Multi-Mode Analysis Software

Multi-Mode Analysis Software
Multi-Mode Analysis Software
SpectraMax® Paradigm® Multi-Mode Detection Platform
FilterMax™ Multi-Mode Microplate Readers
User Guide
5008530 A
September 2010
This document is provided to customers who have purchased Molecular Devices, Inc.
(“Molecular Devices”) equipment, software, reagents, and consumables to use in the
operation of such Molecular Devices equipment, software, reagents, and consumables. This
document is copyright protected and any reproduction of this document, in whole or any part,
is strictly prohibited, except as Molecular Devices may authorize in writing.
Software that may be described in this document is furnished under a license agreement. It
is against the law to copy, modify, or distribute the software on any medium, except as
specifically allowed in the license agreement. Furthermore, the license agreement may
prohibit the software from being disassembled, reverse engineered, or decompiled for any
purpose.
Portions of this document may make reference to other manufacturers and/or their products,
which may contain parts whose names are registered as trademarks and/or function as
trademarks of their respective owners. Any such usage is intended only to designate those
manufacturers' products as supplied by Molecular Devices for incorporation into its
equipment and does not imply any right and/or license to use or permit others to use such
manufacturers' and/or their product names as trademarks.
Molecular Devices makes no warranties or representations as to the fitness of this equipment
for any particular purpose and assumes no responsibility or contingent liability, including
indirect or consequential damages, for any use to which the purchaser may put the
equipment described herein, or for any adverse circumstances arising therefrom.
For research use only. Not for use in diagnostic procedures.
The trademarks mentioned herein are the property of Molecular Devices, Inc. or their respective
owners. These trademarks may not be used in any type of promotion or advertising without the
prior written permission of Molecular Devices, Inc.
ALPHASCREEN is a registered trademark of PerkinElmer, Inc.
CHROMA-GLO is a trademark of Promega Corporation
HTRF is a registered trademark of Cisbio Bioassays.
BRET2 is a trademark of PerkinElmer, Inc.
Product manufactured by Molecular Devices, Inc.
1311 Orleans Drive, Sunnyvale, California, United States of America 94089.
Molecular Devices, Inc. is ISO 9001 registered.
© 2010 Molecular Devices, Inc.
All rights reserved.
Printed in Austria.
Safety
Introduction
This section provides safety information and instructions for the hardware and
accessories of the system. It includes the following topics:
• Safety Terminology on page 3
• Chemical and Biological Safety on page 5
• Electrical Safety on page 5
• Moving Parts on page 6
• Cleaning on page 6
• Disposal and Recycling on page 6
• Maintenance on page 7
• Warnings and Cautions Found in this User Guide on page 7
Safety Terminology
The symbols displayed below and on the instrument should remind you to read
and understand all safety instructions before attempting installation,
operation, maintenance, or repair to this instrument.
WARNING! Paragraphs marked by “WARNING” alert you of a
potential hazard to your personal safety if you do not adhere to the
information stated within the paragraph.
CAUTION! Paragraphs marked by “CAUTION” indicate that there is a potential
danger of equipment damage.
CAUTION! Paragraphs marked by “CAUTION” contain information about a
possible software program failure, draw attention to a specific software setting
or point out that a loss of data may occur if information stated within the
paragraph is not adhered to or if procedures are executed incorrectly.
Note: Paragraphs marked by “Note” contain supplemental or explanatory
information concerning the current topic or procedural step.
The symbols displayed below and on the instrument are reminders that all
safety instructions should be read and understood before installation,
operation, maintenance, or repair to this instrument is attempted.
WARNING! When present, this symbol indicates that a potential
hazard to your personal safety exists if information stated within the
“WARNING” paragraph is not adhered to or procedures are executed
incorrectly.
5008530 A
3
Safety
WARNING! This icon accompanies text and/or other symbols dealing
with potential damage to equipment. When present, it indicates that
there is a potential danger of equipment damage, software program
failure, or that a loss of data may occur if information stated within
the “CAUTION” paragraph is not adhered to or procedures are
executed incorrectly.
WARNING! HIGH VOLTAGE Paragraphs marked by this symbol
indicate that a potential hazard to your personal safety exists from a
high voltage source.
WARNING! BIOHAZARD Paragraphs marked by this symbol indicate
that a potential hazard to your personal safety exists from a
biological source.
WARNING! LASER LIGHT Paragraphs marked by this symbol indicate
that a potential hazard to your personal safety exists from a laser
source.
WARNING! SHARP OBJECTS Paragraphs marked by this symbol
indicate that a potential hazard to your personal safety exists from
unblunted corners or other appendages on the outside or inside of
the equipment.
WARNING! HOT SURFACE Paragraphs marked by this symbol indicate
that a potential hazard to your personal safety exists from heated
surfaces or other appendages on the outside or inside of the
equipment.
WARNING! PROTECTIVE EARTH OR GROUND TERMINAL This symbol
identifies the location of the protective earth or ground terminal lug
on the equipment.
OFF POSITION OF PRINCIPAL POWER SWITCH This symbol graphically represents the
equipment main power push-button switch when it is in the off position.
ON POSITION OF PRINCIPAL POWER SWITCH This symbol graphically represents the
equipment main power push-button switch when it is in the on position.
4
5008530 A
Multi-Mode Analysis Software User Guide
Chemical and Biological Safety
Normal operation of the FilterMax 3 and FilterMax 5 Multi-Mode Microplate
Readers and the SpectraMax Paradigm Multi-Mode Detection Platform may
involve the use of materials that are toxic, flammable, or otherwise biologically
harmful. When using such materials, observe the following precautions:
• Handle infectious samples according to good laboratory procedures and
methods to prevent the spread of disease.
• Observe all cautionary information printed on the original solutions
containers prior to their use.
• Dispose of all waste solutions according to your facility's waste disposal
procedures.
• Operate the FilterMax 3 and FilterMax 5 Multi-Mode Microplate Reader,
and the SpectraMax Paradigm Multi-Mode Detection Platform in
accordance with the instructions outlined in this user guide, and take all
the necessary precautions when using pathological, toxic, or radioactive
materials.
• Splashing of liquids may occur; therefore, take appropriate safety
precautions, such as using safety glasses and wearing protective
clothing, when working with potentially hazardous liquids.
• Use an appropriately contained environment when using hazardous
materials.
• Observe the appropriate cautionary procedures as defined by your
safety officer when using flammable solvents in or near a powered-up
instrument.
• Observe the appropriate cautionary procedures as defined by your
safety officer when using toxic, pathological, or radioactive materials.
Note: Observe all warnings and cautions listed for any external devices
attached or used during operation of the FilterMax 3 and FilterMax 5 MultiMode Microplate Readers and the SpectraMax Paradigm Multi-Mode Detection
Platform. Refer to applicable external device user guides for operating
procedures of that device.
Electrical Safety
To prevent electrically related injuries and property damage, properly inspect
all electrical equipment prior to use and immediately report any electrical
deficiencies. Contact a Molecular Devices Service Engineer for any servicing of
equipment requiring the removal of covers or panels.
