automatically locked after a period of inactivity set using the

UserIdleMin

constant. Please see “Administrator

Constants” on page 392 for more information. The

Login

dialog box will display and a message indicating the session has been locked will be shown. You can choose to log back into the session or log off at this time. Administrator and user sessions will not be locked during experimental data acquisition.

ACCESSING ADMINISTRATOR OPTIONS

The 21 CFR Part 11 software Server Administration options allow administrators to mange users, groups, projects and constants and view associated events.

These options can be accessed in the Data Acquisition and Data Analysis software or by launching the ForteBio GxP Server module directly.

• Data Acquisition and Data Analysis softwareClick

Security

>

Server Administration

:

Figure B-30:

Security Menu

•

ForteBio GxP Server module on network location—Double-click on the



FBServerConfig.exe

file in the

FBServer7

folder from the installed location:

Figure B-31:

Accessing the GxP Server on the Network


page 382

Chapter B:


• ForteBio GxP Server module on a local host computer - Double-click the



ForteBio GxP Server desktop icon:

Figure B-32:

Security Menu

NOTE: When accessing the ForteBio GxP Server module directly, additional

tools are also provided to test server functionality. Please see “Accessing the

GxP Server Module Directly” on page 396 for more information.

The

ForteBio GxP Server Administration

window will display:

Figure B-33:

GxP Server Administration Window



page 383

Administrator Tabs

Five tabs are available in the

ForteBio GxP Server Administration

window that contain the following options:

•

Users Tab

—Allows user and password management and individual privileges selection

•

Groups Tab

—Allows user group management and group privileges selection

•

Projects Tab

—Allows project management and setup

•

Constants Tab

—Allows setup of password requirements, cached server credentials and screen lock due to inactivity.

•

Events Tab

—Displays event logs for individual user accounts, projects or machines

To view the information contained on a tab, just click on the tab.

Tab View

Each tab displays a list of administrator entries and associated setting information that can be sorted by clicking on any of the column headers:

Figure B-34:

Tab Contents Sorted by Password Age

Tab Menu

Right-clicking on an entry or on a blank area in the tab will display the

Tab

menu.

Tab

menu options vary depending on the tab selected.

Figure B-35:

Tab Menu


page 384

Chapter B:


User Account Administration

The

Users Tab

allows administrators to add and delete user accounts as well as set and change individual user account privileges and passwords.

Figure B-36:

Users Tab

Creating a New User Account

To create a new user account:

1.

Right-click anywhere in the

Users Tab

and select

New User

from the

Tab

menu, or double-click in a blank area.

The

New User


Figure B-37:

New User Dialog Box



page 385

2.

Assign Account Details. Enter the user’s

Login name

,

Full name

,

Information

(optional),

Password

, and


(optional).

3.

Assign a User Group. Select a user group from the

Group

drop down list. The following default group selections are available:

•

Administrators

—can add, delete and change user accounts and groups

•

Supervisors

—can review data and events

•

Developers

—can create, run, save and export data

•

Lab Users

—can only run experiments

•

Guests

—have no explicit privileges, these must be assigned by the administrator

If other user groups have been created by an administrator, they will also be available for selection in the

Group

drop down box. For more information, please see “Creating a New

User Group” on page 389.

4.

Assign Privileges. Each user account can be assigned specific privileges. The privileges displayed initially will be those defined in the user group selected in the previous step.

Privileges for the default user groups are shown in Table B-1. If needed, change user

account privileges by selecting or deselecting the check boxes next to each privileges.

•

Administration

—Can administer the user database

•

Review

—Can review changes and events

•

Change

—Can change methods and configuration values

•

Plate

—Can change sample plate properties

•

Run

—Can run experiments and analyses

Table B-1:

Default User Group Privileges

Privilege

Administration

Review

Change

Plate

Run

Administrator Supervisor Developer Lab User Guest

5.

Options—Select the

Password does not expire

check box if desired. This check box is deselected by default. Deselecting this option will let user account passwords expire at the

set PasswordTTL

constant. For more information on setting constants please see

“Administrator Constants” on page 392.

6.

Click

OK



page 386

Chapter B:


Viewing and Changing User Account Settings

To view and change user account settings:

1.

Right-click on the user account and select

Edit User

from the

Tab

menu, or doubleclick on the user account.

The

Edit User


Figure B-38:

Edit User Dialog Box

2.

If needed, modify the user account settings. For more details on individual settings, please refer to “Creating a New User Account” on page 384.

3.

Click

OK


Deleting a User Account

To delete a user account:

1.


Delete User

from the

Tab

menu.

2.

Click

OK

in the dialog box displayed.



Changing User Account Passwords

To change user account passwords:

1.


Set Password

from the

Tab

menu.

The

Change Password

dialog box will display: page 387

Figure B-39:


2.

Enter the


for the user account. Click

?


3.

Enter the

New Password

and


(optional).

4.

Click

OK


Changing the Administrator Password

1.

Initiate a new administrator user session with the existing password.

2.

When the software launches, select

Change Password...

from the

Security

menu.

The

Change Password


NOTE: The

Change Password

dialog box can also be accessed by right-clicking on the administrator account in the

Users Tab

and selecting

Set Password

from the

Tab

menu.


page 388

Chapter B:


Figure B-40:

Administrator Change Password Dialog Box

3.

Enter the


for your user account. Click

?


4.

Enter the

New Password

and


(optional).

5.

Click

OK


Group Administration

The

Groups Tab

allows administrators to add and delete user groups as well as set and change group privileges.

Figure B-41:

Groups Tab

When a user account is assigned to a user group, the privileges defined in the group are also applied to the individual user account. The following default user groups are available and the privileges assigned to each are shown Table B-2:

•

Administrators

- Can add, delete and change user accounts and groups

•

Supervisors

- Can review data and events

•

Developers

- Can create, run, save and export data

•

Lab Users

- Can only run experiments



page 389

•

Guests

- Have no explicit privileges, these must be assigned by the administrator

Table B-2:

Default user group privileges.

Privilege

Administration

Review

Change

Plate

Run

Administrator Supervisor Developer Lab User Guest

Creating a New User Group

1.


Groups Tab

and select

New Group

from the

Tab

menu or double-click in a blank area.

The

New Group


Figure B-42:

New Group Dialog Box

2.

Enter the

Group name

and

Information

(optional).

3.

Privileges - Each group can be assigned specific privileges. Add group privileges by selecting or deselecting the check boxes next to each privilege:

•

Administration -

Can administer the user database

•

Review -

Can review changes and events

•

Change -

Can change methods and configuration values

•

Plate -

Can change sample plate properties

•

Run -

Can run experiments and analyses

4.

Click

OK



page 390

Chapter B:


Viewing and Changing Group Settings

1.

Right-click on the group and select

Edit Group

from the

Tab

menu or double click on the group.

The

Edit Group


Figure B-43:

Edit Group Dialog Box

2.

If needed, modify the group settings. For more details on individual settings, please refer to “Creating a New User Group” on page 389.

3.

Click

OK


Deleting a User Group

1.

Right-click on the group and select

Delete Group

from the

Tab

menu.

2.

Click

OK


Project Administration

The

Projects Tab

allows administrators to add and delete user projects. Projects are selected when a new user session is initiated in the Data Acquisition or Data Analysis software, allowing all user, system and software events for a particular project to be monitored.



page 391

Figure B-44:

Projects Tab

Creating a New Project

1.


Projects Tab

and select

New Project

from the

Tab

menu, or double-click in a blank area.

The

New Project

dialog box will display.

Figure B-45:

New Project Dialog Box

2.

Enter the

Project name

and

Information

(optional).

3.

Click

OK


Viewing and Changing Project Settings

1.

Right-click on the project and select

Edit Project

from the

Tab

menu, or double-click on the project.

The

Edit Project



page 392

Chapter B:


Figure B-46:

Edit Project Dialog Box

2.

If needed, modify the project settings.

3.

Click

OK


Deleting a Project

1.

Right-click on the project and select

Delete Project

from the

Tab

menu.

2.

Click

OK


Administrator Constants

The Constants Tab allows administrators to set GxP Server module constant settings.

Figure B-47:

Constants Tab

Available administrator constants and their associated value ranges are shown in Table B-3.



page 393

Table B-3:

Administrator Constants

Constant

CredentialsTTL

PasswordMin-

Length

PasswordSecure

PasswordTTL

UserIdleMin

Description

The number of days that the server settings are stored in the cache. This allows the software to operate in case the server is temporarily down.

Minimum number of characters that a password must contain.

Level of password complexity.

Setting the constant to 0 has no password restrictions. Setting the constant to 1 requires passwords to contain at least one alpha, one numeric, and one punctuation character.

Amount of time that a password is allowed to remain unchanged.

Idle time allowed during a user session after which the session is automatically closed.

Default

Value

5

0

0

180

15

Value Range

Minimum=0, no max value


0-1



Creating a New Constant

1.


Constants Tab

and select

New Constant

from the

Tab

menu or double-click in a blank area.

The

New Constant


Figure B-48:

New Constant Dialog Box

2.

Enter the

Constant name

and

Value

. Please refer to Table B-3 for a list of available con-

stants and value ranges.


page 394

Chapter B:


3.

Click

OK


Viewing and Changing Constants

1.

Right-click on the constant and select

Edit Constant

from the

Tab

menu or doubleclick on the constant.

The

Edit Constant


Figure B-49:

Edit Constant Dialog Box

2.

If needed, modify the constant settings. For more information on available constants

and their values, please see Table B-3.

3.

Click

OK


Deleting a Constant

1.

Right-click on the constant and select

Delete Constant

from the

Tab

menu.

2.

Click

OK


Event Log

The

Events Tab

allows administrators to view all the user, system and software event information recorded by the GxP Server module.



page 395

Figure B-50:

Events Tab

Events are tracked for individual user accounts, projects and machines. By default, a historical log of all events recorded on the active GxP Server module will display.

To view events for a specific user account, project or computer, click on the

User

,

Project

or

Machine

drop-down list and select an entry:

Figure B-51:

Selecting Events by User Name

NOTE: Selections can be made in either one or all of the

User

,

Project

or

Machine

drop-down lists.


page 396

Chapter B:


The list will then only display events for the entries selected:

Figure B-52:

Events Displayed for User Name

In addition to the specific user, project and machine selections, the following list options are also available:

•

(any)

- Displays all user, project or machine events

•

(none)

- Displays all user and machine events not associated with a specific project

(

Project

list only)

ACCESSING THE GXP SERVER MODULE DIRECTLY

The GxP Server module can be accessed by administrators directly without having to initiate an administrator user session. Direct access provides administrators with server testing options as well as access to all administrative functions discussed earlier in this section.

To access the GxP Server module directly:

• If the GxP Server module is installed on a network location - Double-click on the

FBServerConfig.exe

file in the

FBServer7

folder from the installed location:

Figure B-53:


• If the GxP Server module is installed on a local host computer - Double-click the



ForteBio GxP Server desktop icon:


Accessing the GxP Server Module Directly

Figure B-54:

ForteBio GxP Server Desktop Icon

The

ForteBio GxP Server Configuration

window will display: page 397

Figure B-55:

GxP Server Configuration Window

Use of the

User

,

Groups

,

Projects

,

Constants

and

Events

tabs are described in “Accessing

Administrator Options” on page 381.

Server Testing

The GxP Server module can be tested to ensure it is accessible and functioning properly.

1.

In the

Connections to Clients

box, make changes to the server settings if needed.

Figure B-56:

Connections to Clients Box

2.

Click

Apply & Test

. If the GxP Server module is found and functioning properly, the following message will display:


page 398

Chapter B:


Figure B-57:

Server Found

To return to the originally configured GxP Server module settings, click

Default

at any time.

RESTARTING THE GXP SERVER MODULE

If the host location of the GxP Server module cannot be found during user login or if users are unable to login with valid credentials, the GxP Server module may be offline and need to be restarted.

NOTE: ForteBio recommends contacting your IT department to confirm whether or not network or firewall settings may have been changed. This may also be preventing access to the GxP Server module.

• If the GxP Server module is installed on a network location - Double-click on the

FBServer.exe

file in the FBServer7 folder from the installed location:

Figure B-58:


• If the GxP Server module is installed on a local computer - Double-click the Restart

Server desktop icon:


Restarting the GxP Server Module

page 399

Figure B-59:

Restart Server Desktop Icon

The

Restart Server

window will display momentarily as the GxP Server module restarts:

Figure B-60:

Restart Server Window


page 400

Chapter B:



page 1

Index

Symbols

.csv file for import, creating

90

Numerics

21 CFR Part 11- compliant features, accessing

59

2nd Buffer Time and Shake speed

parameter

136, 213

2nd plate name/barcode

264, 328

2nd Plate Name/Barcode setting

Run Experiment window settings

quantitation 384

196

quantitation 96

119

2nd Time and Shake Speed parameter

Advanced Quantitation

quantitation 384

172

quantitation 96

95

384 Well format (option)

280

384-well Format Reagent Plate (figure)

167


280


167

A

About ForteBio Data Acquisition menu

38

accessing GxP Server module directly

396

accessing Temperature field

12

account details, assigning

385

acquisition for a data column, displaying

267, 331

quantitation 384

199

quantitation 96

122

acquisition options

40

Acquisition rate—advanced settings

Octet QK384 (Kinetics)

330

Octet QK384 (Quantitation)

198

Octet QKe

121

Octet RED

121

Activation (well type)

218

kinetics 384

281

activation steps

237, 303

active biosensor column

122, 199, 267,

331

Active Channels threshold parameter

239,

304

active method file, closing

33

active steps, extending duration

270, 335

Add Sensor dialog box (figure)

49

Adding

49

adding biosensor type

49

replicate assay to a plate

247, 312

Replicate Groups from the Sample Plate

Map kinetics 384

291

kinetics 96

228

quantitation 384 (figure)

160


85

Runtime Binding Chart title

271, 336

quantitation 384

203

quantitation 96

126


page 2 sample annotations from the Sample

Plate Map

kinetics 96 (figure)

225

adjacent steps, selecting

243, 308

administrator account, setting up

374

administrator constants, listed (table)

393

administrator password, changing

387

administrator user session, starting

378

administrator username selection (figure)

379

Advanced Quantitation (shortcut menu option)

166

Advanced Quantitation assay parameters

94, 135, 171, 212


136,

213

Buffer Time and Shake speed

135, 212

Detection Time and Shake speed

136,

213

Enzyme Time and Shake speed

136,

213

Offline

136, 213

Pre-condition sensors

136, 213

quantitation 384

2nd Time and Shake Speed param-

eter

172

Buffer Time and Shake Speed pa-

rameter

172

Detection Time and Shake Speed parameter

172

Enzyme Time and Shake Speed pa-

rameter

172

Multiple Analyte parameter

171

Neutralization Time and Shake

Speed parameter

172

Offline parameter

172

Post-condition sensors parameter

173

Pre-condition sensors parameter

173

Regeneration cycles parameter

173

Regeneration Time and Shake

Speed parameter

172

Reuse Buffer parameter

172

Sample Time and Shake Speed parameter

172

Single Analyte parameter

171

quantitation 96

94


95

Buffer Time and Shake Speed parameter

95

Detection Time and Shake Speed

parameter

95

Enzyme Time and Shake Speed parameter

95


94,

133


Speed parameter

95

Offline parameter

95


96


96


96


Speed parameter

95


95


95


94


page 3

Regeneration cycles

137, 214

Regeneration Time and Shake speed

136, 213

Sample Time and Shake speed

212

Advanced Quantitation, Quantitation (384)

Experiment

142

advanced run experiment settings

120,

197, 329

advanced settings

Acquisition rate—Octet QKe

121

Acquisition rate—Octet RED

121

Default

121

Octet QKe, listed (table)

266

Octet RED, listed (table)

266

Octet RED384, listed (table)

330


266

Sensor offset—Octet QKe

121

Align to Step menu

270

aligning binding data to the beginning of a user-selected step

270, 334

All steps (option)

244, 309

analysis options, viewing

40

analyzing quantitative experiment

68, 140,

216, 276

annotating individual wells in the sample plate table

kinetics 384

289

kinetics 96

226

quantitation 384

157

quantitation 96

82 one or more wells

82, 225, 288

annotations, entering

225, 288

quantitation 384

157

quantitation 96

82

Append as new assay (option)

244, 309

Append to current assay (option)

244, 309

Append to current assay option

243

Application Locked dialog box (figure)

66

applications, closing

34

Arrange Icons menu

37

arranging window icons

37

Assay Definition tab

237

Assay Definition window

237

Assay number

267

assay parameter settings, modifying quantitation 384

167

quantitation 96

91

assay parameter values, editing quantitation 384

208

quantitation 96

131

assay parameters

Advanced Quantitation quantitation 96

94

Basic Quantitation

for 384 model

169

for 96 model

92

Basic Quantitation with Regeneration quantitation 384

170

quantitation 96

93

Assay Parameters box

91

assay parameters, Basic Quantitation

Multiple Analyte quantitation 384

209

quantitation 96

132

Quantitation Shake Speed


page 4

quantitation 384

209

quantitation 96

132

Quantitation Time

quantitation 384

209

quantitation 96

132

Single Analyte

quantitation 384

208

quantitation 96

131

Assay Parameters—Advanced Quantitation

Standard Assay (figure)

94, 135, 171,

212

Assay Parameters—Basic Quantitation

Assay (figure)

92, 131, 169, 208

Assay Parameters—Basic Quantitation with

Regeneration (figure)

93, 133, 170, 210

Assay Settings box

91

Assay Step Definition dialog box

303

assay step name, changing (figure)

247,

311

assay steps adding

243, 308 copying

243, 308

inserting

245, 310

removing

247, 311 reordering

247, 311

assay times, updating (figure)