To reduce risk of electrical shock, all devices employ a three-wire electrical
cable and plug to connect the equipment to earth ground.
• Ensure that the wall outlet receptacle is properly wired and earth
grounded.
• DO NOT use a three-to-two wire plug adapter.
• DO NOT use a two-wire extension cord or a two-wire multiple-outlet
power strip.
• Disconnect power to the system before performing maintenance.
• DO NOT remove any panels; panels should be removed only by
qualified service personnel.
5008530 A
5
Safety
WARNING! This symbol indicates the potential of an electrical shock
hazard existing from a high voltage source and that all safety
instructions should be read and understood before proceeding with
the installation, maintenance, and servicing of all modules.
Do not remove system covers. To avoid electrical shock, use supplied
power cords only and connect to properly grounded (three-holed)
wall outlets. Use only multiplug power strips provided by the
manufacturer.
Moving Parts
To avoid injury due to moving parts, observe the following:
• Never attempt to exchange labware, reagents, or tools while the
instrument is operating.
• Never attempt to physically restrict any of the moving components of
the Multi-Mode Analysis Software.
• Keep the Multi-Mode Analysis Software work area clear to prevent
obstruction of the movement.
Cleaning
Observe the cleaning procedures outlined in this user guide for the Multi-Mode
Analysis Software. Prior to cleaning equipment that has been exposed to
hazardous material:
• Appropriate Chemical and Biological Safety personnel should be
contacted.
• The Chemical and Biological Safety information contained in this user
guide should be reviewed.
Disposal and Recycling
WARNING! It is important to understand and follow all laws
regarding the safe and proper disposal of electrical instrumentation.
The symbol of a crossed-out wheeled bin on the product is required in
accordance with the Waste Electrical and Electronic Equipment (WEEE)
Directive of the European Union. The presence of this marking on the product
indicates that the device:
• Was put on the European Market after August 13, 2005.
• Is not to be disposed via the municipal waste collection system of any
member state of the European Union.
For products under the requirement of WEEE directive, please contact your
dealer or local Molecular Devices office for the proper decontamination
information and take-back program, which will facilitate the proper collection,
treatment, recovery, recycling, and safe disposal of the device.
6
5008530 A
Multi-Mode Analysis Software User Guide
Maintenance
Perform only the maintenance described in this user guide. Maintenance other
than that specified in this user guide should be performed only by service
engineers.
WARNING! It is your responsibility to decontaminate components of
the Multi-Mode Analysis Software before requesting service by a
Molecular Devices Service Engineer or returning parts to Molecular
Devices for repair. Molecular Devices will NOT accept any items which
have not been decontaminated where it is appropriate to do so. If any
parts are retuned, they must be enclosed in a sealed bag stating that
the contents are safe to handle and are not contaminated.
Warnings and Cautions Found in this User Guide
Please read and observe all cautions and instructions. Remember, the most
important key to safety is to operate the FilterMax 3 and FilterMax 5
Multi-Mode Microplate Reader and the SpectraMax Paradigm Multi-Mode
Detection Platform with care.
The WARNINGs and CAUTIONs found within this document are listed below.
WARNING! If the equipment is used in a manner not specified by
Molecular Devices, the protection provided by the equipment may be
impaired.
CAUTION! Settings that vary from the recommended Power Options Properties
may introduce a risk of data transfer interruption and a loss of data.
CAUTION! In any situation (such as when operating the instrument with
integrated systems) where automatic loading and ejection of the cartridge
carrier may cause a potential equipment collision, we recommend disabling the
Automatically load/eject cartridge carrier when running the Validation Plate
feature, and to load and eject the cartridge carrier manually.
CAUTION! Shake low density plates, such as 6-well or 48-well plates, at low
speed only. Shaking low density plates at higher speeds may cause liquid in
wells to spill.
CAUTION! The plate height configured must not be less than that of the actual
plate. Doing so may cause the FilterMax Multi-Mode Microplate Readers to
collide with the plate during a Read Height Optimization. The SpectraMax
Paradigm Multi-Mode Detection Platform has an auto-detection to prevent
collision, if an incorrect plate height is entered for the SpectraMax Paradigm
Multi-Mode Detection Platform an error message appears while running
protocols using the defined labware.
CAUTION! Luminescence light levels visible to the human eye may cause
damage to the detection system.
5008530 A
7
Safety
8
5008530 A
Contents
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Safety Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chemical and Biological Safety . . . . . . . . . . . . . . . . . . . . . . . . . 5
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Moving Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Cleaning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Disposal and Recycling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Warnings and Cautions Found in this User Guide. . . . . . . . . . . . . 7
Chapter 1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Where to Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Chapter 2 Installing, Using, and Configuring
the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Installing Multi-Mode Analysis Software . . . . . . . . . . . . . . . . . . 17
Preparing to Install Multi-Mode Analysis Software . . . . . . . . . . 17
Meeting System Requirements . . . . . . . . . . . . . . . . . . . . . . 18
Upgrading From Previous Versions of the Software . . . . . . . . 19
Installing Multi-Mode Analysis Software on Windows XP . . . . . . 19
Installing Required Components and
Multi-Mode Analysis Software . . . . . . . . . . . . . . . . . . . . . . . 20
Installing the Required Multi-Mode System Updater . . . . . . . . 22
Repairing or Removing the Multi-Mode Analysis
Software Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Using Multi-Mode Analysis Software. . . . . . . . . . . . . . . . . . . . . 24
Launching the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Using the Software Interface . . . . . . . . . . . . . . . . . . . . . . . . 26
About the Navigation Pane . . . . . . . . . . . . . . . . . . . . . . . . . 26
About the Tool Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
About the Selection and Configuration Pane . . . . . . . . . . . . . 31
About the Preview Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Accessing Online Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Configuring Multi-Mode Analysis Software . . . . . . . . . . . . . . . . 32
Configuring Instrument Settings . . . . . . . . . . . . . . . . . . . . . . 33
Configuring Software Settings . . . . . . . . . . . . . . . . . . . . . . . . 35
Selecting Simulated Data Files . . . . . . . . . . . . . . . . . . . . . . 35
Selecting a Directory for Saving Exported
Measurement Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Configuring Print Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Configuring Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
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9
Contents
Configuring the Data Format . . . . . . . . . . . . . . . . . . . . . . . . 43
Configuring Database Settings . . . . . . . . . . . . . . . . . . . . . . . 47
Deleting and Restoring Items . . . . . . . . . . . . . . . . . . . . . . . . . 48
Chapter 3 Configuring and Controlling Instruments . . . . . . . . 51
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Managing Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Adding a New Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Deleting an Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Configuring the Current Instrument . . . . . . . . . . . . . . . . . . . . 54
Controlling Instrument Actions . . . . . . . . . . . . . . . . . . . . . . . . 54
Connecting to the Instrument . . . . . . . . . . . . . . . . . . . . . . . . 55
Ejecting the Plate Carrier . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Loading the Plate Carrier. . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Initializing the Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Enabling Simulation Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Configuring the FilterMax Multi-Mode Microplate Readers