242, 307

Assay Type setting


kinetics 384

328

kinetics 96

264

quantitation 384

196

quantitation 96

119

assays

adding steps

245, 310

adding to sample plates

248, 313

assigning biosensors to samples

249,

313

automatic addition of sensor tray maps

256, 320

building

241

changing biosensor locations

252, 257

changing biosensor type

320

copying steps between

243, 308

editing

246, 311

example using one partial biosensor try and biosensors from a second tray quantitation 384

190

quantitation 96

113

removing steps

247, 311 reordering steps

247, 311

replicating steps

244, 309

starting new

244, 309

assigning

account details

385

biosensors in Multiple Analyte experiments quantitation 384

177

quantitation 96

99

biosensors in single analyte experiments quantitation 384

173

quantitation 96

96

biosensors to samples

249

quantitation 384

173

quantitation 96

96

dilution factor to selected wells quantitation 384

154

quantitation 96

79


page 5 dilution factor to unknowns

quantitation 384

153

quantitation 96

78

heterogeneous biosensor trays

quantitation 96

101

heterogenous biosensor trays

quantitation 384

178

homogenous biosensor trays

quantitation 384

183

quantitation 96

106

molecular weight

kinetics 96

221

molecular weight and molar concentration (kinetics)

283

privileges

385

Replicate Groups in the Sample Plate

Map

kinetics 384

290

kinetics 96

227

quantitation 384

159

quantitation 96

84


Table

kinetics 384

293

kinetics 96

229

quantitation 384

162

quantitation 96

87

sample concentrations by value


223

sample concentrations using dilution series

kinetics 384

286

kinetics 96

223


224

serial dilution to selected wells quantitation 384

154

quantitation 96

79

serial dilution to unknowns quantitation 384

153

quantitation 96

78

standard concentration


151


76

standard concentrations using a dilution series quantitation 384

149

quantitation 96

74

step types in the sample plate (figure)

242, 307

user group

385

user-specified concentration to samples

222, 285

user-specified concentration to standards quantitation 384

151

quantitation 96

76

assigning molar concentration kinetics 96

221

association steps

236, 302

Audit Trail

described

62

illustrated (figure)

62

list options

64

selecting a project

63 sorting

63

viewing

62

Authentication Server dialog box

53


264, 328


page 6

Auto Increment File ID Start


quantitation 384

197

quantitation 96

120

Auto Scroll to bottom check box

39

Automatically save runtime chart (setting)

120, 197, 265, 329

automation for Octet QK384

26

for Octet RED384

19

Automation box

346

Automation Client example application,

connecting

348

automation interface commands

Cleanup

350

Close

350

GetMethodInfo

349

GetRunInfo

349

Present

350

Reset

349

Resume

350

Run

349

Status

350

Stop

350

Version

349

automation interface control setup

346

automation interface design

346

automation session, typical

351

Automation, user option

43

AutomationAPI.h header file

349

AutomationClient.exe

346

B

baseline step

237, 303

basic kinetics experiment

216, 276

Basic Kinetics Experiment window (figure)

277

Basic Quantitation Assay Parameters listed (table)

92, 131, 169, 208


209

quantitation 96

132

quantitation 384

Multiple Analyte and Replicates per

Sensor Type (parameter)

169

Quantitation Shake Speed (param-

eter)

169

Quantitation Time (parameter)

169

Single Analyte (parameter)

169

quantitation 96



92

Quantitation Shake Speed (param-

eter)

92


92


92

Quantitation Shake Speed quantitation 384

209

quantitation 96

132

Quantitation Time quantitation 384

209

quantitation 96

132

Single Analyte quantitation 384

208

quantitation 96

131


page 7 basic quantitation assay parameters, listed

(table)

quantitation 384

208

quantitation 96

131

Basic Quantitation with Regeneration

(shortcut menu option)

166

Basic Quantitation with Regeneration assay

parameter

133, 210

Basic Quantitation with Regeneration assay parameters

Neutralization Time and Shake speed

134, 211


134, 211


134, 211

quantitation 384

170


170


Speed parameter

170


171

Precondition sensors parameter

171

Regeneration Cycles parameter

171


Speed parameter

170


170

quantitation 96

93


93


Speed parameter

93


94


94

Quantitation Time and Shake speed

93


94


Speed parameter

93


93, 133


133, 170, 210

Regeneration cycles

134, 211


133, 210

Basic Quantitation with Regeneration,

Quantitation Experiment

69, 141

Basic Quantitation, Quantitation

Experiment

69, 141

beginning an experiment

216, 276

beginning the next step in the assay

271,

335

binding data aligning kinetics 384

334

kinetics 96

270

exporting quantitation 384

204

quantitation 96

127

saving kinetics 384

337

kinetics 96

273

quantitation 384

204

quantitation 96

127

biosensor column, active

122, 199, 267,

331

biosensor columns, default

252, 316

biosensor pickup tips, cleaning

343

biosensor regeneration, described quantitation 384

188


page 8

quantitation 96

111

biosensor stage (left) and sample stage

(right), figure

116, 261

biosensor tray loading

kinetics 384

324

kinetics 96

260

replacing biosensors

251, 315

biosensor tray type

17, 19, 26

Octet QK instrument

24

Octet QKe instrument

22

Octet RED96 instrument

17, 19, 26

biosensor tray, loading

quantitation 384

193

quantitation 96

116

biosensor type adding

49

changing (figure)

247, 311

Octet QK instrument

24


22


17, 19, 26

removing

49

biosensor type, changing in the Assay

Definition window

258, 322

biosensor type, changing in the Sensor

Assignment window

254, 318

biosensor types, changing

246, 311

biosensors assigning

quantitation 384

173

quantitation 96

96

assigning to samples

249, 313

automatically adding experiment tray

maps

256, 320

changing locations kinetics 96

252

changing type

320

designating reference

105, 110, 182,

187, 257, 321

entering information

252, 315

preparing

68

removing from sensor tray maps

253,

317

replaying in the biosensor tray

251,

315

viewing available

48

biosensors, reference, designating

258

browser window functions

47

Buffer (well type) kinetics 384

280

kinetics 96

218



172

quantitation 96

95

Buffer Time and Shake speed parameter

135, 212

building assays

241

By value option

76, 151, 222, 285

C

capabilities

Octet QK instrument

23

Octet QK384 instrument

25


22


18


17


page 9

cascade arrangement, organizing windows

37

Cascade menu

37

Change Password dialog box (figure)

387

Change Projects menu

64

changing administrator password

387

assay step name (figure)

247, 311

biosensor Location (Method 1)

253,

316

biosensor location (Method 2)

254,

317

biosensor type (figure)

247, 311

biosensor type in the Assay Definition window

258, 322

biosensor type in the Sensor

Assignment window

254, 318

constants

394

group settings

390

project settings

391

projects during a user session

64

sample plate format

kinetics 384

280

quantitation 384

144

sample plate format (figure)

144, 280

user account passwords

387

user account settings

386

user password

65

well designations

kinetics 384

295

kinetics 96

231

changing location of a reserved column

quantitation 384

146

quantitation 96

72

changing projects (figure)

64

Choose Install Location dialog box (figure)

367, 369

Choose Start Menu Folder dialog box

(figure)

367, 370, 373

cleaning biosensor pickup tips

343

cleaning Octet instrument

340, 342

Cleanup (automation interface command)

350

Close (automation interface command)

350

Close Method File menu

33

closing active method file

33

application

34

color codes

122, 199, 267, 331

color-coded wells displaying how biosensors interrogate a 384-well plate, 8 channel or 16-

channel read head

143, 279

a 96-well plate, 8 channel or 16-

channel read head

143, 279

compliance

Octet QK instrument

23


25


21


18


16

compliant features, 21 CFR Part 11

59

Conc column

76, 151

concentration representation in dilution

series (figure)

224

Concentration Units drop-down list

73

Connect as IP address, changing

45


page 10 connecting

Automation Client example application

348

Octet instrument to computer

30

to a TCP/IP socket connection locally using localhost

348

Connections to Clients box (figure)

397

constants

changing

394

creating new

393

deleting

394

viewing

394

Constants tab (figure)

392

constants, administrator, listed (table)

393

contacting ForteBio technical support

13

Control (well type)

218

kinetics 384

280

quantitation 384

145

quantitation 96

71 control, type of well

71, 145

controls

156

defined

81, 156

designating

156 quantitation 384

156

quantitation 96

81

conventions, used in this guide

13

copying assay steps

243, 308

Runtime Binding Chart

kinetics 384

338

kinetics 96

273

quantitation 384

205

quantitation 96

128

step type kinetics 384

305

kinetics 96

240

creating

.csv file for import

90

assay step type (figure) kinetics 384

303

kinetics 96

238

different types of assay steps

237, 303

new constants

393

new user account

384

new user group

389

step types

237, 303

Current Binding Charts box

331

custom assays defining quantitation 384

206

quantitation 96

129

selecting quantitation 384

214

quantitation 96

137

custom biosensors

48

custom steps

237, 303

D

Data Acquisition 21 CFR Part 11 software

overview

52

Data Acquisition desktop icon

30

Data Acquisition Software—New Features

12

Data Acquisition User Guide menu

38


page 11

Data Acquisition User Guide, opening

online version

38

Data Acquisition, icon

8

Data Analysis 21 CFR Part 11 software overview

52

Data Analysis, icon

8

data column, displaying acquisition

267,

331

quantitation 384

199

quantitation 96

122

data display, significant digits

42

data file location and name settings

quantitation 384 (listed)

196

quantitation 96 (listed)

119

Data File repositories, setting

Data File repositories

347

data files kinetics data repository

41

quantitation data repository

41


42

Use old 5.0 file format for FRD files

42

data preferences, setting

40

DataAcquisition-CFR-7_0_0_x.exe

366

default biosensor columns

252, 316

default locations for reserved wells in a 96-

well sample plate map (figure)

72

default server settings localhost

54

Port 2002

54

default temperature value, saving

44

default temperature, defining new

44

default Tray Format

101

default user group privileges

385

default user groups

388

default windows, Octet System Data

Acquisition software

31

Default, advanced settings

121

defining custom assays quantitation 384

206

quantitation 96

129

kinetic assays

236

new assay

35

new assay (figure)

130, 207

new default temperature

44

reagent plates, quantitation 384

166

sample plates kinetics 384

278

kinetics 96

218

quantitation 384

142

quantitation 96

70

samples by entering sample information (figure)

284

step types

237, 303

kinetics 384

305

kinetics 96

240

defining step types

236

Delayed experiment start (setting)

265,

329

Delayed Experiment Start setting quantitation 384

197

quantitation 96

120

deleting

constants

394

factory-loaded biosensor types

49

projects

392

step types

240, 305


page 12

user account

386

user group

390

Description (setting)

121, 199, 331

designating controls

quantitation 384

156

quantitation 96

81 controls (figure)

81, 156

reference biosensor during acquisition

268, 333

reference biosensors

105, 110, 182,

187, 257, 321

reference biosensors during acquisition

quantitation 384

201

quantitation 96

124

reference wells

quantitation 384

156

quantitation 96

81

reference wells (figure)

81, 156

samples (kinetics experiments)

218

unknowns

quantitation 384

153

quantitation 96

78

well type (kinetics 384)

282

well types (kinetics experiments)

282

designating reference biosensors

258

designating standards

quantitation 384

148

quantitation 96

73

designating well types

kinetics 96

219

Detection

95, 136, 172, 213

Detection (reserved well requirements) quantitation 384

146

quantitation 96

72



172

quantitation 96

95

Detection Time and Shake speed parameter

136, 213

determining the GxP Server module host

location

52

developing the automation client

347

dialog boxes

Options

41

setting default temperature

44

Temperature Setting

43

digital signatures, verifying

60

dilution factor, assigning to selected wells quantitation 384

154

quantitation 96

79

dilution factor, assigning to unknowns quantitation 384

153

quantitation 96

78

dilution factor, editing in sample table quantitation 384

155

quantitation 96

80

dilution series assigning sample concentrations kinetics 384

286

kinetics 96

223

assigning standard concentrations quantitation 384

149

quantitation 96

74


page 13

Dilution Series option

75, 223

dimensions

Octet QK instrument

24


27


22


20


17

discontinuing user session

66

displaying

acquisition for a data column

267, 331

quantitation 384

199

quantitation 96

122

GxP Server location (figure)

377

Instrument Status window

34

license information

38

Octet System Data Acquisition software

properties

38

step types (figure)

305

dissociation steps

236, 302

E

Edit Assay Parameters dialog box (figure)

129, 206

Edit Assay Parameters dialog box, opening

35

Edit Assay Parameters menu

35

edit commands

226

Edit Constant dialog box (figure)

394

Edit Project dialog box (figure)

392

Edit Sensor Types menu

35

editing assay parameter values quantitation 384

208

quantitation 96

131

assays

35, 246, 311

biosensor information (figure)

252,

316

dilution factor in the sample table quantitation 384

155

quantitation 96

80

parameter values quantitation 384

208

quantitation 96

131

projects

391

sample data in the Sample Plate Table kinetics 384

295

kinetics 96

231

standard concentration quantitation 384

151

quantitation 96

76

step type (figure)

241, 306

editing step types

240, 305

Electrical hazard symbol

13

electrical requirements

Octet QK instrument

24


27


22


20


17

emptying waste container

340

ending a user session

66

enhanced legend options, in the Runtime

Binding Chart

12

entering annotations


page 14

quantitation 384

157

quantitation 96

82

biosensor information

displayed (figure)

252, 316 procedure

252, 315

entering an individual standard concentration

quantitation 384

151

quantitation 96

76

environmental features

Octet QK instrument

23


25


21


18


16



quantitation 384

172

quantitation 96

95

Enzyme Time and Shake speed parameter

136, 213

equipment classifications

Octet QK instrument

23


25


21


18


16

events list options available

396

viewing

395

Events tab (figure)

395

example .csv plate definition file (figure)

235, 299

example assay using one partial biosensor tray and biosensors from a second tray

113, 190

example experiment using two biosensor trays (figure)

257, 321

Exit menu

34

experiment

prior to running

258, 322

Experiment menu

described

34

figure

35 list of menu commands

35

experiment method files managing

128, 274

quantitation 384

205

quantitation 96

128

saving

33

saving to new name

33

experiment method files, managing

274,

338

experiment methods, saving manually

114,

191

Experiment Run Name setting

Run Experiment window settings quantitation 384

196

quantitation 96

119

experiment settings advanced settings (Octet QK384)

198,

330

data file location and names


264, 328

Assay Type

328

assay type

264


264,


page 15

328

kinetics data repository

264, 328

plate name/barcode (file prefix)

264, 328 run name

264, 328

general information

Description

121, 199, 331

Machine name

121, 199, 330

User name

121, 199, 330

run settings

Automatically save runtime charts

120, 197, 265, 329


265, 329


120, 197, 265, 329

Set Plate Temperature

120, 197,

265, 329

shake sample plate while waiting

120, 197, 265, 329

Start After

265, 329

experiment settings, data file location and names quantitation 384

2nd Plate Name/Barcode

196

Assay Type

196


197

Experiment Run Name

196

Plate Name/Barcode

196

Quantitation Data Repository

196

quantitation 96


119

Assay Type

119


120

Experiment Run Name

119

Plate Name/Barcode

119


119

Experiment type selecting for the Octet RED384

142

for the Octet RED96

70

Experiment Wizard

34

described

40 figure

40

opening

35

starting kinetics experiments

384

277

Experiment Wizard button

69, 141, 217,

277

Experiment wizard, starting experiment quantitation 384

141

experiments adding assays

248, 313

kinetic, starting

384

277

96

217

monitoring remotely

45

remote view via web browser (figure)

47

reviewing (kinetics 96)

258

saving manually

259, 323

saving to the factory-installed

Template folder

260, 324

starting

261, 325

quantitation 384

194

quantitation 96

117

stopping

36

stopping in progress

266, 331


page 16

quantitation 384

199

quantitation 96

122

Export button

88

Sample Plate Map

kinetics 96

233

export options

Copy the Runtime Binding Chart

quantitation 384

205

quantitation 96

128

Export the Runtime Binding Chart to a graphic file

quantitation 384

204

quantitation 96

127

Print the Runtime Binding Chart

quantitation 384

205

quantitation 96

128

save the binding data

quantitation 384

204

quantitation 96

127

Export Plate Definition window

kinetics 384

297

kinetics 96

233

quantitation 384

163

quantitation 96

88

exporting

binding data

127, 204

plate definition

kinetics 384

297

kinetics 96

233

quantitation 384

163

quantitation 96

88

Runtime Binding Chart to a data file

127, 204, 272, 337

Runtime Binding Chart to a graphic

127, 204, 272, 337

Runtime Binding Chart to a graphic file

273, 337

Exporting dialog box (figure)

127, 204

Extend Current Step button

270

Extend Current Step dialog box (figure)

271, 335

extending duration of the active step

270,

335

F

factory-loaded biosensor types, deleting

49

FBServer7 folder, installation location

381

FBServerConfig.exe file

381

File Compliant (figure)

62

File History menu

34

File menu

described

32

figure


33

File menu commands, listed (table)

33

File Not Compliant (figure)

62

File Type selection (figure)

61

Fill Plate (menu)

253, 316

Filtering threshold parameter

239, 305

Flip Data check box

125, 269, 334

Flip Data function

viewing inverted data

269

ForteBio GxP Server 7.0.exe

372

ForteBio GxP Server desktop icon (figure)

397

ForteBio GxP Server module, installing

371


page 17

ForteBio technical support, contacting

13

ForteBio Web Site menu

38

fractional use of regeneration and

neutralization wells (figure)