Instrument Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Modifying and Viewing System Information . . . . . . . . . . . . . . . 58
Defining and Editing Filter Slides . . . . . . . . . . . . . . . . . . . . . . 58
Adding Filter Slides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Configuring Filter Slides . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Removing Filter Slides . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Exporting and Importing All Filter Slide Configurations . . . . . . 61
Exporting and Importing Single Filter Slide Configurations . . . 61
Manually Controlling the FilterMax Multi-Mode
Microplate Readers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Temperature Control (FilterMax 5 Multi-Mode
Microplate Reader only) . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Shake Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Plate Carrier Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Excitation Filter and Emission Filter Slide Control . . . . . . . . . . 64
Configuring SpectraMax Paradigm Multi-Mode
Detection Platform Instrument Settings . . . . . . . . . . . . . . . . . . 64
Configuring SpectraMax Paradigm Multi-Mode
Detection Platform System Information Settings . . . . . . . . . . . . 65
Viewing Installed Detection Cartridges . . . . . . . . . . . . . . . . . . 66
Defining and Editing the Available Detection Cartridges . . . . . . 66
Adding Detection Cartridges to the list of Available
Detection Cartridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Removing Detection Cartridges from the list of
Available Detection Cartridges . . . . . . . . . . . . . . . . . . . . . . . 68
Manually Controlling the SpectraMax Paradigm Multi-Mode
Detection Platform Instrument. . . . . . . . . . . . . . . . . . . . . . . . 69
Temperature Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Shake Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Plate Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Top Read Detection Cartridge Transport Control . . . . . . . . . . 71
Bottom Read Detection Cartridge Transport Control . . . . . . . . 71
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Multi-Mode Analysis Software User Guide
Chapter 4 Setting Up and Using GxP Permissions . . . . . . . . . 73
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Enabling GxP Permissions. . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Performing System Administration Tasks . . . . . . . . . . . . . . . . . 75
Administering User Accounts and Roles . . . . . . . . . . . . . . . . . 75
Configuring Roles for Multi-Mode Analysis Software
User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Restoring the Administrator Password . . . . . . . . . . . . . . . . . . 79
Viewing the System Activity Audit Log . . . . . . . . . . . . . . . . . . 79
Performing GxP Permissions User Actions in
Multi-Mode Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . 80
Logging On and Off the System . . . . . . . . . . . . . . . . . . . . . . 81
Changing the Current User Password . . . . . . . . . . . . . . . . . . . 82
Viewing and Searching the Multi-Mode Analysis
Software Audit Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Reactivating Disabled Message Boxes . . . . . . . . . . . . . . . . . . 83
Adding Electronic Signatures and Comments to Items . . . . . . . 84
Signing Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Viewing or Unlocking Signatures for an Item. . . . . . . . . . . . . 85
Viewing Unlocked Signatures . . . . . . . . . . . . . . . . . . . . . . . 86
Chapter 5 Creating and Editing Detection Methods . . . . . . . . 87
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Viewing Available Detection Methods . . . . . . . . . . . . . . . . . . . . 87
Creating Detection Methods (FilterMax Multi-Mode
Microplate Readers). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Selecting a Method Technique (FilterMax
Multi-Mode Microplate Readers) . . . . . . . . . . . . . . . . . . . . . . 89
Selecting the Method Type (FilterMax
Multi-Mode Microplate Readers) . . . . . . . . . . . . . . . . . . . . . . 90
Defining Method Parameters (FilterMax
Multi-Mode Microplate Readers) . . . . . . . . . . . . . . . . . . . . . . 91
Defining Absorbance Method Parameters . . . . . . . . . . . . . . . 91
Defining Luminescence Method Parameters . . . . . . . . . . . . . 92
Defining Fluorescence Intensity Top Method Parameters . . . . 93
Defining Fluorescence Intensity Bottom Method Parameters
(FilterMax 5 Multi-Mode Microplate Reader only) . . . . . . . . . . 95
Defining Fluorescence Polarization Method Parameters
(FilterMax 5 Multi-Mode Microplate Reader only) . . . . . . . . . . 96
Defining Time-Resolved Fluorescence Method Parameters
(FilterMax 5 Multi-Mode Microplate Reader only) . . . . . . . . . . 97
Signing a Detection Method (FilterMax
Multi-Mode Microplate Readers) . . . . . . . . . . . . . . . . . . . . . . 98
Creating Detection Methods (SpectraMax Paradigm
Multi-Mode Detection Platform) . . . . . . . . . . . . . . . . . . . . . . . . 99
Selecting a Detection Cartridge (SpectraMax Paradigm
Multi-Mode Detection Platform) . . . . . . . . . . . . . . . . . . . . . . 100
Absorbance (ABS) Detection Cartridge . . . . . . . . . . . . . . . . 101
Fluorescence Polarization (FP) Detection Cartridge. . . . . . . . 102
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11
Contents
Multi-Mode (MULTI) Detection Cartridge . . . . . . . . . . .
Fluorescence Intensity (FI) Detection Cartridge . . . . . .
Fluorescence Intensity Dual Label (FI-DL)
(MultiTox-Fluor) Detection Cartridge. . . . . . . . . . . . . .
Time Resolved Fluorescence (TRF) Detection Cartridge .
Cisbio HTRF® Detection Cartridge. . . . . . . . . . . . . . . .
Luminescence (LUM) Detection Cartridge . . . . . . . . . .
AlphaScreen Detection Cartridge . . . . . . . . . . . . . . . .
Signing a Detection Method (SpectraMax Paradigm
Multi-Mode Detection Platform) . . . . . . . . . . . . . . . . . .
Editing Detection Methods. . . . . . . . . . . . . . . . . . . . . . .
Copying Detection Methods . . . . . . . . . . . . . . . . . . . . . .
Deleting Detection Methods. . . . . . . . . . . . . . . . . . . . . .
Exporting and Importing Detection Methods . . . . . . . . . .
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Chapter 6 Creating and Editing Labware . . . . . . . . . . . . . . . . 127
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Creating Labware. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Defining Labware Information . . . . . . . . . . . . . . . . . . . . . . . 129
General Labware Selection Guidelines. . . . . . . . . . . . . . . . . 131
Configuring Offsets and Well Dimensions for
the Default Labware Lot . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Signing Labware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Editing Labware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Viewing and Editing Labware Information . . . . . . . . . . . . . . . 134
Selecting and Editing Labware Lots . . . . . . . . . . . . . . . . . . . 135
Copying Labware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Deleting Labware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Optimizing Labware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Creating a Copy of the Labware to be Optimized . . . . . . . . . . 138
Start the Optimization Wizard . . . . . . . . . . . . . . . . . . . . . . . 138
Selecting the Detection Method . . . . . . . . . . . . . . . . . . . . . . 138
Preparing and Loading the Labware . . . . . . . . . . . . . . . . . . . 139
Performing the Optimization Read . . . . . . . . . . . . . . . . . . . . 140
Selecting the Centers of the Four Corner Wells . . . . . . . . . . . 141
Verifying Well Centers . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Exporting and Importing Labware . . . . . . . . . . . . . . . . . . . . . 143
Chapter 7 Creating and Running Protocols . . . . . . . . . . . . . . 145
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Creating Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Configuring General Settings . . . . . . . . . . . . . . . . . . . . . . . . 148
Selecting the Technique Type . . . . . . . . . . . . . . . . . . . . . . . 149
Selecting the Labware Type Used in the Protocol . . . . . . . . . . 150
Configuring Labware Layout Settings . . . . . . . . . . . . . . . . . . 151
Configuring Dilution Factors . . . . . . . . . . . . . . . . . . . . . . . . 154
Adding Detection and Preparation Methods
for Analysis Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Configuring Method Properties . . . . . . . . . . . . . . . . . . . . . . 159
Configuring Methods for Quantitation Protocols . . . . . . . . . . . 165
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5008530 A
Multi-Mode Analysis Software User Guide
Determining the Normalization Factor . . . . . . . . . . . .
Configuring Variables . . . . . . . . . . . . . . . . . . . . . . . . .
Configuring the Data Reduction. . . . . . . . . . . . . . . . . .
Configuring a Transformation Formula . . . . . . . . . . . . .
Configuring Concentration . . . . . . . . . . . . . . . . . . . . .
Configuring Cutoff Values . . . . . . . . . . . . . . . . . . . . . .
Configuring Validation Rules . . . . . . . . . . . . . . . . . . . .
Configuring Output Settings . . . . . . . . . . . . . . . . . . . .
User Defined Excel Export. . . . . . . . . . . . . . . . . . . . .
Workbook Export Options . . . . . . . . . . . . . . . . . . . . .
Worksheet Export Options . . . . . . . . . . . . . . . . . . . .
New Sheet and Existing Sheet Export Options . . . . . . .
Exporting Measurement Data to SoftMax Pro Software .
Exporting Data to SoftMax Pro File Format . . . . . . . . .
Starting SoftMax Pro Software and Importing Data . . .
Configuring a Program to Execute after
a Protocol Run Completes . . . . . . . . . . . . . . . . . . . . .
Signing a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . .
Creating a Protocol from a Template . . . . . . . . . . . . . . .
Running Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Running a Protocol on an Instrument . . . . . . . . . . . . . .
Optimizing Read Height (FilterMax 5 Multi-Mode
Microplate Reader). . . . . . . . . . . . . . . . . . . . . . . . . .
Optimizing Read Height (SpectraMax Paradigm
Multi-Mode Detection Platform) . . . . . . . . . . . . . . . . .
Viewing the Run Protocol Runtime Display . . . . . . . . .
Running a Protocol When Simulation Mode is Enabled . .
Editing Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Copying Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Deleting Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Printing Protocol Configuration Information . . . . . . . . . .
Exporting and Importing Protocols. . . . . . . . . . . . . . . . .
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Chapter 8 Viewing Measurement Results . . . . . . . . . . . . . . . 215
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Viewing Measurement Results in the Result Viewer . . . . . . . . . 217
Viewing Raw Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Viewing Blanked Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Viewing Reduced Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Viewing Mean Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
Viewing Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Viewing Two-Dimensional Graphs . . . . . . . . . . . . . . . . . . . 225
Viewing Three-Dimensional Graphs . . . . . . . . . . . . . . . . . . 226
Recalculating Data Reduction . . . . . . . . . . . . . . . . . . . . . . . 227
Exporting Measurement Results to Microsoft Excel. . . . . . . . . 228
Saving Measurement Results . . . . . . . . . . . . . . . . . . . . . . . 228
Viewing and Reevaluating Results from an
Analysis Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Viewing Results From an Analysis Protocol . . . . . . . . . . . . . . 230
Changing the Standard Curve Graph View . . . . . . . . . . . . . 231
5008530 A
13
Contents
Reevaluating Results from an Analysis Protocol . .
Viewing Exported Measurement Results . . . . . . . .
Viewing Measurement Results in Microsoft Excel .
Viewing Protocol and Measurement Information.
Viewing Raw Data . . . . . . . . . . . . . . . . . . . . .
Viewing Reduced and Transformed Data . . . . . .
Signing Measurement Results . . . . . . . . . . . . . . .
Deleting Measurement Results. . . . . . . . . . . . . . .
Printing Measurement Results . . . . . . . . . . . . . . .
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Appendix A Data Reduction Techniques . . . . . . . . . . . . . . . . 241
Supported Data Reduction Techniques . . . . . . . . . . . . . . . . . . 241
Appendix B PathCheck® Pathlength Measurement
Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Using the PathCheck Pathlength Measurement Technology
Water Constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
Background Constant Subtraction and Blanking
Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Use Plate Background Constant . . . . . . . . . . . . . . . . . . . . . 247
PathCheck Pathlength Measurement Technology and
Interfering Substances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Determining Color Interference . . . . . . . . . . . . . . . . . . . . . . 248
Appendix C Mathematical Operators and Functions . . . . . . . 249
Supported Mathematical Operators and Functions . . . . . . . . . . 249
14
5008530 A
1
Overview
Introduction
Multi-Mode Analysis Software configures and controls all measurement
protocols and actions performed by the FilterMax Multi-Mode Microplate
Readers and the SpectraMax Paradigm Multi-Mode Detection Platform. The
software supports detection for absorbance, glow luminescence, fluorescence
intensity, fluorescence polarization, and time-resolved fluorescence (TRF)
measurements including HTRF. The measurement methods available to users
depend on the capabilities of the instrument being controlled. Measurement
results can be viewed in the Multi-Mode Analysis Software or easily exported
to compatible applications such as Microsoft Excel.
Optional modules such as GxP Permissions lend support for electronic
signature regulations such as 21 CFR Part 11.
This user guide covers the functionality supplied by the Multi-Mode Analysis
Software and the Multi-Mode Analysis Software with GxP Permissions modules,
including:
• Configuring and Controlling Instruments on page 51
• Setting Up and Using GxP Permissions on page 73
• Creating and Editing Detection Methods on page 87
• Creating and Editing Labware on page 127
• Creating and Running Protocols on page 145
• Viewing Measurement Results on page 215
Where to Begin
To correctly use the software it is important that initial configuration is done in
a specific order.
1. Installing Multi-Mode Analysis Software on page 17.
2. Configuring Multi-Mode Analysis Software on page 32.
3. Configuring and Controlling Instruments on page 51.
4. Setting Up and Using GxP Permissions on page 73 (optional module).
5. Creating Detection Methods (FilterMax Multi-Mode Microplate Readers)
on page 88 or Creating Detection Methods (SpectraMax Paradigm MultiMode Detection Platform) on page 99. The measurement configuration
parameters are stored in detection methods.
6. Creating and Editing Labware on page 127. Labware types must be
configured and ready for use in protocols.
7. Creating Protocols on page 146 using the detection methods created in
Step 5. A protocol stores all parameters required to perform a
measurement, including technique types, detection methods, labware
types, and preparation methods, such as shaking.
8. Running Protocols on page 197.
9. Viewing Measurement Results on page 215.
10. When required, create additional detection methods, labware, and
protocols.