112, 189

Fuse symbol

13

G

general settings, kinetics 384

330

GetMethodInfo (automation interface

command)

349

GetRunInfo (automation interface

command)

349

GetRunInfo command

347

Gradient threshold parameter

239, 305

group administration

388

group settings

changing

390

viewing

390

Groups tab (figure)

388

GxP Server Address search results (figure)

54

GxP Server Configuration window (figure)

397

GxP Server module accessing directly

396

restarting

398

H

Heat/hot symbol

13

Help menu described

38

figure

38

I

list of menu commands

38

heterogeneous biosensor trays assigning biosensors quantitation 384

178

quantitation 96

101

using kinetics 384

317

kinetics 96

254

hiding main toolbar

34

status bar

34

higher acquisition rate

120, 197, 329

Homogeneous biosensor trays assigning biosensors quantitation 384

183

quantitation 96

106

icons

Data Acquisition

8

Data Analysis

8

Import button

89

Import button (figure)

234

Import Plate Definition window quantitation 384

164

quantitation 96

89

Import Plate Definition window (figure)

234

importing plate definitions kinetics 384

298

kinetics 96

234


page 18 importing plate definition

quantitation 384

164

quantitation 96

89

inserting assay steps

245, 310

installing

Data Acquisition 7.0 CFR Part 11

software

366

Data Analysis 7.0 CFR Part 11 software

369

ForteBio GxP Server

372

ForteBio GxP Server module

371

Instrument menu described

36

figure

36


36

Instrument Status (menu)

34

instrument status log (figure)

119, 196,

263, 327


36

described

39

figure

39

logging

36

inverted data, viewing in the Runtime

Binding Chart

269, 334

K

kinetic data analysis

40

kinetics assays

building

248

defining

236

step type requirements

236, 302


264, 328

kinetics data repository, user option

41

kinetics experiments designating samples

218

designating well types

282

Plate Definition window

282

starting

384

277

96

217

L

launching the Octet System Data


30

legend, for Runtime Binding Chart,

selecting

271, 336

quantitation 384

203

quantitation 96

126

license information, displaying

38

list options available for events

396

listing windows currently open in the Main

Screen

37

Load (well type) kinetics 384

281

kinetics 96

218

loading biosensor tray kinetics 384

324

kinetics 96

260

quantitation 384

193

quantitation 96

116

reagent plates, kinetics 384

324

sample plate kinetics 384

324


page 19

kinetics 96

260

quantitation 384

193

quantitation 96

116

steps

236, 302

LoadSensors

353

Localhost option

347

localhost, default server settings

54

locking

Data Acquisition software

65

Data Analysis software

65

logging in the Instrument Status window

36

Login dialog box administrator session (figure)

378

user session (figure)

56

Lot Number column

252

lower acquisition rate

121, 198, 329

M

Machine drop-down list

63

Machine name (setting)

121, 199, 330

magnification, undoing

125, 202, 271,

335

magnifying Runtime Binding Chart

271,

335

quantitation 384

202

quantitation 96

125

Main Menu, Octet System Data Acquisition

software

31

main screen, Octet System Data Acquisition

software

31

main toolbar hiding

34

showing

34

managing experiment method files

128, 274,

338

quantitation 384

205

quantitation 96

128

Runtime Binding Chart kinetics 96

267

managing experiment method files

274

manually save an experiment

259, 323

mechanics

Octet QK instrument

24


26


22


19


17

menu bar, Octet System Data Acquisition software

32

menu commands, listed

33, 34, 35, 36

method file (.fmf)

68, 140, 216, 276

method file (.fmf), described

32

method files

closing

33 saving

33

saving all

33

Modify Plates dialog box

166

modifying assay parameter settings quantitation 384

167

quantitation 96

91

reagent plate quantitation 384

166, 299

molar concentration units

222, 284


page 20 molar concentration, assigning

kinetics 96

221

molecular weight, assigning

kinetics 96

221

monitoring experiments remotely

45

Multiple Analyte assay parameter

quantitation 384

209

quantitation 96

132

Multiple Analyte experiments assigning biosensors

quantitation 384

177

quantitation 96

99

used with Replicate Groups

quantitation 384

163

quantitation 96

88



quantitation 384

171

quantitation 96

94, 133


quantitation 384

170

quantitation 96

93

multiple runtime binding charts

12

quantitation 96

72

Neutralization Time and Shake Speed parameter


172

quantitation 96

95


170

quantitation 96

93

Neutralization Time and Shake speed parameter

134, 211

Neutralization Time(s) and Shake speed

136, 213

New Experiment Wizard (menu)

217, 277

New Experiment Wizard menu

35

new features, Octet System Data


12

New Group dialog box (figure)

389

New Kinetics Experiment (menu)

217, 277

New Quantitation Experiment

69, 141

New Window menu

37

non-adjacent steps, selecting

243, 308

N

Negative Control (well type)

kinetics 384

280

kinetics 96

218

quantitation 384

145

quantitation 96

71

Neutralization (reserved well requirements)

quantitation 384

146

O

Octet instrument cleaning

340, 342

resetting

36

Octet instrument labels

13

Octet instrument power supply, back panel

341, 344

Octet instrument to computer, connecting

30

Octet instrument, side panel removed

343


page 21

Octet QK instrument

23

biosensor tray type

24

biosensor type

24

capabilities

23

compliance

23

dimensions

24


24

environment

23 equipment classifications

23

mechanics

24

optics

24

orbital flow capacity

24

sample types

24

sample volume

24

sampling format

24 temperature range

24

throughput

24

Octet QK system specifications

23

Octet QK384

sensor offset

20, 27 well volumes

20, 27


automation

26

capabilities

25

compliance

25

dimensions

27


27

environment


25

mechanics

26

optics

26

sample types

26 sampling format

26

weight

27

Octet QK384 instrument (figure)

25

Octet QK384 system specifications, listed

(table)

25

Octet QKe and Octet RED Run Experiment window advanced settings, listed (table)

266


biosensor tray type

22

biosensor type

22

capabilities

22

compliance

21

dimensions

22

displayed (figure)

21


22

environment

21

equipment classifications

21

mechanics

22 optics

22 orbital flow capacity

22 sample types

22 sample volume

22 sampling format

22

temperature range

22 throughput

22 weight

22

Octet QKe system specifications, listed

(table)

21

Octet RED instrument, replacing fuses

341

Octet RED system, warm-up

30

Octet RED384 sensor offset

20, 27

starting


page 22 kinetics experiment with the Experiment wizard (figure)

278

well volumes

20, 27


automation

19

capabilities

18

compliance

18

dimensions

20


20

environment


18

mechanics

19

optics

19

sample types

19

sampling format

19

weight

20

Octet RED384 instrument (figure)

18

Octet RED384 stage platform, figure

193

Octet RED96 instrument biosensor tray type

17, 19, 26

biosensor type

17, 19, 26 capabilities

17

compliance

16

dimensions

17


17

environment


16

mechanics

17

optics

17


17, 20, 27

sample types

17

sampling format

17

sampling volume

17

temperature range

17 throughput

17, 19, 26 weight

17


16

Octet RED96 system specifications displayed (figure)

18

listed (table)

16, 18, 25

Octet system biosensor stage (left) and sample stage (right) (figure)

325


Main Menu

31

main toolbar

32

new features

12

starting

30

toolbar

31


Main Screen

31

Octet System Data Acquisition, analysis options, viewing

40

Octet system, described

8

Offline parameter

136, 213


172

quantitation 96

95

Offset steps (option)

244, 309

Offset steps check box

243

Open Experiment (menu)

268, 332

Open Experiment menu

33

Open Method File menu

33

Open runtime charts automatically (setting)

120, 197, 265, 329

Open runtime charts automatically check box

267


page 23

Open runtime charts automatically option

326

Open Windows menu

37

opening dialog box to select an experiment

method file

33

Edit Assay Parameters dialog box

35

Experiment Wizard

35

online Data Acquisition User Guide

38


268, 332

quantitation 384

200

quantitation 96

123

Sensor Types dialog box

35

Temperature Setting dialog box

35

web browser

38

optics

Octet QK instrument

24


26


22


19


17

Options dialog box

displayed (figure)

41

setting

FRD file format to the earlier 5.0 format

34

significant digits

34

viewing analysis options

41

Options dialog box (figure)

41

Options dialog box—Automation Interface selection (figure)

347

Options menu

34


Octet QK instrument

24


22


17, 20, 27

organizing windows in a cascade arrangement

37

P

panel, Octet instrument, removing

343

parameter settings, assay, modifying quantitation 384

167

quantitation 96

91

parameter values, editing quantitation 384

208

quantitation 96

131

partial biosensor trays, using

256

kinetics 384

320

password reminder, user and administrator

(figure)

57

plate definition exporting kinetics 384

297

kinetics 96

233

quantitation 384

163

quantitation 96

88

importing quantitation 384

164

quantitation 96

89


Designate Unknown Wells (figure)

78,

153

Designating Standards (figure)

74, 149

Export button (figure)

233, 234


234


page 24

kinetics experiments

282

selecting

concentration units (figure)

222,

285

molar concentration units (figure)

222, 285

plate definitions importing

kinetics 384

298

kinetics 96

234

plate name/barcode (file prefix)

264, 328

Plate Name/Barcode setting


quantitation 384

196

quantitation 96

119

plate temperature range

43

plate temperature, setting

43

Port 2002, default server settings

54

Positive control

218

Positive Control (well type)

kinetics 384

280

quantitation 384

145

quantitation 96

71

post-condition biosensors

12


134,

211


quantitation 384

173

quantitation 96

96


quantitation 384

171

quantitation 96

94



136, 213

quantitation 384

173

quantitation 96

96


134, 211



171

quantitation 96

94

preparing biosensors

68

preparing samples for quantitation or

kinetics experiments

8

Present (automation interface command)

350

Present Stage menu

36

Print menu

33

Print Preview menu

33

print preview window

33

Print Setup dialog box

33

Print Setup menu

33

printing files

33


128, 205, 273,

338

prior to running an experiment

258, 322

privileges, assigning

385

project administration

390

Project drop-down list

63

project selection (figure)

58

project settings changing

391 viewing

391

project-based Audit Trail events (figure)

64


page 25 projects

changing (figure)

64

deleting

392

editing

391

Projects tab

391

projects, changing during a user session

64

properties, for Octet System software,

displaying

38

Q

QKe instrument, replacing fuses

341

quantitation 384

144

Quantitation Data Repository setting


quantitation 384

196

quantitation 96

119

quantitation data repository, user option

41



quantitation 384

142

Basic Quantitation 384

141


69


69, 141

quantitation experiment defined

68, 140

starting

69, 141

Quantitation Shake Speed assay parameter

quantitation 384

209

quantitation 96

132

Quantitation Shake Speed parameter quantitation 384

169

quantitation 96

92

Quantitation Time and Shake speed parameter

133, 170, 210


93

Quantitation Time assay parameter quantitation 384

209

quantitation 96

132

Quantitation Time parameter quantitation 384

169

quantitation 96

92

quantitative experiment analyzing

68, 140, 216, 276

setting up

68, 140, 216, 276

Quench (well type) kinetics 384

281

kinetics 96

218

quenching steps

237, 303

R

raw reference-subtracted data, viewing quantitation 384

201

quantitation 96

123

read head configuration kinetics 384

278

quantitation 384

143

reagent plate defining quantitation 384

166

modifying quantitation 384

299


page 26 reagent plate definitions saving

301

Reagent Plate Map

166

Reagent Plate Map (figure)

166, 300

Reagent Plate radio button

166

reagent plates, loading

kinetics 384

324

Received (well type)

quantitation 384

145

quantitation 96

71

recommended sensor offset

198, 330

Reference (well type)

218

kinetics 384

280

quantitation 384

145

quantitation 96

71

reference biosensors

designating

105, 110, 182, 187, 257,

258, 321

designating during acquisition

268,

333

reference biosensors, designating during acquisition

quantitation 384

201

quantitation 96

124

Reference menu

124, 201, 268, 333

reference wells defined

81, 156

designating

quantitation 384

156

quantitation 96

81

reference, type of well

71, 145

reference-subtracted data viewing kinetics 384

332

kinetics 96

268

reference-subtracted data, viewing quantitation 384

201

quantitation 96

123

Refresh settings

45

Regeneration (reserved well requirements) quantitation 384

146

quantitation 96

72

Regeneration (well type) kinetics 384

281

kinetics 96

218



171

quantitation 96

94



137, 214

quantitation 384

173

quantitation 96

96


134, 211

Regeneration Time and Shake Speed parameter


172

quantitation 96

95


170

quantitation 96

93

Regeneration Time and Shake speed parameter

133, 136, 210, 213

remote view of experiment via web browser (figure)

47


page 27 removing assay from the quantitation application

35

assay steps

247, 311

biosensor type

49

side panel of Octet instrument

343

step alignment of data

270, 334

well designation

282

well designations

controls or reference wells

81, 157

quantitation 384

149, 153

quantitation 96

74, 78


167

reordering assay steps

247, 311

Replace sensors in tray after use check box

176

replacing biosensors in the biosensor tray

251,

315

fuses for Octet RED instrument

341

for QKe instrument

341

replicate assay steps

244, 309

replicate assay, adding to a plate

247, 312

Replicate Group color-coding (figure)

227,

290

Replicate Groups assigning in the Sample Plate Table

quantitation 384

162

quantitation 96

87

defined

226

quantitation 384

159

quantitation 96

84

displayed in Sample Plate Map


161


86

displayed in Sample Plate Table


161


86

Replicate Groups displayed in Sample Plate

Map (figure)

229

Replicate Groups in Sample Plate Table

(figure)

229

replicate steps

All steps (option)

244, 309


244,

309


244,

309


244, 309 options (table)

244, 309

Sample steps only (option)

244, 309

Sample steps will be adjusted by

vertically by one row (option)

244,

309

Sample steps will be adjusted by X

column (option)

244, 309

Replicate Steps dialog box (figure)

243

requirements, for reserved wells

72

reserved column, changing location quantitation 384

146

quantitation 96

72

Reserved Well requirements

72, 146 reserved well requirements

72

Detection quantitation 384

146

quantitation 96

72


page 28

Neutralization

quantitation 384

146

quantitation 96

72

Regeneration

quantitation 384

146

quantitation 96

72 reserved wells

72

reserved, type of well

71, 145

Reset (automation interface command)

349

Reset menu

36 resetting Octet instrument

36

Restart Server desktop icon (figure)

399

Restart Server window (figure)

399

restarting the GxP Server module

398

Resume (automation interface command)

350

resuming user session

66



quantitation 384

172

quantitation 96

95

Review Experiment window

114, 191,

258, 322

Review Experiment window (figure)

114,

191, 259, 323

reviewing experiments (kinetics 96)

258

Run (automation interface command)

349

Run Experiment tab

117

Run Experiment window

Octet RED, RED96, and QKe (figure)

117, 194



119, 196

Assay Type

119, 196


120, 197

Experiment Run Name

119, 196

Plate Name/Barcode

119, 196


119, 196

Run Experiment window—Octet RED and

Octet RED96 (figure)

262, 326

run name

264, 328

run settings quantitation 384

Delayed Experiment Start

197

Start After setting

197

quantitation 96


120

Start After setting

120

run settings, listed quantitation 384

197

quantitation 96

120

running experiment settings

119, 196


adding title

271, 336

quantitation 384

203

quantitation 96

126

copying kinetics 384

338

kinetics 96

273

exporting to a graphic file

273, 337

exporting to a graphic or data file

127,

204, 272, 337

magnifying

271, 335

quantitation 384

202

quantitation 96

125

managing


page 29

kinetics 96

267

opening

268, 332

quantitation 384

200

quantitation 96

123

printing

273, 338

scaling

271, 335

quantitation 384

202

quantitation 96

126

selecting legend

271, 336

quantitation 384

203

quantitation 96

126

updating

kinetics 384

331

kinetics 96

267

quantitation 384

199

quantitation 96

122

viewing inverted data

269, 334

viewing multiple

kinetics 384

336

kinetics 96

272

quantitation 384

204

quantitation 96

127

Runtime Binding Chart (figure)

118, 195,

263, 327

Runtime Binding Chart Export options copy the Runtime Binding Chart to a graphic file

quantitation 384

205

quantitation 96

128

export the Runtime Binding Chart to a graphic file

quantitation 384

204

quantitation 96

127

print the Runtime Binding Chart to a graphic file quantitation 384

205

quantitation 96

128

save the binding data quantitation 384

204

quantitation 96

127

Runtime Binding Chart options, listed

(table) quantitation 384

204

quantitation 96

127

Runtime Binding Chart window (figure)

267, 332

Runtime Binding Chart, copying quantitation 384

205

quantitation 96

128

Runtime Binding Chart, enhanced legend

options

12

Runtime Binding Chart, printing

128, 205

Runtime Graph Properties dialog box

126,

203, 271, 336

S

Sample (well type) kinetics 384

280

kinetics 96

218

sample plate loading kinetics 384

324

kinetics 96

260

quantitation 384

193

quantitation 96

116


page 30

Sample Plate and Reagent Plate Layouts for an Advanced Quantitation Experiment—

16 Channel Read Head (figure)

167

Sample Plate File (.csv), example (figure)

90,

165

sample plate format, changing

kinetics 384

280

quantitation 384

144

Sample Plate Map—Setting a Dilution

Series (figure)

75, 150, 223, 286

sample plate shaker, stopper

36

Sample Plate Table—Shortcut Menu of Edit

Commands (figure)