5008530 A
15
Overview
16
5008530 A
Installing, Using, and Configuring
the Software
2
Overview
This section introduces users to the software and gives the instructions for:
• Installing Multi-Mode Analysis Software on page 17
• Using Multi-Mode Analysis Software on page 24
• Configuring Multi-Mode Analysis Software on page 32
• Deleting and Restoring Items on page 48
Installing Multi-Mode Analysis Software
The Multi-Mode Analysis Software installer provides the ability to install the
software onto a new system or update from a previous version of the software.
Installing the software requires:
• Preparing to Install Multi-Mode Analysis Software on page 17
• Meeting System Requirements on page 18
• Installing Multi-Mode Analysis Software on Windows XP on page 19
Preparing to Install Multi-Mode Analysis Software
Before installing Multi-Mode Analysis Software, confirm that the host computer
meets the minimum system requirements listed in Meeting System
Requirements on page 18.
If upgrading from previous versions of Multi-Mode Analysis Software, see
Upgrading From Previous Versions of the Software on page 19 before
installing. The information in this section helps to ensure the update is
successful.
5008530 A
17
Installing, Using, and Configuring the Software
Meeting System Requirements
To install and use the software successfully, the host computer must meet the
minimum system requirements listed in Table 2-1. Where relevant, Table 2-1
also lists recommended specifications.
Table 2-1 Host Computer System Requirements
Component
Minimum System Requirements
CPU
Pentium III 600 Mhz
RAM
256 MB minimum
512 MB or more recommended
Hard Drive
600 MB free space
CD-ROM Drive
4X
Monitor
800x600 resolution
Keyboard
101 key
Mouse
IBM compatible
Serial Port
USB Port
1 free serial port or 1 free USB port
Operating System
Microsoft Windows XP (Service Pack 2)
Operating System
Language
English (U.S.)
Database
Microsoft SQL Server 2000 (Desktop Edition included on the
installation CD)
Note: SQL Server 2000 Desktop Edition has a 2GB
storage limit. Contact Molecular Devices Technical
Support if this limit is reached.
Web Browser
Microsoft Internet Explorer 6.0 or later (included on the
installation CD)
Programs
Microsoft Excel 2003 recommended
Power Options
Properties
Turn off hard disks: Never
System standby: Never
System hibernates: Never
Note: System power options properties are set in Control
Panel > Power Options.
CAUTION! Settings that vary from the recommended
Power Options Properties can introduce a risk of data
transfer interruption and a loss of data.
18
5008530 A
Multi-Mode Analysis Software User Guide
Upgrading From Previous Versions of the Software
If upgrading from a previous Multi-Mode Analysis Software version, follow the
steps in this section to make sure that the update is successful.
To update the software from a previous version:
1. Launch Multi-Mode Analysis Software and open Instrument Settings.
2. For FilterMax instruments: If the filter slides have been customized by
installing new filters or moving existing filters to other slots, these
settings need to be saved and later imported after software installation.
In Instrument Settings, select the Filter Slides tab and select Export
Slides before proceeding with installation. See Exporting and Importing
All Filter Slide Configurations on page 61.
3. Install the software by following the steps in Installing Multi-Mode
Analysis Software on page 17.
Note: Installing a newer version of Multi-Mode Analysis Software
replaces the previous version.
4. When the installation is complete, launch Multi-Mode Analysis Software.
The software automatically checks if any default detection methods,
labware types, and protocols provided with the install have the same
name as those imported to the database from the previous versions.
Note: If a prompt appears asking whether a detection method, labware
type, or protocol should be overwritten, click Yes to overwrite the
existing item or click No to keep the existing item in the database.
Note: SpectraMax Paradigm Multi-Mode Detection Platform: For each
new detected cartridge, example Protocols and Methods are imported
automatically. The automatic importing function may be disabled. To do
this, go to the Multi-Mode Analysis Software main window. Then from
the File menu click Settings > Properties > Allow Protocol Auto-Import.
Installing Multi-Mode Analysis Software on Windows XP
On a Windows XP system, the Multi-Mode Analysis Software installer uses a
simple interface to guide the installation using the two CDs provided with your
purchase. Installation proceeds in two phases:
• Installing Required Components and Multi-Mode Analysis Software on
page 20
• Installing the Required Multi-Mode System Updater on page 22
5008530 A
19
Installing, Using, and Configuring the Software
Installing Required Components and
Multi-Mode Analysis Software
To install the components and software:
1. Exit all Windows programs before starting installation.
2. Ensure the current user account has Administrator privileges. Accounts
with Standard or Restricted access are not allowed to run the setup
program. Contact the site system administrator for more information
about account privileges.
3. Insert the installation CD 1 into the CD drive and browse to the
contents of the CD.
4. Double-click on Installer.exe. The Multi-Mode Analysis Software Installer
appears Figure 2-1. All components required to successfully install the
software are listed along with the current status of each component:
 A check icon indicates the correct version of the component is
already installed on the system.
 A caution icon indicates that an older version of the component is
installed and must be updated before the software can be installed.
 An X icon indicates that the component must be installed before the
Multi-Mode Analysis Software can be installed.
Figure 2-1 Starting the Installation
5. Select Update or Install for the first component indicated. The
components are installed one at a time and must be installed in the
order listed.
6. Follow the steps in the component installer until the component
installation is complete. Restart the system as required. For example, a
restart might required after the Microsoft SQL Server installation.
Note: If a component installation requires restarting the system,
restart before installing the next component listed. After the system
restarts, browse to the contents of the installer CD and launch the
installer again to continue installing components.
20
5008530 A
Multi-Mode Analysis Software User Guide
Note: Some components can give the option to Repair or Remove the
component. First click Remove to remove the component and then click
Install to reinstall the component.
7. Repeat Step 5 and Step 6 for each component required.
When all components are installed correctly, the Install Multi-Mode
Software button launches the Multi-Mode Analysis Software System
Updater.
8. Click Install Multi-Mode Software to launch the Multi-Mode System
Updater.
Figure 2-2 System Updater Window
9. Follow the steps as described in Installing the Required Multi-Mode
System Updater on page 22.
10. In the Multi-Mode Analysis Software Installer, click Finish.
CAUTION! Settings that vary from the recommended Power Options Properties
may introduce a risk of data transfer interruption and a loss of data.
11. Open the Power Options Properties by selecting Start > Control Panel >
Power Options.
12. Set Turn off Hard Disks to Never.
13. Set System standby to Never.
14. Set System hibernates to Never.
The software is ready for use.
5008530 A
21
Installing, Using, and Configuring the Software
Installing the Required Multi-Mode System Updater
Upon installing, reinstalling, or updating Multi-Mode Analysis Software from a
previous version, running the System Updater will provide vital updates to
firmware, detection cartridge files and other components specific to your
instrument’s needs.
Note: If new detection platform products are purchased (such as SpectraMax
Paradigm detection cartridges), or you intend to update your Multi-Mode
Analysis Software installation, it is recommended that you use the Multi-Mode
System Updater CD Package to consistently update your system.
Note: SpectraMax Paradigm Multi-Mode Detection Platform: Ensure the
instrument is turned on, not in the standby mode, and all your detection
cartridges are installed.
To run the System Updater:
1. If installing the Multi-Mode System Updater as a part of the Multi-Mode
Analysis Software installation, remove installation CD 1 from the CD
drive and insert CD 2 into the CD drive.
If installing the System Updater separately, exit all Windows programs
before starting system update as shown in Installing the Required
Multi-Mode System Updater on page 22. Insert CD 2 into the CD drive
and browse to the contents of the CD. Double click installer.exe
The System Updater window appears Figure2.3.
Figure 2-3 System Updater Window
22
5008530 A
Multi-Mode Analysis Software User Guide
Note: Depending on the host system’s firewall configuration, a
Windows firewall message might request that you unblock Multi-Mode
System Updater’s executable file, SystemUpdater.exe. If this message
does show, allow unblocking.
2. Click the Install or Update links to add components as required by the
System Updater.
Note: During the install/update process, the instrument might initialize
and produce sounds while the System Updater runs.
3. When finished, the System updater window appears Figure 2-4.
Figure 2-4 System Updater Window Showing Fully Updated Controller
PC System
4. Upon completion of the entire update process, click Finish. The MultiMode Software Installer window appears.
5. Click Finish.
Note: If the System Updater ran as a part of the Multi-Mode Analysis
Software installation, click Finish to close that installation also.
The software is ready for use.
5008530 A
23
Installing, Using, and Configuring the Software
Repairing or Removing the Multi-Mode Analysis
Software Installation
In the event required components are missing or damaged, or if the software
does not open or does not run correctly, repair should be made by uninstalling
the Multi-Mode Analysis Software from the controlling PC system.
To repair or remove the software:
1. Exit all open Windows programs.
2. Make sure the current user account has Administrator privileges.
Accounts with Standard or Restricted access are not permitted to
modify or remove software. Contact the site system administrator for
more information about account privileges.
3. If repairing the installation, insert the Multi-Mode Analysis Software
installation CD into the CD-ROM drive.
4. From the Start menu, click Settings > Control Panel. The Control Panel
appears.
5. In Control Panel, double-click Add or Remove Programs. The Windows
Add or Remove Programs dialog appears.
6. In the Add or Remove Programs dialog, select Multi-Mode Analysis
Software. Repair and removal options for Multi-Mode Analysis Software
appear.
7. Click Remove and follow the instructions until the removal process is
completed. Proceed to step 8.
Note: When removing the software, only files installed during the initial
installation are removed. The software database and files created after
the installation, such as exported measurement results, remain.
8. When finished, reinstall Multi-Mode Analysis Software from the original
installation CD.
Using Multi-Mode Analysis Software
The Multi-Mode Analysis Software uses a simple interface that divides the main
window into four basic sections: navigation pane, tool bar, selection and
configuration pane, and preview pane (Figure2.5). The interface provides
access to the selection lists that enables system functionality and
comprehensive, context-sensitive online help.
This section covers:
• Launching the Software on page 25
• Using the Software Interface on page 26
• Accessing Online Help on page 31
Note: To correctly use the software it is important that the initial configuration
is done in a particular order. Please see Where to Begin regarding important
setup information.
24
5008530 A
Multi-Mode Analysis Software User Guide
Launching the Software
To launch Multi-Mode Analysis Software:
• From the Windows Start menu, click Programs > Molecular Devices >
Multi-Mode Analysis Software> Multi-Mode Analysis Software. The MultiMode Analysis Software window appears (Figure 2-5).
Note: If the Multi-Mode Analysis Software is not found in the Start
menu, the software may have been installed for a single user account
on the system instead of all accounts. Check with the site system
administrator or login to the user account with permission to access
the software. See Installing Multi-Mode Analysis Software on Windows
XP on page 19 for more information about installing the software for a
single or multiple user accounts.
Figure 2-5 Multi-Mode Analysis Software Main Window
Note: The first time the software is launched, depending on the host
system’s firewall configuration, a Windows firewall message might
request that you unblock Multi-Mode Analysis Software’s executable
file, Apex.exe. If this message does show, allow unblocking.
5008530 A
25
Installing, Using, and Configuring the Software
Using the Software Interface
Multi-Mode Analysis Software uses a simple interface that is divided into four
basic sections:
• Navigation Pane (See About the Navigation Pane on page 26)
• Tool Bar (See About the Tool Bar on page 27)
• Selection and Configuration Pane (See About the Selection and
Configuration Pane on page 31)
• Preview Pane (See About the Preview Pane on page 31)
The navigation pane provides access to the selection lists that provide the
majority of the functionality built into the software. Items selected in the
selection list determine the options available in the tool bar and configuration
pane.
About the Navigation Pane
The navigation pane is the narrow pane on the left of the Multi-Mode Analysis
Software window (Figure 2-5). Use the navigation pane to switch between
selection lists.
Table 2-2 The Navigation Pane
Name
26
Button
Description
Protocols
Contains the Protocols Selection List
and provides the ability to define,
run, edit, copy, delete, and print
measurement protocols. See
Creating and Running Protocols.
A protocol stores all parameters
required to perform a measurement,
including technique types, detection
methods, labware types, and
preparation methods such as
shaking.
Detection Methods
Contains the Detection Method
Selection List and provides the ability
to create, edit, copy, and delete
detection methods. See Creating and
Editing Detection Methods.
Measurement configuration
parameters are stored in detection
methods.
Results
Contains the Results Selection List
and provides the ability to view
saved measurement results and
modify data reduction parameters in
the Result Viewer. Measurement
results may be reevaluated using
parameters different from those
configured in the original protocol.
See Viewing Measurement Results.
Measurement results from each
protocol run are stored in the MultiMode Analysis Software database
and are accessed only from the
Results Selection List.
Labware
Contains the Labware Selection List
and provides the ability to create,
edit, optimize, copy, and delete
labware types. See Creating and
Editing Labware.
5008530 A
Multi-Mode Analysis Software User Guide
Table 2-2 The Navigation Pane (cont’d)
Name
Button
Description
Instruments
Contains the Instrument Selection
List and provides the ability to
manually control instrument actions
(such as shaking, or loading and
ejecting the plate carrier) and
configure instrument settings and
filter slides or detection cartridges.
See Configuring and Controlling
Instruments. The active instrument
is controlled using the Instrument
Selection List.
Users
Appears in the navigation pane only
when the Multi-Mode Analysis
Software with GxP Permissions
module is installed and enabled on
the system. GxP Permissions is an
integrated set of features that help
Multi-Mode Analysis Software users
comply with electronic signature
regulations, such as 21 CFR Part 11.
See Performing GxP Permissions
User Actions in Multi-Mode Analysis
Software on page 80.
Trash
Contains the Trash List containing
labware, detection methods, and
protocols pending deletion. This
section provides the ability to restore
or permanently delete items from
the database. See Deleting and
Restoring Items on page 48.
About the Tool Bar
The tool bar provides easy access to common software actions. The module
chosen in the navigation pane determines which actions are available on the
tool bar; for example, Optimize Labware is only available when the Labware
module is active. A description of each tool bar is included for each view:
• Protocols Selection List Tool Bar. See Table 2-3.