77, 80, 152, 155,

231, 232, 295, 296

sample plate temperature, recorded in log

file

12

sample plates

adding assays

248, 313

assigning biosensors to samples

249,

313

assigning step types to

242, 307

defining

kinetics 96

218

quantitation 384

142

quantitation 96

70

defining kinetics 384

278

importing definitions

kinetics 384

298

kinetics 96

234

sample step types for kinetic assays, listed

(table)

236


244, 309

Sample steps will be adjusted by vertically

by one row (option)

244, 309

Sample steps will be adjusted by X columns

(option) kinetics 384

309

kinetics 96

244



172

quantitation 96

95

sample types

Octet QK instrument

24


26


22


19


17

sample volume

Octet QK instrument

24


22

samples

changing biosensor type

320

designating (kinetics experiments)

218

specifying analyte concentration

221,

283

specifying concentration units

222,

284

sampling format

Octet QK instrument

24


26


22


19


17 sampling volume, Octet RED96 instrument

17

Save All Method Files menu

33

Save Experiment menu

33


page 31

Save Method File As menu

33

Save Method File menu

33

Save to File menu

39

saved experiments in the Template folder

(figure)

260, 324

saving

all method files

33

binding data

127, 204, 273, 337

default temperature value

44

experiment method files

33

experiment method files to a new name

33

experiment methods

114, 191

experiments manually

259, 323

experiments to the factory-installed

Template folder

kinetics 384

324

kinetics 96

260

quantitation 384

192

quantitation 96

115

modified parameter settings

91, 167

reagent plate definition

kinetics 384

301

quantitation 384

167

scaling Runtime Binding Chart

kinetics 384

335

kinetics 96

271

quantitation 384

202

quantitation 96

126

screen components, Octet System Data


31

Security menu

availability

32

compliance features (figure)

59

described

36

figure

37

selecting

adjacent steps, to copy and add

243,

308

concentration units

222, 284

concentration units in the Plate

Definition window (figure)

222, 285

custom assays quantitation 384

214

quantitation 96

137

experiment method file, opening

function

33

Experiment type for the Octet RED384

142

for the Octet RED96

70

in the Experiment Wizard

70

from a set of predefined ForteBio quantitation or kinetics method templates

35

molar concentration units

222, 284

molar concentration units in the Plate


222, 285

non-adjacent steps, to add and copy

243, 308

project in the Audit Trail

63

Runtime Binding Chart legend kinetics 384

336

kinetics 96

271

quantitation 384

203

quantitation 96

126

server location

53

wells in the Sample Plate Map kinetics 384

282


page 32

kinetics 96

219

quantitation 384

148

quantitation 96

73

wells in the Sample Plate Map (kinetics

384)

281

selecting the Web Server in the Options

dialog box (figure)

45

selectively display the acquisition for a data

column

267, 331

quantitation 384

199

quantitation 96

122

Send Commands—Command Field (figure)

349

Sensor Assignment tab

48, 96, 100, 173,

177, 303

Sensor Assignment window

96, 100, 173,

177, 303

displayed (figure)

250, 314

Sensor Assignment Window for Basic

Quantitation without Regeneration

(figure)

97, 100, 174, 177

sensor offset

198, 330

Octet QK384

20, 27

Octet RED384

20, 27

Sensor offset—Octet QKe, advanced settings

121

Sensor Tray map, color codes

122, 199,

267, 331

sensor tray maps

256 automatically adding

256, 320

changing biosensor locations

252, 257

removing biosensors

253, 317

returning to default layout

253, 316

Sensor Type arrow

246

Sensor Type table column

249

Sensor Types dialog box opening

35

Sensor Types dialog box (figure)

48

Sensors to Chart box (figure)

267

serial dilution, assigning to selected wells quantitation 384

154

quantitation 96

79

serial dilution, assigning to unknowns quantitation 384

153

quantitation 96

78

serial port (RS-232)

346

server location, selecting

53

server testing

397

Set Plate Temperature (setting) kinetics 384

329

kinetics 96

265

quantitation 384

197

quantitation 96

120

Set Plate Temperature menu

35

Set Well Data dialog box

76, 151, 221

Set Well Data dialog box (figure)

290

setting assay step threshold parameters

(figure)

239, 304

plate temperature

43

system and data preferences

40

setting assay step threshold parameters

(figure)

239

Setting Default Temperature dialog box

44

setting temperature (figure)

43

setting up administrator account

374

setting up quantitative experiment

68,

140, 216, 276


page 33 settings, advanced run experiment

120,

197, 329

shake sample plate while waiting (setting)

120, 197, 265, 329

Shake Speed parameter

quantitation 384

169

quantitation 96

92

shortcut keys

226

showing

main toolbar

34 status bar

34

Signal Change threshold parameter

239,

304

significant digits

data display

42 user option

42

simulation, user option

43

Single Analyte assay parameter

quantitation 384

208

quantitation 96

131

single analyte experiment assigning biosensors

quantitation 384

173

quantitation 96

96



quantitation 384

171

quantitation 96

94


quantitation 384

170

quantitation 96

93, 133

quantitation 384

169

quantitation 96

92

Skip Step menu

35

specifying number of significant digits for the values of Molecular Weight,

Concentration and Dilution used during data analysis

42

Standard (well type) quantitation 384

145

quantitation 96

71

Standard button

73, 148

standard concentration, entering quantitation 384

151

quantitation 96

76

standard, type of well

71, 145

standards, designating quantitation 384

148

quantitation 96

73

Start After setting kinetics 384

329

kinetics 96

265

quantitation 384

197

quantitation 96

120

starting administrator user session

378

an experiment

261, 325

quantitation 384

194

quantitation 96

117

basic kinetics experiment

384

277

96

217

experiment from the Experiment wizard

141

kinetics experiment with the

Experiment wizard (figure)

Octet RED384

278


page 34 new assay

244, 309


30

quantitation experiment

69, 141

user session

56

starting concentration value

76, 151, 222,

285

startup, temperature, user option

42

Status (automation interface command)

350

status bar described

38

figure

38

hiding

34 showing

34

Status Bar (menu)

34

Step Data List, displaying step types (figure)

305

Step Name arrow

246

Step Name drop-down list

246

step types activation

237, 303

applying a threshold

238, 304

assigning to columns in sample plate

242, 307

association

236, 302

changing

246, 311

copying

kinetics 384

305

kinetics 96

240

creating

237, 303

custom

237, 303

defining

236

kinetics 384

305

kinetics 96

240 deleting

240, 305

dissociation

236, 302

editing

240, 305

loading

236, 302

quenching

237, 303

requirements for kinetics assays

236,

302

step types (sample) for kinetic assays

236

steps adding to assays

245, 310

copying between assays

243, 308

replicate

244, 309

Stop (automation interface command)

350

Stop menu

36

Stop Shaker menu

36

stopping

experiment

36

experiment in progress

266, 331

quantitation 384

199

quantitation 96

122

sample plate shaker

36

Subtract Reference Biosensor check box

268, 332

Subtract reference sensors check box

124,

201, 268, 333

symbols electrical hazard

13

fuse

13

heat/hot

13

system preferences, setting

40

system specifications

Octet QK

23


page 35

Octet QKe

21

Octet RED96

16, 18, 25

T

Tab menu

383

TCP/IP socket

346

TCP/IP socket connection, connecting

348

technical support, contacting

13

Temperature field, accessing

12

temperature range

Octet QK instrument

24


22


17


displayed (figure)

43

opening

35

temperature value, default, saving

44

temperature, startup, user option

42

Templates menu

35

templates, viewing

kinetics 384

324

kinetics 96

260

terminating a step in the assay

271, 335

testing server

397

Threshold check box

238

threshold parameters

Active Channels

239, 304

Filtering

239, 305

Gradient

239, 305 listed (table)

239, 304

Signal Change

239, 304

Threshold Parameters dialog box

304

threshold, applying to assay steps

238, 304

throughput

Octet QK instrument

24


22


17, 19, 26

Tile menu

37

tiling, windows vertically

37

Toolbar (menu)

34

toolbar, Octet System Data Acquisition software

31

tooltip of well information

241

Tray Format button

106

types of wells control

71, 145

reference

71, 145 reserved

71, 145

standard

71, 145

unassigned

71, 145

Unknown

71

unknown

145

U

Unaligned menu

270, 334

unassigned, type of well

71, 145

UNC folder names

347

undo magnification

125, 202, 271, 335

Unknown (well type) quantitation 384

145

quantitation 96

71

unknowns assigning a dilution factor quantitation 384

153


page 36

quantitation 96

78

assigning serial dilution

quantitation 384

153

quantitation 96

78

designating

quantitation 384

153

quantitation 96

78

updating assay times as steps are added to the assay (figure)

242, 307


kinetics 384

331

kinetics 96

267

quantitation 384

199

quantitation 96

122

Use extended sample types, user option

42

Use old 5.0 file format for FRD files, user

option

42

user account creating new

384

deleting

386

user account passwords, changing

387


changing

386

viewing

386

user data files options

41

user data options

42

user group assigning

385

creating new

389

deleting

390

privileges

385

user groups, default

388

User name (setting)

121, 199, 330

user options

Automation

43


41

listed (table)

41 quantitation data repository

41

significant digits

42

Simulation

43

temperature

42


42


42

viewing

40

Web Server

43

user password, changing

65

user session

changing projects during

64

starting

56

starting an administrator

378

user sessions

discontinuing

66 ending

66

Login dialog box

56

resuming

66

user startup options

42

user-defined default start-up temperature

12

UserIdleMin constant

381

user-modifiable settings for an assay quantitation 384

167

quantitation 96

91

username selection (figure)

57

Users tab

384

using


page 37 heterogeneous biosensor trays

kinetics 384

317

kinetics 96

254

partial biosensor trays

kinetics 384

320

kinetics 96

256

quantitation 96

112

V

Verify Digital Signature dialog box (figure)

60 verifying digital signatures

60

Version (automation interface command)

349

View menu described

34

figure

34


34

viewing analysis options

40

Audit Trail

62

available types of biosensors

48

constants

394

events

395

events for a specific project or

computer

63

group settings

390

inverted data displayed in the Runtime

Binding Chart

269, 334

multiple Runtime Binding Charts

kinetics 384

336

kinetics 96

272

quantitation 384

204

quantitation 96

127

project settings

391

raw reference-subtracted data quantitation 384

201

quantitation 96

123

reference-subtracted data kinetics 384

332

kinetics 96

268

quantitation 384

201

quantitation 96

123

templates

260, 324


386

user options

40

user-modifiable settings for an assay quantitation 384

167

quantitation 96

91

W

warm-up time

30

Wash (well type) kinetics 384

281

kinetics 96

218

waste container

emptying

340

for the Octet instrument (figure)

341

web browser opening

38

remote view of experiment

47

Web Server check box

45

URL (figure)

46

user option

43


page 38 weight

Octet QK instrument

24


27


22


20


17

well designations changing

kinetics 384

295

kinetics 96

231

defined

144

removing

quantitation 384

149, 153

quantitation 96

74, 78


167

removing controls or reference wells

quantitation 384

157

quantitation 96

81

well information, tooltip

241

well types

Activation

kinetics 384

281

kinetics 96

218

Buffer

kinetics 384

280

kinetics 96

218

Control

kinetics 384

280

kinetics 96

218

quantitation 384

145

quantitation 96

71

designating kinetics 384

282

kinetics 96

219

designating (kinetics experiments)

282

for kinetics experiments

220, 282

Load kinetics 384

281

kinetics 96

218

Negative Control kinetics 384

280

quantitation 384

145

quantitation 96

71

Positive Control kinetics 384

280

quantitation 384

145

quantitation 96

71

Quench kinetics 384

281

kinetics 96

218

Received quantitation 384

145

quantitation 96

71

Reference kinetics 384

280

kinetics 96

218

quantitation 384

145

quantitation 96

71

Regeneration kinetics 384

281

kinetics 96

218

removing designated type

220

Sample kinetics 384

280


page 39

kinetics 96

218

Standard

quantitation 384

145

quantitation 96

71

Unknown

quantitation 384

145

quantitation 96

71

Wash

kinetics 384

281

kinetics 96

218

well volumes

Octet QK384

20, 27

Octet RED384

20, 27

wells annotating

82, 225, 288

annotating individual

kinetics 384

289

kinetics 96

226

quantitation 384

157

quantitation 96

82

assigning dilution factor

quantitation 384

154

quantitation 96

79

assigning serial dilution

quantitation 384

154

quantitation 96

79

selecting in the Sample Plate Map

kinetics 96

219

quantitation 384

148

quantitation 96

73

window icons, arranging

37

Window menu

described


37

windows organizing in a cascade arrangement

37

tiling vertically

37


page 40


page 1

Index

Symbols


90

Numerics


59

2nd Buffer Time and Shake speed parameter

136, 213


264, 328



196 quantitation 96

119



172 quantitation 96

95


280


167


280


167

A


38 accessing GxP Server module directly

396 accessing Temperature field

12 account details, assigning

385 acquisition for a data column, displaying

267, 331 quantitation 384

199 quantitation 96

122 acquisition options

40



330


198

Octet QKe

121

Octet RED

121


218 kinetics 384

281 activation steps

237, 303 active biosensor column

122, 199, 267,

331


239,

304 active method file, closing

33 active steps, extending duration

270, 335


49

Adding

49 adding biosensor type

49 replicate assay to a plate

247, 312


Map kinetics 384

291 kinetics 96

228 quantitation 384 (figure)


85



203 quantitation 96

126



Plate Map kinetics 96 (figure)

225 adjacent steps, selecting

243, 308 administrator account, setting up

374 administrator constants, listed (table)

393 administrator password, changing

387 administrator user session, starting

378 administrator username selection (figure)

379


166


94, 135, 171, 212


136,

213


135, 212


136,

213


136,

213

Offline

136, 213




172


172


172


172


171


Speed parameter

172

Offline parameter

172


173


173


173


Speed parameter

172


172


172


171 quantitation 96

94


95


95


95


95


94,

133


Speed parameter

95

Offline parameter

95


96


96


96


Speed parameter

95


95


95


94


page 3

Regeneration cycles

137, 214


136, 213


212


Experiment

142 advanced run experiment settings

120,

197, 329 advanced settings


121


121

Default

121


266


266


330


266


121

Align to Step menu

270 aligning binding data to the beginning of a user-selected step

270, 334

All steps (option)

244, 309 analysis options, viewing

40 analyzing quantitative experiment

68, 140,

216, 276 annotating individual wells in the sample plate table kinetics 384

289 kinetics 96


157 quantitation 96


82, 225, 288 annotations, entering


157 quantitation 96

82


244, 309


244, 309


243


66 applications, closing

34

Arrange Icons menu

37 arranging window icons

37


237


237

Assay number

267 assay parameter settings, modifying quantitation 384

167 quantitation 96

91 assay parameter values, editing quantitation 384

208 quantitation 96

131 assay parameters


94

Basic Quantitation for 384 model

169 for 96 model

92


170 quantitation 96

93


91 assay parameters, Basic Quantitation


209 quantitation 96

132



page 4 quantitation 384

209 quantitation 96

132


209 quantitation 96

132


208 quantitation 96

131



94, 135, 171,

212


Assay (figure)

92, 131, 169, 208



93, 133, 170, 210

Assay Settings box

91


303 assay step name, changing (figure)

247,

311 assay steps adding

243, 308 copying

243, 308 inserting

245, 310 removing

247, 311 reordering

247, 311 assay times, updating (figure)

242, 307

Assay Type setting

Run Experiment window settings kinetics 384

328 kinetics 96


196 quantitation 96

119 assays adding steps

245, 310 adding to sample plates

248, 313 assigning biosensors to samples

249,

313 automatic addition of sensor tray maps

256, 320 building

241 changing biosensor locations

252, 257 changing biosensor type

320 copying steps between

243, 308 editing

246, 311 example using one partial biosensor try and biosensors from a second tray quantitation 384

190 quantitation 96

113 removing steps


247, 311 replicating steps

244, 309 starting new

244, 309 assigning account details

385 biosensors in Multiple Analyte experiments quantitation 384

177 quantitation 96

99 biosensors in single analyte experiments quantitation 384

173 quantitation 96

96 biosensors to samples


173 quantitation 96

96 dilution factor to selected wells quantitation 384

154 quantitation 96

79


page 5 dilution factor to unknowns quantitation 384

153 quantitation 96

78 heterogeneous biosensor trays quantitation 96

101 heterogenous biosensor trays quantitation 384

178 homogenous biosensor trays quantitation 384

183 quantitation 96

106 molecular weight kinetics 96

221 molecular weight and molar concentration (kinetics)

283 privileges

385


Map kinetics 384

290 kinetics 96


159 quantitation 96

84


Table kinetics 384

293 kinetics 96


162 quantitation 96

87 sample concentrations by value kinetics 96 (figure)

223 sample concentrations using dilution series kinetics 384

286 kinetics 96

223 kinetics 96 (figure)

224 serial dilution to selected wells quantitation 384

154 quantitation 96

79 serial dilution to unknowns quantitation 384

153 quantitation 96

78 standard concentration quantitation 384 (figure)


76 standard concentrations using a dilution series quantitation 384

149 quantitation 96

74 step types in the sample plate (figure)

242, 307 user group

385 user-specified concentration to samples

222, 285 user-specified concentration to standards quantitation 384

151 quantitation 96

76 assigning molar concentration kinetics 96

221 association steps

236, 302

Audit Trail described

62 illustrated (figure)