• Detection Method Selection List Tool Bar. See Table 2-4.
• Results Selection List Tool Bar. See Table 2-5.
• Labware Selection List Tool Bar. See Table 2-6.
• Instrument Selection List Tool Bar. See Table 2-7.
• Users Tool Bar. See Table 2-8.
• Trash Tool Bar. See Table 2-9.
The Protocols Selection List tool bar provides access for creating, editing, and
running protocols. A protocol stores all parameters required to perform a
measurement, including technique types, detection methods, labware types,
and preparation methods, such as shaking.
5008530 A
27
Installing, Using, and Configuring the Software
Table 2-3 Protocols Selection List Tool Bar
Button
Description
Creates a new protocol, see Creating Protocols on page 146.
Runs the currently selected protocol, see Running Protocols on
page 197.
Edits the currently selected protocol, see Editing Protocols on
page 211.
Copies the currently selected protocol, see Copying Protocols on
page 212.
Prints the configuration information for the currently selected protocol,
see Printing Protocol Configuration Information on page 213.
Deletes the currently selected protocol, see Deleting Protocols on
page 212.
The Detection Method Selection List tool bar provides access for creating and
editing detection methods. Measurement configuration parameters are stored
in detection methods.
Table 2-4 Detection Method Selection List Tool Bar
Button
Description
Creates a new detection method, see Creating Detection Methods
(FilterMax Multi-Mode Microplate Readers) on page 88 or Creating
Detection Methods (SpectraMax Paradigm Multi-Mode Detection
Platform) on page 99.
Edits the currently selected detection method, see Editing Detection
Methods on page 123.
Copies the currently selected detection method, see Copying Detection
Methods on page 124.
Deletes the currently selected detection method, see Deleting
Detection Methods on page 124.
28
5008530 A
Multi-Mode Analysis Software User Guide
The Results Selection List tool bar provides access to viewing, printing, and
deleting results. Measurement results from each protocol run are stored in the
Multi-Mode Analysis Software database and are accessed only from the Results
Selection List.
Table 2-5 Results Selection List Tool Bar
Button
Description
Deletes all displayed results, see Deleting Measurement Results on
page 239.
Deletes currently selected result, see Deleting Measurement Results
on page 239.
Views the currently selected result, see Viewing Measurement Results
in the Result Viewer on page 217.
Prints the currently selected result, see Printing Measurement Results
on page 239
The Labware Selection List tool bar provides access to creating, copying,
optimizing, and deleting labware.
Table 2-6 Labware Selection List Tool Bar
Button
Description
Creates a new labware type, see Creating Labware on page 128.
Edits the currently selected labware type, see Editing Labware on
page 133.
Copies the currently selected labware type, see Copying Labware on
page 136.
Optimizes the currently selected labware type, see Optimizing Labware
on page 137.
Deletes the currently selected labware type, see Deleting Labware on
page 136.
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The Instrument Selection List tool bar provides access to adding, deleting,
configuring, managing, and connecting to an instrument.
Table 2-7 Instrument Selection List Tool Bar
Button
Description
Adds a new instrument to the instrument selection list, see Adding a
New Instrument on page 52.
Deletes the currently selected instrument, see Deleting an
Instrument on page 53.
Sets the currently selected instrument to the current instrument, see
Configuring the Current Instrument on page 54.
Configures instrument settings, see Configuring the FilterMax MultiMode Microplate Readers Instrument Settings on page 57 or
Configuring SpectraMax Paradigm Multi-Mode Detection Platform
System Information Settings on page 65.
Ejects the currently selected instrument’s plate carrier, see
Connecting to the Instrument on page 55.
Loads the currently selected instrument’s plate carrier, see Loading
the Plate Carrier on page 55.
Initialize the currently selected instrument, see Initializing the
Instrument on page 56.
Connects to the currently selected instrument, see Enabling
Simulation Mode on page 56.
The Users tool bar provides access to logging out the current user, changing
the password, viewing the audit log, and reactivating disabled message boxes.
Table 2-8 Users Tool Bar
Button
Description
Logs out the current user, see Logging On and Off the
System on page 81.
Changes the password of the user currently logged in,
see Changing the Current User Password on page 82.
Views the audit log for the Multi-Mode Analysis
Software, see Viewing and Searching the Multi-Mode
Analysis Software Audit Log on page 83.
Reactivates disabled message boxes for the current
user, see Reactivating Disabled Message Boxes on
page 83.
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The Trash tool bar provides access for permanently removing and restoring
items pending deletion from the database.
Table 2-9 Trash Tool Bar
Button
Description
Restores currently selected item, see Deleting and Restoring
Items on page 48.
Restores all items in trash, see Deleting and Restoring Items on
page 48.
Permanently removes the selected item from the database, see
Deleting and Restoring Items on page 48.
Permanently removes all items in trash from the database, see
Deleting and Restoring Items on page 48.
About the Selection and Configuration Pane
The selection and configuration pane is the large pane to the right of the
navigation pane. Options available in this pane change depending on which
module is currently selected in the navigation pane. For example, when
Protocols is selected, the Protocol Selection List is displayed, which provides
access to configured protocols and functionality specific to the Protocols
module.
About the Preview Pane
The preview pane appears below the selection and configuration pane. It
contains additional information about the selected object in the Protocols,
Detection Methods, Labware, or Instruments selection lists. For example,
when an instrument is selected in the Instrument Selection List, the
parameters of the instrument appear in the preview pane. To hide the preview
pane click Hide Preview. To display the preview pane click Show Preview.
Accessing Online Help
The Multi-Mode Analysis Software contains detailed online help that covers
defining and editing labware, detection methods, and protocols, performing
measurements, and exporting measurement results. The online help is context
sensitive, which provides instant access to help for the active screen.
To access online help:
• Press F1 at any time to display online help for the active screen.
• From the Help menu, select Help > Contents to display the table of
contents.
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Configuring Multi-Mode Analysis Software
After installing the software, physically connecting the instrument to a serial
port on the host computer and turning the instrument on, instrument and
software settings must be configured.
Configuration activities include:
• Configuring Instrument Settings on page 33
• Configuring Software Settings on page 35
To set up Multi-Mode Analysis Software:
1. From the Windows Start menu, select Programs > Molecular Devices >
Multi-Mode Analysis Software > Multi-Mode Analysis Software. The MultiMode Analysis Software appears (Figure 2-6).
Note: If Multi-Mode Analysis Software is not found from the Windows
Start menu, the software may have been installed for a single user
account on the system instead of for all accounts. Check with the site
system administrator or log in to the user account with permission to
access the software. See Using Multi-Mode Analysis Software on
page 24 for more information about installing the software for a single
or multiple user accounts.
Figure 2-6 Multi-Mode Analysis Software Main Screen
2. If the Protocol Selection List (Figure 2-6) appears immediately, the
instrument was automatically detected by the software. Proceed to
Configuring Software Settings on page 35, to configure system
settings.
OR
If a warning dialog appears (Figure 2-7), the instrument was not
detected by the software. Click OK to work in simulation mode.
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Note: Upon establishing a physical connection from the controlling PC, in
many cases Multi-Mode Analysis Software may automatically detect and
initialize the instrument.