62 list options

64 selecting a project

63 sorting

63 viewing

62


53


264, 328


page 6



197 quantitation 96

120


39


120, 197, 265, 329 automation for Octet QK384

26 for Octet RED384

19

Automation box

346

Automation Client example application, connecting

348 automation interface commands

Cleanup

350

Close

350

GetMethodInfo

349

GetRunInfo

349

Present

350

Reset

349

Resume

350

Run

349

Status

350

Stop

350

Version

349 automation interface control setup

346 automation interface design

346 automation session, typical

351


43


349


346

B

baseline step

237, 303 basic kinetics experiment

216, 276


277


92, 131, 169, 208


209 quantitation 96




169

Quantitation Shake Speed (parameter)

169


169


169 quantitation 96



92


92


92


92


209 quantitation 96

132


209 quantitation 96

132


208 quantitation 96

131




208 quantitation 96

131



166

Basic Quantitation with Regeneration assay parameter

133, 210



134, 211


134, 211



170


170


Speed parameter

170


171


171


171


Speed parameter

170


170 quantitation 96

93


93


Speed parameter

93


94


94


93


94


Speed parameter

93


93, 133


133, 170, 210

Regeneration cycles

134, 211


133, 210



69, 141


Experiment

69, 141 beginning an experiment

216, 276 beginning the next step in the assay

271,

335 binding data aligning kinetics 384

334 kinetics 96

270 exporting quantitation 384

204 quantitation 96

127 saving kinetics 384

337 kinetics 96


204 quantitation 96

127 biosensor column, active

122, 199, 267,

331 biosensor columns, default

252, 316 biosensor pickup tips, cleaning

343 biosensor regeneration, described quantitation 384

188



111 biosensor stage (left) and sample stage

(right), figure

116, 261 biosensor tray loading kinetics 384

324 kinetics 96

260 replacing biosensors

251, 315 biosensor tray type

17, 19, 26

Octet QK instrument

24


22


17, 19, 26 biosensor tray, loading quantitation 384

193 quantitation 96

116 biosensor type adding

49 changing (figure)

247, 311

Octet QK instrument

24


22


17, 19, 26 removing

49 biosensor type, changing in the Assay

Definition window

258, 322 biosensor type, changing in the Sensor

Assignment window

254, 318 biosensor types, changing

246, 311 biosensors assigning quantitation 384

173 quantitation 96

96 assigning to samples

249, 313 automatically adding experiment tray maps

256, 320 changing locations kinetics 96

252 changing type

320 designating reference

105, 110, 182,

187, 257, 321 entering information

252, 315 preparing

68 removing from sensor tray maps

253,

317 replaying in the biosensor tray

251,

315 viewing available

48 biosensors, reference, designating

258 browser window functions

47


280 kinetics 96

218



172 quantitation 96

95


135, 212 building assays

241

By value option

76, 151, 222, 285

C

capabilities

Octet QK instrument

23


25


22


18


17


page 9 cascade arrangement, organizing windows

37

Cascade menu

37


387


64 changing administrator password

387 assay step name (figure)

247, 311 biosensor Location (Method 1)

253,

316 biosensor location (Method 2)

254,

317 biosensor type (figure)

247, 311 biosensor type in the Assay Definition window

258, 322 biosensor type in the Sensor

Assignment window

254, 318 constants

394 group settings

390 project settings

391 projects during a user session

64 sample plate format kinetics 384


144 sample plate format (figure)

144, 280 user account passwords

387 user account settings

386 user password

65 well designations kinetics 384

295 kinetics 96

231 changing location of a reserved column quantitation 384

146 quantitation 96

72 changing projects (figure)

64


367, 369


(figure)

367, 370, 373 cleaning biosensor pickup tips

343 cleaning Octet instrument

340, 342


350


350


33 closing active method file

33 application

34 color codes

122, 199, 267, 331 color-coded wells displaying how biosensors interrogate a 384-well plate, 8 channel or 16channel read head

143, 279 a 96-well plate, 8 channel or 16channel read head

143, 279 compliance

Octet QK instrument

23


25


21


18


16 compliant features, 21 CFR Part 11

59

Conc column

76, 151 concentration representation in dilution series (figure)

224


73


45


page 10 connecting


348


30 to a TCP/IP socket connection locally using localhost

348


397 constants changing

394 creating new

393 deleting

394 viewing

394


392 constants, administrator, listed (table)

393 contacting ForteBio technical support

13

Control (well type)

218 kinetics 384


145 quantitation 96


71, 145 controls

156 defined

81, 156 designating


156 quantitation 96

81 conventions, used in this guide

13 copying assay steps

243, 308


338 kinetics 96


205 quantitation 96

128 step type kinetics 384

305 kinetics 96

240 creating


90 assay step type (figure) kinetics 384

303 kinetics 96

238 different types of assay steps

237, 303 new constants

393 new user account

384 new user group

389 step types

237, 303


331 custom assays defining quantitation 384

206 quantitation 96

129 selecting quantitation 384

214 quantitation 96

137 custom biosensors

48 custom steps

237, 303

D

Data Acquisition 21 CFR Part 11 software overview

52


30


12


38


page 11

Data Acquisition User Guide, opening online version

38


8


52

Data Analysis, icon

8 data column, displaying acquisition

267,


199 quantitation 96

122 data display, significant digits

42 data file location and name settings quantitation 384 (listed)

196 quantitation 96 (listed)

119



347 data files kinetics data repository


41


42


42 data preferences, setting

40


366 default biosensor columns

252, 316 default locations for reserved wells in a 96well sample plate map (figure)

72 default server settings localhost

54

Port 2002

54 default temperature value, saving

44 default temperature, defining new

44 default Tray Format

101 default user group privileges

385 default user groups

388 default windows, Octet System Data


31


121 defining custom assays quantitation 384

206 quantitation 96

129 kinetic assays

236 new assay

35 new assay (figure)

130, 207 new default temperature

44 reagent plates, quantitation 384

166 sample plates kinetics 384

278 kinetics 96


142 quantitation 96

70 samples by entering sample information (figure)

284 step types

237, 303 kinetics 384

305 kinetics 96

240 defining step types

236


265,

329


197 quantitation 96

120 deleting constants

394 factory-loaded biosensor types

49 projects

392 step types

240, 305


page 12 user account

386 user group

390


121, 199, 331 designating controls quantitation 384

156 quantitation 96


81, 156 reference biosensor during acquisition

268, 333 reference biosensors

105, 110, 182,

187, 257, 321 reference biosensors during acquisition quantitation 384

201 quantitation 96

124 reference wells quantitation 384

156 quantitation 96

81 reference wells (figure)

81, 156 samples (kinetics experiments)

218 unknowns quantitation 384

153 quantitation 96

78 well type (kinetics 384)

282 well types (kinetics experiments)

282 designating reference biosensors

258 designating standards quantitation 384

148 quantitation 96

73 designating well types kinetics 96

219

Detection

95, 136, 172, 213


146 quantitation 96

72



172 quantitation 96

95


136, 213 determining the GxP Server module host location

52 developing the automation client

347 dialog boxes

Options

41 setting default temperature

44

Temperature Setting

43 digital signatures, verifying

60 dilution factor, assigning to selected wells quantitation 384

154 quantitation 96

79 dilution factor, assigning to unknowns quantitation 384

153 quantitation 96

78 dilution factor, editing in sample table quantitation 384

155 quantitation 96

80 dilution series assigning sample concentrations kinetics 384

286 kinetics 96

223 assigning standard concentrations quantitation 384

149 quantitation 96

74


page 13


75, 223 dimensions

Octet QK instrument

24


27


22


20


17 discontinuing user session

66 displaying acquisition for a data column


199 quantitation 96

122


377


34 license information

38

Octet System Data Acquisition software properties

38 step types (figure)

305 dissociation steps

236, 302

E


129, 206


35


35 edit commands

226


394


392


35 editing assay parameter values quantitation 384

208 quantitation 96

131 assays

35, 246, 311 biosensor information (figure)

252,

316 dilution factor in the sample table quantitation 384

155 quantitation 96

80 parameter values quantitation 384

208 quantitation 96

131 projects

391 sample data in the Sample Plate Table kinetics 384

295 kinetics 96

231 standard concentration quantitation 384

151 quantitation 96

76 step type (figure)

241, 306 editing step types

240, 305


13 electrical requirements

Octet QK instrument

24


27


22


20


17 emptying waste container

340 ending a user session

66 enhanced legend options, in the Runtime

Binding Chart

12 entering annotations



157 quantitation 96

82 biosensor information displayed (figure)

252, 316 procedure

252, 315 entering an individual standard concentration quantitation 384

151 quantitation 96

76 environmental features

Octet QK instrument

23


25


21


18


16



172 quantitation 96

95


136, 213 equipment classifications

Octet QK instrument

23


25


21


18


16 events list options available

396 viewing

395

Events tab (figure)

395 example .csv plate definition file (figure)

235, 299 example assay using one partial biosensor tray and biosensors from a second tray

113, 190 example experiment using two biosensor trays (figure)

257, 321

Exit menu

34 experiment prior to running

258, 322

Experiment menu described

34 figure


35 experiment method files managing


205 quantitation 96

128 saving

33 saving to new name

33 experiment method files, managing

274,

338 experiment methods, saving manually

114,

191



196 quantitation 96

119 experiment settings advanced settings (Octet QK384)

198,

330 data file location and names


264, 328

Assay Type

328 assay type

264


264,


page 15

328 kinetics data repository

264, 328 plate name/barcode (file prefix)

264, 328 run name

264, 328 general information

Description

121, 199, 331

Machine name

121, 199, 330

User name

121, 199, 330 run settings


120, 197, 265, 329


265, 329


120, 197, 265, 329


120, 197,

265, 329 shake sample plate while waiting

120, 197, 265, 329

Start After

265, 329 experiment settings, data file location and names quantitation 384


196

Assay Type

196


197

Experiment Run Name

196

Plate Name/Barcode

196


196 quantitation 96


119

Assay Type

119


120

Experiment Run Name

119

Plate Name/Barcode

119


119


142 for the Octet RED96

70

Experiment Wizard

34 described

40 figure

40 opening

35 starting kinetics experiments

384

277


69, 141, 217,

277


141 experiments adding assays

248, 313 kinetic, starting

384

277

96

217 monitoring remotely

45 remote view via web browser (figure)

47 reviewing (kinetics 96)

258 saving manually

259, 323 saving to the factory-installed

Template folder

260, 324 starting


194 quantitation 96

117 stopping

36 stopping in progress

266, 331



199 quantitation 96

122

Export button

88

Sample Plate Map kinetics 96

233 export options

Copy the Runtime Binding Chart quantitation 384

205 quantitation 96

128

Export the Runtime Binding Chart to a graphic file quantitation 384

204 quantitation 96

127

Print the Runtime Binding Chart quantitation 384

205 quantitation 96

128 save the binding data quantitation 384

204 quantitation 96

127

Export Plate Definition window kinetics 384

297 kinetics 96


163 quantitation 96

88 exporting binding data

127, 204 plate definition kinetics 384

297 kinetics 96


163 quantitation 96

88


127, 204, 272, 337


127, 204, 272, 337


273, 337


127, 204


270


271, 335 extending duration of the active step

270,

335

F


49


381


381


62

File History menu

34

File menu described

32 figure


33


33


62


61

Fill Plate (menu)

253, 316


239, 305

Flip Data check box

125, 269, 334

Flip Data function viewing inverted data

269


372


397


371


page 17


13


38 fractional use of regeneration and neutralization wells (figure)

112, 189

Fuse symbol

13

G


330

GetMethodInfo (automation interface command)

349

GetRunInfo (automation interface command)

349

GetRunInfo command

347


239, 305 group administration

388 group settings changing

390 viewing

390

Groups tab (figure)

388


54


397


396 restarting

398

H

Heat/hot symbol

13

Help menu described

38 figure

38

I


38 heterogeneous biosensor trays assigning biosensors quantitation 384

178 quantitation 96

101 using kinetics 384

317 kinetics 96

254 hiding main toolbar

34 status bar

34 higher acquisition rate

120, 197, 329


183 quantitation 96

106 icons

Data Acquisition

8

Data Analysis

8

Import button

89


234


164 quantitation 96

89


234 importing plate definitions kinetics 384

298 kinetics 96

234


page 18 importing plate definition quantitation 384

164 quantitation 96

89 inserting assay steps

245, 310 installing

Data Acquisition 7.0 CFR Part 11 software

366


369

ForteBio GxP Server

372


371


36 figure


36


34 instrument status log (figure)

119, 196,

263, 327


36 described

39 figure

39 logging

36 inverted data, viewing in the Runtime

Binding Chart

269, 334

K


40 kinetics assays building

248 defining

236 step type requirements

236, 302 kinetics data repository

264, 328 kinetics data repository, user option

41 kinetics experiments designating samples

218 designating well types

282


282 starting

384

277

96

217

L



30 legend, for Runtime Binding Chart, selecting


203 quantitation 96

126 license information, displaying

38 list options available for events

396 listing windows currently open in the Main

Screen

37


281 kinetics 96

218 loading biosensor tray kinetics 384

324 kinetics 96


193 quantitation 96

116 reagent plates, kinetics 384

324 sample plate kinetics 384

324


page 19 kinetics 96


193 quantitation 96

116 steps

236, 302

LoadSensors

353

Localhost option

347 localhost, default server settings

54 locking


65


65 logging in the Instrument Status window

36


378 user session (figure)

56

Lot Number column

252 lower acquisition rate

121, 198, 329

M


63


121, 199, 330 magnification, undoing

125, 202, 271,

335 magnifying Runtime Binding Chart

271,


202 quantitation 96

125

Main Menu, Octet System Data Acquisition software

31 main screen, Octet System Data Acquisition software

31 main toolbar hiding

34 showing

34 managing experiment method files

128, 274,


205 quantitation 96

128



274 manually save an experiment

259, 323 mechanics

Octet QK instrument

24


26


22


19


17 menu bar, Octet System Data Acquisition software

32 menu commands, listed

33, 34, 35, 36 method file (.fmf)

68, 140, 216, 276 method file (.fmf), described

32 method files closing

33 saving

33 saving all

33


166 modifying assay parameter settings quantitation 384

167 quantitation 96

91 reagent plate quantitation 384

166, 299 molar concentration units

222, 284


page 20 molar concentration, assigning kinetics 96

221 molecular weight, assigning kinetics 96

221 monitoring experiments remotely

45

Multiple Analyte assay parameter quantitation 384

209 quantitation 96

132

Multiple Analyte experiments assigning biosensors quantitation 384

177 quantitation 96

99 used with Replicate Groups quantitation 384

163 quantitation 96

88



171 quantitation 96

94, 133


170 quantitation 96

93 multiple runtime binding charts

12 quantitation 96

72



172 quantitation 96

95


170 quantitation 96

93


134, 211


136, 213


217, 277


35 new features, Octet System Data


12


389


217, 277


69, 141

New Window menu

37 non-adjacent steps, selecting

243, 308

N

Negative Control (well type) kinetics 384

280 kinetics 96


145 quantitation 96

71

Neutralization (reserved well requirements) quantitation 384

146

O


340, 342 resetting

36


13


341, 344


30


343


page 21

Octet QK instrument

23 biosensor tray type

24 biosensor type

24 capabilities

23 compliance

23 dimensions


24 environment


23 mechanics

24 optics


24 sample types

24 sample volume

24 sampling format


24 throughput

24


23

Octet QK384 sensor offset

20, 27 well volumes

20, 27

Octet QK384 instrument automation

26 capabilities

25 compliance

25 dimensions


27 environment


25 mechanics

26 optics

26 sample types

26 sampling format

26 weight

27


25


(table)

25


266

Octet QKe instrument biosensor tray type

22 biosensor type

22 capabilities

22 compliance

21 dimensions

22 displayed (figure)


22 environment


21 mechanics

22 optics


22 sample types

22 sample volume

22 sampling format


22 throughput

22 weight

22


(table)

21


341


30


20, 27 starting



278 well volumes

20, 27

Octet RED384 instrument automation

19 capabilities

18 compliance

18 dimensions


20 environment


18 mechanics

19 optics

19 sample types

19 sampling format

19 weight

20


18


193


17, 19, 26 biosensor type


17 compliance

16 dimensions


17 environment


16 mechanics

17 optics


17, 20, 27 sample types

17 sampling format

17 sampling volume


17 throughput

17, 19, 26 weight

17


16


18 listed (table)

16, 18, 25


325


Main Menu

31 main toolbar

32 new features

12 starting

30 toolbar

31


Main Screen

31


40


8

Offline parameter

136, 213


172 quantitation 96

95


244, 309


243


268, 332


33


33


120, 197, 265, 329


267


page 23


326

Open Windows menu

37 opening dialog box to select an experiment method file

33


35

Experiment Wizard

35 online Data Acquisition User Guide

38



200 quantitation 96

123


35


35 web browser

38 optics

Octet QK instrument

24


26


22


19


17

Options dialog box displayed (figure)

41 setting


34 significant digits

34 viewing analysis options

41


41


347

Options menu


Octet QK instrument

24


22


17, 20, 27 organizing windows in a cascade arrangement

37

P


343 parameter settings, assay, modifying quantitation 384

167 quantitation 96

91 parameter values, editing quantitation 384

208 quantitation 96

131 partial biosensor trays, using

256 kinetics 384

320 password reminder, user and administrator

(figure)

57 plate definition exporting kinetics 384

297 kinetics 96


163 quantitation 96

88 importing quantitation 384

164 quantitation 96

89



78,

153


74, 149


233, 234


234


page 24 kinetics experiments

282 selecting concentration units (figure)

222,

285 molar concentration units (figure)

222, 285 plate definitions importing kinetics 384

298 kinetics 96

234 plate name/barcode (file prefix)

264, 328



196 quantitation 96

119 plate temperature range

43 plate temperature, setting

43


54

Positive control

218

Positive Control (well type) kinetics 384


145 quantitation 96

71 post-condition biosensors

12


134,

211


173 quantitation 96

96


171 quantitation 96

94




173 quantitation 96

96


134, 211



171 quantitation 96

94 preparing biosensors

68 preparing samples for quantitation or kinetics experiments

8


350

Present Stage menu

36

Print menu

33

Print Preview menu

33 print preview window

33


33

Print Setup menu

33 printing files

33


128, 205, 273,

338 prior to running an experiment

258, 322 privileges, assigning

385 project administration

390


63 project selection (figure)

58 project settings changing

391 viewing

391 project-based Audit Trail events (figure)

64


page 25 projects changing (figure)

64 deleting

392 editing

391

Projects tab

391 projects, changing during a user session

64 properties, for Octet System software, displaying

38

Q



144



196 quantitation 96

119 quantitation data repository, user option

41



142


141


69


69, 141 quantitation experiment defined

68, 140 starting

69, 141

Quantitation Shake Speed assay parameter quantitation 384

209 quantitation 96

132


169 quantitation 96

92


133, 170, 210


93


209 quantitation 96

132


169 quantitation 96

92 quantitative experiment analyzing

68, 140, 216, 276 setting up

68, 140, 216, 276


281 kinetics 96

218 quenching steps

237, 303

R


201 quantitation 96

123 read head configuration kinetics 384


143 reagent plate defining quantitation 384

166 modifying quantitation 384

299



301

Reagent Plate Map

166


166, 300


166 reagent plates, loading kinetics 384

324

Received (well type) quantitation 384

145 quantitation 96

71 recommended sensor offset

198, 330


218 kinetics 384


145 quantitation 96

71 reference biosensors designating

105, 110, 182, 187, 257,

258, 321 designating during acquisition

268,

333 reference biosensors, designating during acquisition quantitation 384

201 quantitation 96

124

Reference menu

124, 201, 268, 333 reference wells defined

81, 156 designating quantitation 384

156 quantitation 96

81 reference, type of well

71, 145 reference-subtracted data viewing kinetics 384

332 kinetics 96

268 reference-subtracted data, viewing quantitation 384

201 quantitation 96

123

Refresh settings

45


146 quantitation 96

72


281 kinetics 96

218



171 quantitation 96

94




173 quantitation 96

96


134, 211



172 quantitation 96

95


170 quantitation 96

93


133, 136, 210, 213 remote view of experiment via web browser (figure)

47



35 assay steps

247, 311 biosensor type

49 side panel of Octet instrument

343 step alignment of data

270, 334 well designation

282 well designations controls or reference wells



74, 78 reagent plates, quantitation 384

167 reordering assay steps

247, 311


176 replacing biosensors in the biosensor tray

251,

315 fuses for Octet RED instrument

341 for QKe instrument

341 replicate assay steps

244, 309 replicate assay, adding to a plate

247, 312


227,

290

Replicate Groups assigning in the Sample Plate Table quantitation 384

162 quantitation 96

87 defined


159 quantitation 96

84 displayed in Sample Plate Map quantitation 384 (figure)


86 displayed in Sample Plate Table quantitation 384 (figure)


86


Map (figure)

229


(figure)

229 replicate steps

All steps (option)

244, 309


244,

309


244,

309



244, 309


244, 309

Sample steps will be adjusted by vertically by one row (option)

244,

309

Sample steps will be adjusted by X column (option)

244, 309


243 requirements, for reserved wells

72 reserved column, changing location quantitation 384

146 quantitation 96

72



72


146 quantitation 96

72


page 28

Neutralization quantitation 384

146 quantitation 96

72

Regeneration quantitation 384

146 quantitation 96

72 reserved wells

72 reserved, type of well

71, 145


349

Reset menu


36


399


399 restarting the GxP Server module

398


350 resuming user session

66



172 quantitation 96

95


114, 191,

258, 322


114,

191, 259, 323 reviewing experiments (kinetics 96)

258


349

Run Experiment tab

117



117, 194



119, 196

Assay Type

119, 196


120, 197

Experiment Run Name

119, 196

Plate Name/Barcode

119, 196


119, 196



262, 326 run name

264, 328 run settings quantitation 384


197

Start After setting

197 quantitation 96


120

Start After setting

120 run settings, listed quantitation 384

197 quantitation 96

120 running experiment settings

119, 196

Runtime Binding Chart adding title


203 quantitation 96

126 copying kinetics 384

338 kinetics 96

273 exporting to a graphic file

273, 337 exporting to a graphic or data file

127,

204, 272, 337 magnifying


202 quantitation 96

125 managing


page 29 kinetics 96

267 opening


200 quantitation 96

123 printing

273, 338 scaling


202 quantitation 96

126 selecting legend


203 quantitation 96

126 updating kinetics 384

331 kinetics 96


199 quantitation 96

122 viewing inverted data

269, 334 viewing multiple kinetics 384

336 kinetics 96


204 quantitation 96

127


118, 195,

263, 327

Runtime Binding Chart Export options copy the Runtime Binding Chart to a graphic file quantitation 384

205 quantitation 96

128 export the Runtime Binding Chart to a graphic file quantitation 384

204 quantitation 96

127 print the Runtime Binding Chart to a graphic file quantitation 384

205 quantitation 96


204 quantitation 96

127



204 quantitation 96

127


267, 332


205 quantitation 96

128

Runtime Binding Chart, enhanced legend options

12


128, 205


126,

203, 271, 336

S


280 kinetics 96

218 sample plate loading kinetics 384

324 kinetics 96


193 quantitation 96

116


page 30



167


90,

165 sample plate format, changing kinetics 384


144


Series (figure)

75, 150, 223, 286 sample plate shaker, stopper

36


Commands (figure)

77, 80, 152, 155,

231, 232, 295, 296 sample plate temperature, recorded in log file

12 sample plates adding assays


249,

313 assigning step types to

242, 307 defining kinetics 96


142 quantitation 96

70 defining kinetics 384

278 importing definitions kinetics 384

298 kinetics 96

234 sample step types for kinetic assays, listed

(table)

236


244, 309


244, 309



309 kinetics 96

244



172 quantitation 96

95 sample types

Octet QK instrument

24


26


22


19


17 sample volume

Octet QK instrument

24


22 samples changing biosensor type

320 designating (kinetics experiments)

218 specifying analyte concentration

221,

283 specifying concentration units

222,

284 sampling format

Octet QK instrument

24


26


22


19



17


33


33


page 31


33


33

Save to File menu

39 saved experiments in the Template folder

(figure)

260, 324 saving all method files

33 binding data

127, 204, 273, 337 default temperature value

44 experiment method files

33 experiment method files to a new name

33 experiment methods

114, 191 experiments manually

259, 323 experiments to the factory-installed

Template folder kinetics 384

324 kinetics 96


192 quantitation 96

115 modified parameter settings

91, 167 reagent plate definition kinetics 384


167 scaling Runtime Binding Chart kinetics 384

335 kinetics 96


202 quantitation 96

126 screen components, Octet System Data


31

Security menu availability

32 compliance features (figure)

59 described

36 figure

37 selecting adjacent steps, to copy and add

243,

308 concentration units

222, 284 concentration units in the Plate


222, 285 custom assays quantitation 384

214 quantitation 96

137 experiment method file, opening function

33



70 in the Experiment Wizard

70 from a set of predefined ForteBio quantitation or kinetics method templates

35 molar concentration units

222, 284 molar concentration units in the Plate


222, 285 non-adjacent steps, to add and copy

243, 308 project in the Audit Trail

63


336 kinetics 96


203 quantitation 96

126 server location

53 wells in the Sample Plate Map kinetics 384

282


page 32 kinetics 96


148 quantitation 96

73 wells in the Sample Plate Map (kinetics

384)

281 selecting the Web Server in the Options dialog box (figure)

45 selectively display the acquisition for a data column


199 quantitation 96

122


349


48, 96, 100, 173,

177, 303


96, 100, 173,

177, 303 displayed (figure)

250, 314



(figure)

97, 100, 174, 177 sensor offset

198, 330

Octet QK384

20, 27

Octet RED384

20, 27


121


122, 199,

267, 331 sensor tray maps


256, 320 changing biosensor locations

252, 257 removing biosensors

253, 317 returning to default layout

253, 316

Sensor Type arrow

246


249


35


48


267 serial dilution, assigning to selected wells quantitation 384

154 quantitation 96

79 serial dilution, assigning to unknowns quantitation 384

153 quantitation 96

78 serial port (RS-232)

346 server location, selecting

53 server testing

397


329 kinetics 96


197 quantitation 96

120


35


76, 151, 221


290 setting assay step threshold parameters

(figure)

239, 304 plate temperature

43 system and data preferences


(figure)

239


44 setting temperature (figure)

43 setting up administrator account

374 setting up quantitative experiment

68,

140, 216, 276



120,

197, 329 shake sample plate while waiting (setting)

120, 197, 265, 329

Shake Speed parameter quantitation 384

169 quantitation 96

92 shortcut keys

226 showing main toolbar

34 status bar

34


239,

304 significant digits data display

42 user option

42 simulation, user option

43

Single Analyte assay parameter quantitation 384

208 quantitation 96

131 single analyte experiment assigning biosensors quantitation 384

173 quantitation 96

96



171 quantitation 96

94


170 quantitation 96


169 quantitation 96

92

Skip Step menu

35 specifying number of significant digits for the values of Molecular Weight,


42


145 quantitation 96

71

Standard button

73, 148 standard concentration, entering quantitation 384

151 quantitation 96

76 standard, type of well

71, 145 standards, designating quantitation 384

148 quantitation 96

73


329 kinetics 96


197 quantitation 96

120 starting administrator user session

378 an experiment


194 quantitation 96

117 basic kinetics experiment

384

277

96

217 experiment from the Experiment wizard

141 kinetics experiment with the


Octet RED384

278


page 34 new assay

244, 309


30 quantitation experiment

69, 141 user session

56 starting concentration value

76, 151, 222,

285 startup, temperature, user option

42


350 status bar described

38 figure

38 hiding

34 showing

34

Status Bar (menu)

34


305

Step Name arrow

246


246 step types activation

237, 303 applying a threshold

238, 304 assigning to columns in sample plate

242, 307 association

236, 302 changing

246, 311 copying kinetics 384

305 kinetics 96

240 creating

237, 303 custom

237, 303 defining

236 kinetics 384

305 kinetics 96

240 deleting

240, 305 dissociation

236, 302 editing

240, 305 loading

236, 302 quenching

237, 303 requirements for kinetics assays

236,

302 step types (sample) for kinetic assays

236 steps adding to assays

245, 310 copying between assays

243, 308 replicate

244, 309


350

Stop menu

36

Stop Shaker menu

36 stopping experiment

36 experiment in progress


199 quantitation 96

122 sample plate shaker

36


268, 332


124,

201, 268, 333 symbols electrical hazard

13 fuse

13 heat/hot

13 system preferences, setting

40 system specifications

Octet QK

23


page 35

Octet QKe

21

Octet RED96

16, 18, 25

T

Tab menu

383

TCP/IP socket

346


348 technical support, contacting

13



Octet QK instrument

24


22


17

Temperature Setting dialog box displayed (figure)

43 opening

35 temperature value, default, saving

44 temperature, startup, user option

42

Templates menu

35 templates, viewing kinetics 384

324 kinetics 96

260 terminating a step in the assay

271, 335 testing server

397

Threshold check box

238 threshold parameters

Active Channels

239, 304

Filtering

239, 305

Gradient


239, 304

Signal Change

239, 304


304 threshold, applying to assay steps

238, 304 throughput

Octet QK instrument

24


22


17, 19, 26

Tile menu

37 tiling, windows vertically

37

Toolbar (menu)

34 toolbar, Octet System Data Acquisition software

31 tooltip of well information

241

Tray Format button

106 types of wells control

71, 145 reference

71, 145 reserved

71, 145 standard

71, 145 unassigned

71, 145

Unknown

71 unknown

145

U

Unaligned menu

270, 334 unassigned, type of well

71, 145

UNC folder names

347 undo magnification

125, 202, 271, 335


145 quantitation 96

71 unknowns assigning a dilution factor quantitation 384

153



78 assigning serial dilution quantitation 384

153 quantitation 96

78 designating quantitation 384

153 quantitation 96

78 updating assay times as steps are added to the assay (figure)

242, 307


331 kinetics 96


199 quantitation 96

122


42

Use old 5.0 file format for FRD files, user option

42 user account creating new

384 deleting

386 user account passwords, changing

387 user account settings changing

386 viewing

386 user data files options

41 user data options

42 user group assigning

385 creating new

389 deleting

390 privileges

385 user groups, default

388

User name (setting)

121, 199, 330 user options

Automation


41 listed (table)



42

Simulation

43 temperature

42


42


42 viewing

40

Web Server

43 user password, changing

65 user session changing projects during

64 starting

56 starting an administrator

378 user sessions discontinuing

66 ending

66

Login dialog box

56 resuming

66 user startup options

42 user-defined default start-up temperature

12


381 user-modifiable settings for an assay quantitation 384

167 quantitation 96

91 username selection (figure)

57

Users tab

384 using


page 37 heterogeneous biosensor trays kinetics 384

317 kinetics 96

254 partial biosensor trays kinetics 384

320 kinetics 96

256 quantitation 96

112

V



60


349

View menu described

34 figure



40

Audit Trail

62 available types of biosensors

48 constants

394 events

395 events for a specific project or computer

63 group settings

390 inverted data displayed in the Runtime

Binding Chart

269, 334 multiple Runtime Binding Charts kinetics 384

336 kinetics 96


204 quantitation 96


391 raw reference-subtracted data quantitation 384

201 quantitation 96

123 reference-subtracted data kinetics 384

332 kinetics 96


201 quantitation 96

123 templates

260, 324 user account settings

386 user options


167 quantitation 96

91

W

warm-up time

30


281 kinetics 96

218 waste container emptying

340 for the Octet instrument (figure)

341 web browser opening

38 remote view of experiment

47


45

URL (figure)

46 user option

43


page 38 weight

Octet QK instrument

24


27


22


20


17 well designations changing kinetics 384

295 kinetics 96

231 defined

144 removing quantitation 384



167 removing controls or reference wells quantitation 384

157 quantitation 96

81 well information, tooltip

241 well types

Activation kinetics 384

281 kinetics 96

218

Buffer kinetics 384

280 kinetics 96

218

Control kinetics 384

280 kinetics 96


145 quantitation 96

71 designating kinetics 384

282 kinetics 96


282 for kinetics experiments

220, 282

Load kinetics 384

281 kinetics 96

218



145 quantitation 96

71



145 quantitation 96

71

Quench kinetics 384

281 kinetics 96

218


145 quantitation 96

71


280 kinetics 96


145 quantitation 96

71


281 kinetics 96

218 removing designated type

220

Sample kinetics 384

280


page 39 kinetics 96

218

Standard quantitation 384

145 quantitation 96

71

Unknown quantitation 384

145 quantitation 96

71

Wash kinetics 384

281 kinetics 96

218 well volumes

Octet QK384

20, 27

Octet RED384

20, 27 wells annotating

82, 225, 288 annotating individual kinetics 384

289 kinetics 96


157 quantitation 96

82 assigning dilution factor quantitation 384

154 quantitation 96


154 quantitation 96

79 selecting in the Sample Plate Map kinetics 96


148 quantitation 96

73 window icons, arranging

37

Window menu described


37 windows organizing in a cascade arrangement

37 tiling vertically

37


page 40


page 1

Index

Symbols


90

Numerics


59

2nd Buffer Time and Shake speed parameter

136, 213


264, 328



196 quantitation 96

119



172 quantitation 96

95


280


167


280


167

A


38 accessing GxP Server module directly

396 accessing Temperature field

12 account details, assigning

385 acquisition for a data column, displaying


199 quantitation 96

122 acquisition options

40



330


198

Octet QKe

121

Octet RED

121


218 kinetics 384

281 activation steps

237, 303 active biosensor column

122, 199, 267,

331


239,

304 active method file, closing

33 active steps, extending duration

270, 335


49

Adding

49 adding biosensor type

49 replicate assay to a plate

247, 312


Map kinetics 384

291 kinetics 96



85



203 quantitation 96

126



Plate Map kinetics 96 (figure)

225 adjacent steps, selecting

243, 308 administrator account, setting up

374 administrator constants, listed (table)

393 administrator password, changing

387 administrator user session, starting

378 administrator username selection (figure)

379


166


94, 135, 171, 212


136,

213


135, 212


136,

213


136,

213

Offline

136, 213




172


172


172


172


171


Speed parameter

172

Offline parameter

172


173


173


173


Speed parameter

172


172


172


171 quantitation 96

94


95


95


95


95


94,

133


Speed parameter

95

Offline parameter

95


96


96


96


Speed parameter

95


95


95


94


page 3

Regeneration cycles

137, 214


136, 213


212


Experiment

142 advanced run experiment settings

120,

197, 329 advanced settings


121


121

Default

121


266


266


330


266


121

Align to Step menu

270 aligning binding data to the beginning of a user-selected step

270, 334

All steps (option)

244, 309 analysis options, viewing

40 analyzing quantitative experiment

68, 140,

216, 276 annotating individual wells in the sample plate table kinetics 384

289 kinetics 96


157 quantitation 96


82, 225, 288 annotations, entering


157 quantitation 96

82


244, 309


244, 309


243


66 applications, closing

34

Arrange Icons menu

37 arranging window icons

37


237


237

Assay number

267 assay parameter settings, modifying quantitation 384

167 quantitation 96

91 assay parameter values, editing quantitation 384

208 quantitation 96

131 assay parameters


94

Basic Quantitation for 384 model

169 for 96 model

92


170 quantitation 96

93


91 assay parameters, Basic Quantitation


209 quantitation 96

132




209 quantitation 96

132


209 quantitation 96

132


208 quantitation 96

131



94, 135, 171,

212


Assay (figure)

92, 131, 169, 208



93, 133, 170, 210

Assay Settings box

91


303 assay step name, changing (figure)

247,

311 assay steps adding

243, 308 copying

243, 308 inserting

245, 310 removing

247, 311 reordering

247, 311 assay times, updating (figure)

242, 307

Assay Type setting

Run Experiment window settings kinetics 384

328 kinetics 96


196 quantitation 96

119 assays adding steps

245, 310 adding to sample plates


249,

313 automatic addition of sensor tray maps

256, 320 building

241 changing biosensor locations

252, 257 changing biosensor type

320 copying steps between

243, 308 editing

246, 311 example using one partial biosensor try and biosensors from a second tray quantitation 384

190 quantitation 96

113 removing steps


247, 311 replicating steps

244, 309 starting new

244, 309 assigning account details

385 biosensors in Multiple Analyte experiments quantitation 384

177 quantitation 96

99 biosensors in single analyte experiments quantitation 384

173 quantitation 96

96 biosensors to samples


173 quantitation 96

96 dilution factor to selected wells quantitation 384

154 quantitation 96

79


page 5 dilution factor to unknowns quantitation 384

153 quantitation 96

78 heterogeneous biosensor trays quantitation 96

101 heterogenous biosensor trays quantitation 384

178 homogenous biosensor trays quantitation 384

183 quantitation 96

106 molecular weight kinetics 96

221 molecular weight and molar concentration (kinetics)

283 privileges

385


Map kinetics 384

290 kinetics 96


159 quantitation 96

84


Table kinetics 384

293 kinetics 96


162 quantitation 96

87 sample concentrations by value kinetics 96 (figure)

223 sample concentrations using dilution series kinetics 384

286 kinetics 96

223 kinetics 96 (figure)

224 serial dilution to selected wells quantitation 384

154 quantitation 96

79 serial dilution to unknowns quantitation 384

153 quantitation 96

78 standard concentration quantitation 384 (figure)


76 standard concentrations using a dilution series quantitation 384

149 quantitation 96

74 step types in the sample plate (figure)

242, 307 user group

385 user-specified concentration to samples

222, 285 user-specified concentration to standards quantitation 384

151 quantitation 96

76 assigning molar concentration kinetics 96

221 association steps

236, 302

Audit Trail described

62 illustrated (figure)

62 list options

64 selecting a project

63 sorting

63 viewing

62


53


264, 328


page 6



197 quantitation 96

120


39


120, 197, 265, 329 automation for Octet QK384

26 for Octet RED384

19

Automation box

346

Automation Client example application, connecting

348 automation interface commands

Cleanup

350

Close

350

GetMethodInfo

349

GetRunInfo

349

Present

350

Reset

349

Resume

350

Run

349

Status

350

Stop

350

Version

349 automation interface control setup

346 automation interface design

346 automation session, typical

351


43


349


346

B

baseline step

237, 303 basic kinetics experiment

216, 276


277


92, 131, 169, 208


209 quantitation 96




169


169


169


169 quantitation 96



92


92


92


92


209 quantitation 96

132


209 quantitation 96

132


208 quantitation 96

131




208 quantitation 96

131



166

Basic Quantitation with Regeneration assay parameter

133, 210



134, 211


134, 211



170


170


Speed parameter

170


171


171


171


Speed parameter

170


170 quantitation 96

93


93


Speed parameter

93


94


94


93


94


Speed parameter

93


93, 133


133, 170, 210

Regeneration cycles

134, 211


133, 210



69, 141


Experiment

69, 141 beginning an experiment

216, 276 beginning the next step in the assay

271,

335 binding data aligning kinetics 384

334 kinetics 96

270 exporting quantitation 384

204 quantitation 96

127 saving kinetics 384

337 kinetics 96


204 quantitation 96

127 biosensor column, active

122, 199, 267,

331 biosensor columns, default

252, 316 biosensor pickup tips, cleaning

343 biosensor regeneration, described quantitation 384

188



111 biosensor stage (left) and sample stage

(right), figure

116, 261 biosensor tray loading kinetics 384

324 kinetics 96

260 replacing biosensors

251, 315 biosensor tray type

17, 19, 26

Octet QK instrument

24


22


17, 19, 26 biosensor tray, loading quantitation 384

193 quantitation 96

116 biosensor type adding

49 changing (figure)

247, 311

Octet QK instrument

24


22


17, 19, 26 removing

49 biosensor type, changing in the Assay

Definition window

258, 322 biosensor type, changing in the Sensor

Assignment window

254, 318 biosensor types, changing

246, 311 biosensors assigning quantitation 384

173 quantitation 96

96 assigning to samples

249, 313 automatically adding experiment tray maps

256, 320 changing locations kinetics 96

252 changing type

320 designating reference

105, 110, 182,

187, 257, 321 entering information

252, 315 preparing

68 removing from sensor tray maps

253,

317 replaying in the biosensor tray

251,

315 viewing available

48 biosensors, reference, designating

258 browser window functions

47


280 kinetics 96

218



172 quantitation 96

95


135, 212 building assays

241

By value option

76, 151, 222, 285

C

capabilities

Octet QK instrument

23


25


22


18


17


page 9 cascade arrangement, organizing windows

37

Cascade menu

37


387


64 changing administrator password

387 assay step name (figure)

247, 311 biosensor Location (Method 1)

253,

316 biosensor location (Method 2)

254,

317 biosensor type (figure)

247, 311 biosensor type in the Assay Definition window

258, 322 biosensor type in the Sensor

Assignment window

254, 318 constants

394 group settings


391 projects during a user session

64 sample plate format kinetics 384


144 sample plate format (figure)

144, 280 user account passwords

387 user account settings

386 user password

65 well designations kinetics 384

295 kinetics 96

231 changing location of a reserved column quantitation 384

146 quantitation 96

72 changing projects (figure)

64


367, 369


(figure)

367, 370, 373 cleaning biosensor pickup tips

343 cleaning Octet instrument

340, 342


350


350


33 closing active method file

33 application

34 color codes

122, 199, 267, 331 color-coded wells displaying how biosensors interrogate a 384-well plate, 8 channel or 16channel read head

143, 279 a 96-well plate, 8 channel or 16channel read head

143, 279 compliance

Octet QK instrument

23


25


21


18


16 compliant features, 21 CFR Part 11

59

Conc column

76, 151 concentration representation in dilution series (figure)

224


73


45


page 10 connecting


348


30 to a TCP/IP socket connection locally using localhost

348


397 constants changing

394 creating new

393 deleting

394 viewing

394


392 constants, administrator, listed (table)

393 contacting ForteBio technical support

13

Control (well type)

218 kinetics 384


145 quantitation 96


71, 145 controls

156 defined

81, 156 designating


156 quantitation 96

81 conventions, used in this guide

13 copying assay steps

243, 308


338 kinetics 96


205 quantitation 96

128 step type kinetics 384

305 kinetics 96

240 creating


90 assay step type (figure) kinetics 384

303 kinetics 96

238 different types of assay steps

237, 303 new constants

393 new user account

384 new user group

389 step types

237, 303


331 custom assays defining quantitation 384

206 quantitation 96

129 selecting quantitation 384

214 quantitation 96

137 custom biosensors

48 custom steps

237, 303

D

Data Acquisition 21 CFR Part 11 software overview

52


30


12


38


page 11

Data Acquisition User Guide, opening online version

38


8


52

Data Analysis, icon

8 data column, displaying acquisition

267,


199 quantitation 96

122 data display, significant digits

42 data file location and name settings quantitation 384 (listed)

196 quantitation 96 (listed)

119



347 data files kinetics data repository


41


42


42 data preferences, setting

40


366 default biosensor columns

252, 316 default locations for reserved wells in a 96well sample plate map (figure)

72 default server settings localhost

54

Port 2002

54 default temperature value, saving

44 default temperature, defining new

44 default Tray Format

101 default user group privileges

385 default user groups

388 default windows, Octet System Data


31


121 defining custom assays quantitation 384

206 quantitation 96

129 kinetic assays

236 new assay

35 new assay (figure)

130, 207 new default temperature

44 reagent plates, quantitation 384

166 sample plates kinetics 384

278 kinetics 96


142 quantitation 96

70 samples by entering sample information (figure)

284 step types

237, 303 kinetics 384

305 kinetics 96

240 defining step types

236


265,

329


197 quantitation 96

120 deleting constants

394 factory-loaded biosensor types

49 projects

392 step types

240, 305


page 12 user account

386 user group

390


121, 199, 331 designating controls quantitation 384

156 quantitation 96


81, 156 reference biosensor during acquisition

268, 333 reference biosensors

105, 110, 182,

187, 257, 321 reference biosensors during acquisition quantitation 384

201 quantitation 96

124 reference wells quantitation 384

156 quantitation 96

81 reference wells (figure)

81, 156 samples (kinetics experiments)

218 unknowns quantitation 384

153 quantitation 96

78 well type (kinetics 384)

282 well types (kinetics experiments)

282 designating reference biosensors

258 designating standards quantitation 384

148 quantitation 96

73 designating well types kinetics 96

219

Detection

95, 136, 172, 213


146 quantitation 96

72



172 quantitation 96

95


136, 213 determining the GxP Server module host location

52 developing the automation client

347 dialog boxes

Options

41 setting default temperature

44

Temperature Setting

43 digital signatures, verifying

60 dilution factor, assigning to selected wells quantitation 384

154 quantitation 96

79 dilution factor, assigning to unknowns quantitation 384

153 quantitation 96

78 dilution factor, editing in sample table quantitation 384

155 quantitation 96

80 dilution series assigning sample concentrations kinetics 384

286 kinetics 96

223 assigning standard concentrations quantitation 384

149 quantitation 96

74


page 13


75, 223 dimensions

Octet QK instrument

24


27


22


20


17 discontinuing user session

66 displaying acquisition for a data column


199 quantitation 96

122


377


34 license information

38

Octet System Data Acquisition software properties

38 step types (figure)

305 dissociation steps

236, 302

E


129, 206


35


35 edit commands

226


394


392


35 editing assay parameter values quantitation 384

208 quantitation 96

131 assays

35, 246, 311 biosensor information (figure)

252,

316 dilution factor in the sample table quantitation 384

155 quantitation 96

80 parameter values quantitation 384

208 quantitation 96

131 projects

391 sample data in the Sample Plate Table kinetics 384

295 kinetics 96

231 standard concentration quantitation 384

151 quantitation 96

76 step type (figure)

241, 306 editing step types

240, 305



Octet QK instrument

24


27


22


20


17 emptying waste container

340 ending a user session

66 enhanced legend options, in the Runtime

Binding Chart

12 entering annotations



157 quantitation 96

82 biosensor information displayed (figure)

252, 316 procedure

252, 315 entering an individual standard concentration quantitation 384

151 quantitation 96

76 environmental features

Octet QK instrument

23


25


21


18


16



172 quantitation 96

95


136, 213 equipment classifications

Octet QK instrument

23


25


21


18


16 events list options available

396 viewing

395

Events tab (figure)

395 example .csv plate definition file (figure)

235, 299 example assay using one partial biosensor tray and biosensors from a second tray

113, 190 example experiment using two biosensor trays (figure)

257, 321

Exit menu

34 experiment prior to running

258, 322

Experiment menu described

34 figure


35 experiment method files managing


205 quantitation 96

128 saving

33 saving to new name

33 experiment method files, managing

274,

338 experiment methods, saving manually

114,

191



196 quantitation 96

119 experiment settings advanced settings (Octet QK384)

198,

330 data file location and names


264, 328

Assay Type

328 assay type

264


264,


page 15


264, 328 plate name/barcode (file prefix)

264, 328 run name

264, 328 general information

Description

121, 199, 331

Machine name

121, 199, 330

User name

121, 199, 330 run settings


120, 197, 265, 329


265, 329


120, 197, 265, 329


120, 197,

265, 329 shake sample plate while waiting

120, 197, 265, 329

Start After

265, 329 experiment settings, data file location and names quantitation 384


196

Assay Type

196


197

Experiment Run Name

196

Plate Name/Barcode

196


196 quantitation 96


119

Assay Type

119


120

Experiment Run Name

119

Plate Name/Barcode

119


119



70

Experiment Wizard

34 described

40 figure

40 opening

35 starting kinetics experiments

384

277


69, 141, 217,

277


141 experiments adding assays

248, 313 kinetic, starting

384

277

96

217 monitoring remotely

45 remote view via web browser (figure)

47 reviewing (kinetics 96)

258 saving manually

259, 323 saving to the factory-installed

Template folder

260, 324 starting


194 quantitation 96

117 stopping

36 stopping in progress

266, 331



199 quantitation 96

122

Export button

88

Sample Plate Map kinetics 96

233 export options

Copy the Runtime Binding Chart quantitation 384

205 quantitation 96

128

Export the Runtime Binding Chart to a graphic file quantitation 384

204 quantitation 96

127

Print the Runtime Binding Chart quantitation 384

205 quantitation 96


204 quantitation 96

127

Export Plate Definition window kinetics 384

297 kinetics 96


163 quantitation 96

88 exporting binding data

127, 204 plate definition kinetics 384

297 kinetics 96


163 quantitation 96

88


127, 204, 272, 337


127, 204, 272, 337


273, 337


127, 204


270


271, 335 extending duration of the active step

270,

335

F


49


381


381


62

File History menu

34

File menu described

32 figure


33


33


62


61

Fill Plate (menu)

253, 316


239, 305

Flip Data check box

125, 269, 334

Flip Data function viewing inverted data

269


372


397


371


page 17


13


38 fractional use of regeneration and neutralization wells (figure)

112, 189

Fuse symbol

13

G


330

GetMethodInfo (automation interface command)

349

GetRunInfo (automation interface command)

349

GetRunInfo command

347


239, 305 group administration

388 group settings changing

390 viewing

390

Groups tab (figure)

388


54


397


396 restarting

398

H

Heat/hot symbol

13

Help menu described

38 figure

38

I


38 heterogeneous biosensor trays assigning biosensors quantitation 384

178 quantitation 96

101 using kinetics 384

317 kinetics 96

254 hiding main toolbar

34 status bar

34 higher acquisition rate

120, 197, 329


183 quantitation 96

106 icons

Data Acquisition

8

Data Analysis

8

Import button

89


234


164 quantitation 96

89


234 importing plate definitions kinetics 384

298 kinetics 96

234


page 18 importing plate definition quantitation 384

164 quantitation 96

89 inserting assay steps

245, 310 installing

Data Acquisition 7.0 CFR Part 11 software

366


369

ForteBio GxP Server

372


371


36 figure


36


34 instrument status log (figure)

119, 196,

263, 327


36 described

39 figure

39 logging

36 inverted data, viewing in the Runtime

Binding Chart

269, 334

K


40 kinetics assays building

248 defining

236 step type requirements

236, 302 kinetics data repository

264, 328 kinetics data repository, user option

41 kinetics experiments designating samples

218 designating well types

282


282 starting

384

277

96

217

L



30 legend, for Runtime Binding Chart, selecting


203 quantitation 96

126 license information, displaying

38 list options available for events

396 listing windows currently open in the Main

Screen

37


281 kinetics 96

218 loading biosensor tray kinetics 384

324 kinetics 96


193 quantitation 96

116 reagent plates, kinetics 384

324 sample plate kinetics 384

324


page 19 kinetics 96


193 quantitation 96

116 steps

236, 302

LoadSensors

353

Localhost option

347 localhost, default server settings

54 locking


65


65 logging in the Instrument Status window

36


378 user session (figure)

56

Lot Number column

252 lower acquisition rate

121, 198, 329

M


63


121, 199, 330 magnification, undoing

125, 202, 271,

335 magnifying Runtime Binding Chart

271,


202 quantitation 96

125

Main Menu, Octet System Data Acquisition software

31 main screen, Octet System Data Acquisition software

31 main toolbar hiding

34 showing


128, 274,


205 quantitation 96

128



274 manually save an experiment

259, 323 mechanics

Octet QK instrument

24


26


22


19


17 menu bar, Octet System Data Acquisition software

32 menu commands, listed

33, 34, 35, 36 method file (.fmf)

68, 140, 216, 276 method file (.fmf), described

32 method files closing

33 saving

33 saving all

33


166 modifying assay parameter settings quantitation 384

167 quantitation 96

91 reagent plate quantitation 384

166, 299 molar concentration units

222, 284


page 20 molar concentration, assigning kinetics 96

221 molecular weight, assigning kinetics 96

221 monitoring experiments remotely

45

Multiple Analyte assay parameter quantitation 384

209 quantitation 96

132

Multiple Analyte experiments assigning biosensors quantitation 384

177 quantitation 96

99 used with Replicate Groups quantitation 384

163 quantitation 96

88



171 quantitation 96

94, 133


170 quantitation 96

93 multiple runtime binding charts

12 quantitation 96

72



172 quantitation 96

95


170 quantitation 96

93


134, 211


136, 213


217, 277


35 new features, Octet System Data


12


389


217, 277


69, 141

New Window menu

37 non-adjacent steps, selecting

243, 308

N

Negative Control (well type) kinetics 384

280 kinetics 96


145 quantitation 96

71

Neutralization (reserved well requirements) quantitation 384

146

O


340, 342 resetting

36


13


341, 344


30


343


page 21

Octet QK instrument

23 biosensor tray type

24 biosensor type

24 capabilities

23 compliance

23 dimensions


24 environment


23 mechanics

24 optics


24 sample types

24 sample volume

24 sampling format


24 throughput

24


23

Octet QK384 sensor offset

20, 27 well volumes

20, 27

Octet QK384 instrument automation

26 capabilities

25 compliance

25 dimensions


27 environment


25 mechanics

26 optics

26 sample types

26 sampling format

26 weight

27


25


(table)

25


266

Octet QKe instrument biosensor tray type

22 biosensor type

22 capabilities

22 compliance

21 dimensions

22 displayed (figure)


22 environment


21 mechanics

22 optics


22 sample types

22 sample volume

22 sampling format


22 throughput

22 weight

22


(table)

21


341


30


20, 27 starting



278 well volumes

20, 27

Octet RED384 instrument automation

19 capabilities

18 compliance

18 dimensions


20 environment


18 mechanics

19 optics

19 sample types

19 sampling format

19 weight

20


18


193


17, 19, 26 biosensor type


17 compliance

16 dimensions


17 environment


16 mechanics

17 optics


17, 20, 27 sample types

17 sampling format

17 sampling volume


17 throughput

17, 19, 26 weight

17


16


18 listed (table)

16, 18, 25


325


Main Menu

31 main toolbar

32 new features

12 starting

30 toolbar

31


Main Screen

31


40


8

Offline parameter

136, 213


172 quantitation 96

95


244, 309


243


268, 332


33


33


120, 197, 265, 329


267


page 23


326

Open Windows menu

37 opening dialog box to select an experiment method file

33


35

Experiment Wizard

35 online Data Acquisition User Guide

38



200 quantitation 96

123


35


35 web browser

38 optics

Octet QK instrument

24


26


22


19


17

Options dialog box displayed (figure)

41 setting




41


41


347

Options menu


Octet QK instrument

24


22


17, 20, 27 organizing windows in a cascade arrangement

37

P


343 parameter settings, assay, modifying quantitation 384

167 quantitation 96

91 parameter values, editing quantitation 384

208 quantitation 96

131 partial biosensor trays, using

256 kinetics 384

320 password reminder, user and administrator

(figure)

57 plate definition exporting kinetics 384

297 kinetics 96


163 quantitation 96

88 importing quantitation 384

164 quantitation 96

89



78,

153


74, 149


233, 234


234


page 24 kinetics experiments

282 selecting concentration units (figure)

222,

285 molar concentration units (figure)

222, 285 plate definitions importing kinetics 384

298 kinetics 96

234 plate name/barcode (file prefix)

264, 328



196 quantitation 96

119 plate temperature range

43 plate temperature, setting

43


54

Positive control

218

Positive Control (well type) kinetics 384


145 quantitation 96

71 post-condition biosensors

12


134,

211


173 quantitation 96

96


171 quantitation 96

94




173 quantitation 96

96


134, 211



171 quantitation 96

94 preparing biosensors

68 preparing samples for quantitation or kinetics experiments

8


350

Present Stage menu

36

Print menu

33

Print Preview menu

33 print preview window

33


33

Print Setup menu

33 printing files

33


128, 205, 273,

338 prior to running an experiment

258, 322 privileges, assigning

385 project administration

390


63 project selection (figure)

58 project settings changing

391 viewing

391 project-based Audit Trail events (figure)

64


page 25 projects changing (figure)

64 deleting

392 editing

391

Projects tab

391 projects, changing during a user session

64 properties, for Octet System software, displaying

38

Q



144



196 quantitation 96

119 quantitation data repository, user option

41



142


141


69


69, 141 quantitation experiment defined

68, 140 starting

69, 141

Quantitation Shake Speed assay parameter quantitation 384

209 quantitation 96

132


169 quantitation 96

92


133, 170, 210


93


209 quantitation 96

132


169 quantitation 96

92 quantitative experiment analyzing

68, 140, 216, 276 setting up

68, 140, 216, 276


281 kinetics 96

218 quenching steps

237, 303

R


201 quantitation 96

123 read head configuration kinetics 384


143 reagent plate defining quantitation 384

166 modifying quantitation 384

299



301

Reagent Plate Map

166


166, 300


166 reagent plates, loading kinetics 384

324

Received (well type) quantitation 384

145 quantitation 96

71 recommended sensor offset

198, 330


218 kinetics 384


145 quantitation 96

71 reference biosensors designating

105, 110, 182, 187, 257,

258, 321 designating during acquisition

268,

333 reference biosensors, designating during acquisition quantitation 384

201 quantitation 96

124

Reference menu

124, 201, 268, 333 reference wells defined

81, 156 designating quantitation 384

156 quantitation 96

81 reference, type of well

71, 145 reference-subtracted data viewing kinetics 384

332 kinetics 96

268 reference-subtracted data, viewing quantitation 384

201 quantitation 96

123

Refresh settings

45


146 quantitation 96

72


281 kinetics 96

218



171 quantitation 96

94




173 quantitation 96

96


134, 211



172 quantitation 96

95


170 quantitation 96

93


133, 136, 210, 213 remote view of experiment via web browser (figure)

47



35 assay steps

247, 311 biosensor type

49 side panel of Octet instrument

343 step alignment of data

270, 334 well designation

282 well designations controls or reference wells




167 reordering assay steps

247, 311


176 replacing biosensors in the biosensor tray

251,

315 fuses for Octet RED instrument

341 for QKe instrument

341 replicate assay steps

244, 309 replicate assay, adding to a plate

247, 312


227,

290

Replicate Groups assigning in the Sample Plate Table quantitation 384

162 quantitation 96

87 defined


159 quantitation 96

84 displayed in Sample Plate Map quantitation 384 (figure)


86 displayed in Sample Plate Table quantitation 384 (figure)


86


Map (figure)

229


(figure)

229 replicate steps

All steps (option)

244, 309


244,

309


244,

309



244, 309


244, 309


244,

309

Sample steps will be adjusted by X column (option)

244, 309


243 requirements, for reserved wells

72 reserved column, changing location quantitation 384

146 quantitation 96

72



72


146 quantitation 96

72


page 28

Neutralization quantitation 384

146 quantitation 96

72

Regeneration quantitation 384

146 quantitation 96

72 reserved wells

72 reserved, type of well

71, 145


349

Reset menu


36


399


399 restarting the GxP Server module

398


350 resuming user session

66



172 quantitation 96

95


114, 191,

258, 322


114,

191, 259, 323 reviewing experiments (kinetics 96)

258


349

Run Experiment tab

117



117, 194



119, 196

Assay Type

119, 196


120, 197

Experiment Run Name

119, 196

Plate Name/Barcode

119, 196


119, 196



262, 326 run name

264, 328 run settings quantitation 384


197

Start After setting

197 quantitation 96


120

Start After setting

120 run settings, listed quantitation 384

197 quantitation 96

120 running experiment settings

119, 196

Runtime Binding Chart adding title


203 quantitation 96

126 copying kinetics 384

338 kinetics 96

273 exporting to a graphic file

273, 337 exporting to a graphic or data file

127,

204, 272, 337 magnifying


202 quantitation 96

125 managing


page 29 kinetics 96

267 opening


200 quantitation 96

123 printing

273, 338 scaling


202 quantitation 96

126 selecting legend


203 quantitation 96

126 updating kinetics 384

331 kinetics 96


199 quantitation 96

122 viewing inverted data

269, 334 viewing multiple kinetics 384

336 kinetics 96


204 quantitation 96

127


118, 195,

263, 327

Runtime Binding Chart Export options copy the Runtime Binding Chart to a graphic file quantitation 384

205 quantitation 96

128 export the Runtime Binding Chart to a graphic file quantitation 384

204 quantitation 96

127 print the Runtime Binding Chart to a graphic file quantitation 384

205 quantitation 96


204 quantitation 96

127



204 quantitation 96

127


267, 332


205 quantitation 96

128

Runtime Binding Chart, enhanced legend options

12


128, 205


126,

203, 271, 336

S


280 kinetics 96

218 sample plate loading kinetics 384

324 kinetics 96


193 quantitation 96

116


page 30



167


90,

165 sample plate format, changing kinetics 384


144


Series (figure)

75, 150, 223, 286 sample plate shaker, stopper

36


Commands (figure)

77, 80, 152, 155,

231, 232, 295, 296 sample plate temperature, recorded in log file

12 sample plates adding assays


249,

313 assigning step types to

242, 307 defining kinetics 96


142 quantitation 96

70 defining kinetics 384

278 importing definitions kinetics 384

298 kinetics 96

234 sample step types for kinetic assays, listed

(table)

236


244, 309


244, 309



309 kinetics 96

244



172 quantitation 96

95 sample types

Octet QK instrument

24


26


22


19


17 sample volume

Octet QK instrument

24


22 samples changing biosensor type


218 specifying analyte concentration

221,

283 specifying concentration units

222,

284 sampling format

Octet QK instrument

24


26


22


19



17


33


33


page 31


33


33

Save to File menu

39 saved experiments in the Template folder

(figure)

260, 324 saving all method files

33 binding data

127, 204, 273, 337 default temperature value

44 experiment method files

33 experiment method files to a new name

33 experiment methods

114, 191 experiments manually

259, 323 experiments to the factory-installed

Template folder kinetics 384

324 kinetics 96


192 quantitation 96

115 modified parameter settings

91, 167 reagent plate definition kinetics 384


167 scaling Runtime Binding Chart kinetics 384

335 kinetics 96


202 quantitation 96

126 screen components, Octet System Data


31

Security menu availability

32 compliance features (figure)

59 described

36 figure

37 selecting adjacent steps, to copy and add

243,

308 concentration units

222, 284 concentration units in the Plate


222, 285 custom assays quantitation 384

214 quantitation 96

137 experiment method file, opening function

33



70 in the Experiment Wizard

70 from a set of predefined ForteBio quantitation or kinetics method templates

35 molar concentration units

222, 284 molar concentration units in the Plate


222, 285 non-adjacent steps, to add and copy

243, 308 project in the Audit Trail

63


336 kinetics 96


203 quantitation 96

126 server location

53 wells in the Sample Plate Map kinetics 384

282


page 32 kinetics 96


148 quantitation 96

73 wells in the Sample Plate Map (kinetics

384)

281 selecting the Web Server in the Options dialog box (figure)

45 selectively display the acquisition for a data column


199 quantitation 96

122


349


48, 96, 100, 173,

177, 303


96, 100, 173,

177, 303 displayed (figure)

250, 314



(figure)

97, 100, 174, 177 sensor offset

198, 330

Octet QK384

20, 27

Octet RED384

20, 27


121


122, 199,

267, 331 sensor tray maps


256, 320 changing biosensor locations

252, 257 removing biosensors

253, 317 returning to default layout

253, 316

Sensor Type arrow

246


249


35


48


267 serial dilution, assigning to selected wells quantitation 384

154 quantitation 96

79 serial dilution, assigning to unknowns quantitation 384

153 quantitation 96

78 serial port (RS-232)

346 server location, selecting

53 server testing

397


329 kinetics 96


197 quantitation 96

120


35


76, 151, 221



(figure)

239, 304 plate temperature

43 system and data preferences


(figure)

239


44 setting temperature (figure)

43 setting up administrator account

374 setting up quantitative experiment

68,

140, 216, 276



120,

197, 329 shake sample plate while waiting (setting)

120, 197, 265, 329

Shake Speed parameter quantitation 384

169 quantitation 96

92 shortcut keys

226 showing main toolbar

34 status bar

34


239,

304 significant digits data display

42 user option

42 simulation, user option

43

Single Analyte assay parameter quantitation 384

208 quantitation 96

131 single analyte experiment assigning biosensors quantitation 384

173 quantitation 96

96



171 quantitation 96

94


170 quantitation 96


169 quantitation 96

92

Skip Step menu

35 specifying number of significant digits for the values of Molecular Weight,


42


145 quantitation 96

71

Standard button

73, 148 standard concentration, entering quantitation 384

151 quantitation 96

76 standard, type of well

71, 145 standards, designating quantitation 384

148 quantitation 96

73


329 kinetics 96


197 quantitation 96

120 starting administrator user session

378 an experiment


194 quantitation 96

117 basic kinetics experiment

384

277

96

217 experiment from the Experiment wizard

141 kinetics experiment with the


Octet RED384

278


page 34 new assay

244, 309


30 quantitation experiment

69, 141 user session

56 starting concentration value

76, 151, 222,

285 startup, temperature, user option

42


350 status bar described

38 figure

38 hiding

34 showing

34

Status Bar (menu)

34


305

Step Name arrow

246


246 step types activation

237, 303 applying a threshold

238, 304 assigning to columns in sample plate

242, 307 association

236, 302 changing

246, 311 copying kinetics 384

305 kinetics 96

240 creating

237, 303 custom

237, 303 defining

236 kinetics 384

305 kinetics 96

240 deleting

240, 305 dissociation

236, 302 editing

240, 305 loading

236, 302 quenching

237, 303 requirements for kinetics assays

236,

302 step types (sample) for kinetic assays

236 steps adding to assays

245, 310 copying between assays

243, 308 replicate

244, 309


350

Stop menu

36

Stop Shaker menu

36 stopping experiment

36 experiment in progress


199 quantitation 96

122 sample plate shaker

36


268, 332


124,

201, 268, 333 symbols electrical hazard

13 fuse

13 heat/hot

13 system preferences, setting

40 system specifications

Octet QK

23


page 35

Octet QKe

21

Octet RED96

16, 18, 25

T

Tab menu

383

TCP/IP socket

346


348 technical support, contacting

13



Octet QK instrument

24


22


17

Temperature Setting dialog box displayed (figure)

43 opening

35 temperature value, default, saving

44 temperature, startup, user option

42

Templates menu

35 templates, viewing kinetics 384

324 kinetics 96

260 terminating a step in the assay

271, 335 testing server

397

Threshold check box

238 threshold parameters

Active Channels

239, 304

Filtering

239, 305

Gradient


239, 304

Signal Change

239, 304


304 threshold, applying to assay steps

238, 304 throughput

Octet QK instrument

24


22


17, 19, 26

Tile menu

37 tiling, windows vertically

37

Toolbar (menu)

34 toolbar, Octet System Data Acquisition software

31 tooltip of well information

241

Tray Format button

106 types of wells control

71, 145 reference

71, 145 reserved

71, 145 standard

71, 145 unassigned

71, 145

Unknown

71 unknown

145

U

Unaligned menu

270, 334 unassigned, type of well

71, 145

UNC folder names

347 undo magnification

125, 202, 271, 335


145 quantitation 96

71 unknowns assigning a dilution factor quantitation 384

153




153 quantitation 96

78 designating quantitation 384

153 quantitation 96

78 updating assay times as steps are added to the assay (figure)

242, 307


331 kinetics 96


199 quantitation 96

122


42

Use old 5.0 file format for FRD files, user option

42 user account creating new

384 deleting

386 user account passwords, changing

387 user account settings changing

386 viewing

386 user data files options

41 user data options

42 user group assigning

385 creating new

389 deleting

390 privileges

385 user groups, default

388

User name (setting)

121, 199, 330 user options

Automation


41 listed (table)



42

Simulation

43 temperature

42


42


42 viewing

40

Web Server

43 user password, changing

65 user session changing projects during

64 starting

56 starting an administrator

378 user sessions discontinuing

66 ending

66

Login dialog box

56 resuming

66 user startup options

42 user-defined default start-up temperature

12



167 quantitation 96

91 username selection (figure)

57

Users tab

384 using


page 37 heterogeneous biosensor trays kinetics 384

317 kinetics 96

254 partial biosensor trays kinetics 384

320 kinetics 96

256 quantitation 96

112

V



60


349

View menu described

34 figure



40

Audit Trail

62 available types of biosensors

48 constants

394 events

395 events for a specific project or computer

63 group settings

390 inverted data displayed in the Runtime

Binding Chart

269, 334 multiple Runtime Binding Charts kinetics 384

336 kinetics 96


204 quantitation 96


391 raw reference-subtracted data quantitation 384

201 quantitation 96

123 reference-subtracted data kinetics 384

332 kinetics 96


201 quantitation 96

123 templates

260, 324 user account settings

386 user options


167 quantitation 96

91

W

warm-up time

30


281 kinetics 96

218 waste container emptying

340 for the Octet instrument (figure)

341 web browser opening

38 remote view of experiment

47


45

URL (figure)

46 user option

43


page 38 weight

Octet QK instrument

24


27


22


20


17 well designations changing kinetics 384

295 kinetics 96

231 defined

144 removing quantitation 384



167 removing controls or reference wells quantitation 384

157 quantitation 96

81 well information, tooltip

241 well types

Activation kinetics 384

281 kinetics 96

218

Buffer kinetics 384

280 kinetics 96

218

Control kinetics 384

280 kinetics 96


145 quantitation 96

71 designating kinetics 384

282 kinetics 96


282 for kinetics experiments

220, 282

Load kinetics 384

281 kinetics 96

218



145 quantitation 96

71



145 quantitation 96

71

Quench kinetics 384

281 kinetics 96

218


145 quantitation 96

71


280 kinetics 96


145 quantitation 96

71


281 kinetics 96

218 removing designated type

220

Sample kinetics 384

280


page 39 kinetics 96

218

Standard quantitation 384

145 quantitation 96

71

Unknown quantitation 384

145 quantitation 96

71

Wash kinetics 384

281 kinetics 96

218 well volumes

Octet QK384

20, 27

Octet RED384

20, 27 wells annotating

82, 225, 288 annotating individual kinetics 384

289 kinetics 96


157 quantitation 96

82 assigning dilution factor quantitation 384

154 quantitation 96


154 quantitation 96

79 selecting in the Sample Plate Map kinetics 96


148 quantitation 96

73 window icons, arranging

37

Window menu described


37 windows organizing in a cascade arrangement

37 tiling vertically

37


page 40