Note: If the instrument is not detected check to see that the instrument is
turned on, the instrument is connected to the controlling PC on which the
software is installed, and that the instrument LED is not flashing. After
turning on or plugging in the instrument click Connect on the Instrument
Selection List toolbar. If the instrument does not connect automatically
contact your local Molecular Devices Field Service Representative.
Figure 2-7 Warning Dialog Instrument Not Connected
Note: Upon software start up, the software will check if the instrument is
locked, or is detected as a new instrument. If the software detects the
instrument in either state, the unlock wizard will start up. Proceed to unlock
the instrument before continuing.
Configuring Instrument Settings
Before an instrument is connected, a simulated instrument appears in the
Instrument Selection List (Figure 2-8). When an actual instrument is detected
by the software and has successfully connected, the simulated instrument is
replaced in the list by the connected instrument.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Instrument Settings permission may configure instrument
settings. See Configuring Roles for Multi-Mode Analysis Software User
Accounts on page 76 for more information about roles and permissions.
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To configure instrument settings:
1. From the navigation pane, select Instruments. The Instrument Selection
List appears (Figure 2-8).
Figure 2-8 Instrument Selection List with Simulated Instrument
Selected
2. From the tool bar, select Settings.
OR
From the menu bar select Actions > Instrument Settings.
3. The Instrument Settings dialog appears (Figure 2-9).
Figure 2-9 SpectraMax Paradigm Multi-Mode Detection Platform
Instrument Settings
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4. Select the System Information tab, if necessary.
5. In Instrument Name, modify the instrument’s name if desired.
6. Click OK to close the Instrument Settings dialog.
Configuring Software Settings
The Multi-Mode Analysis Software can be customized using the options
available in Software Settings (Figure 2-10). Use the menu in Software
Settings to configure print options, default simulated data files, and the
directory where measurement results are stored.
To configure Software Settings:
1. Select File > Settings. The Software Settings window appears
(Figure 2-10).
Figure 2-10 Software Settings Window
2. Configure the settings using the menus:
 Selecting Simulated Data Files
 Selecting a Directory for Saving Exported Measurement Results
 Configuring Print Settings
 Configuring Properties
 Configuring the Data Format
 Configuring Database Settings
Selecting Simulated Data Files
Protocols may be run in simulation mode, which allows the protocol
configuration to be tested using simulated data before performing the protocol
on actual samples. In simulation mode, all features for the instrument type
currently selected in the Instrument Selection List are available, but
measurement results are either randomly generated by the software or read
from a data file.
Use the Directories menu option to select the default data files for simulated
absorbance, luminescence, and fluorescence measurements (Figure 2-11).
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Figure 2-11 Selecting the Simulated Data Files
To select different simulated data files:
1. Select the Directories menu. The Simulated Data window appears
(Figure 2-11).
2. In the desired field, enter the full path to the new simulated data file.
For example: c:\detection software templates\DefaultSimulatedData.dat
Any data file with a .dat extension may be selected, including prior
measurement results. Proceed to step 3.
OR
Click the browse (...) button next to the desired measurement type.
The Open dialog appears.
Note: Simulated data files are used when the number of measurement
points in the simulated protocol run is the same as those present in the
data file. When the number of measurement points is different, the
software generates random data.
3. In the Open dialog, browse to and select the desired data file. Any data
file with a .dat extension may be selected, including prior measurement
results.
4. Click the Open button to select the data file and return to the Software
Settings tab.
5. Repeat steps 2 through 4 for each simulated data file, as desired.
6. Click OK to set the new default data files.
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Selecting a Directory for Saving Exported
Measurement Results
Exported measurement results files, regardless of format, are saved into a
single directory. The default storage directory is:
C:\Documents and Settings\All Users\Application Data\Multi-Mode\Detection
Software\data
Use the Directories menu (Figure 2-12) to change the storage directory, as
desired.
Note: All measurement results are also stored in the Multi-Mode Analysis
Software database and may be accessed using the Result Viewer. See Viewing
Measurement Results in the Result Viewer on page 217.
Figure 2-12 Directories Window for Data Storage Locations
To select a different storage directory:
1. Select the Directories menu. The directories window appears
(Figure 2-12).
2. In the Data Directory path field, enter the complete path of the desired
storage directory;
3. for example: C:\documents\Multi-Mode measurement results\MyResults\
OR
Click the browse (...) button for a directory and use the Open window
to browse to and select the desired directory.
4. Click OK to set the new storage directory.
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Configuring Print Settings
Measurement results and protocol configurations may be printed. Printing
parameters, such as headers and footers are configured in the Print Settings
window (Figure 2-13).
Figure 2-13 Print Settings Window
To configure print settings:
1. Select the Print Settings menu. The Print Settings window appears
(Figure 2-13).
2. In the Print Header section, enter text for each header line, as desired.
Header lines may be left blank.
3. In the Footer section, enter text for the Footer and Comment, as
desired. The comment will display on printed pages below the footer.
The footer and comment may be left blank.
4. In the Print Options section, select Print Preview to preview the page
layout each time a protocol configuration or measurement results are
printed.
5. In the Print Options section, select Show printer settings to display
printing options each time a protocol or measurement results are
printed.
6. In the Print Options section, select the desired Font and Font Size for
printed text.
7. Click OK to save the new print settings.
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Configuring Properties
Certain settings (described below) may be configured from the Properties
window.
1. In the Software Settings window, select the Properties menu. The List
View Settings and some other general settings appear (Figure 2-14).
Figure 2-14 Software Settings Window
2. Select Show all Methods and Protocols in list view to display all methods
and protocols on the Protocol Selection List window. Those protocols
not available will be grayed out (Figure 2-15). When deselected
unavailable methods and protocols are not displayed at all
(Figure 2-16).
3. Select Show enabled state icon in list view for methods and protocols to
display an enabled column in the Detection Methods List view and the
Protocols Selection list view (Figure 2-17 and Figure 2-18). This allows
the user to easily view if the detection method or protocol is currently
enabled.
4. Select Allow Protocol Auto-Import when new instrument or detection
cartridge detected to allow import of new example protocols when a new
instrument or detection cartridge is detected.
Note: New cartridge detection is available for the SpectraMax Paradigm
Multi-Mode Detection Platform only.
5. Select Initialize Instrument on Connect to allow initialization of the
instrument when the software automatically connects to the
instrument, or after the user clicks the Connect button.
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6. Select Automatically load/eject cartridge carrier when running a Validation
Plate to allow automatic loading and ejection of the cartridge carrier at
appropriate times within the Validation Plate process.
CAUTION! In any situation (such as when operating the instrument with
integrated systems) where automatic loading and ejection of the cartridge
carrier may cause a potential equipment collision, we recommend disabling the
Automatically load/eject cartridge carrier when running the Validation Plate
feature, and to load and eject the cartridge carrier manually.
7. Select Disable all sample wells without sample ID to disable processing of
sample wells not bearing a sample ID.
8. Select Show elapsed time during measurement to allow indication of the
elapsed time while running protocols. By deselecting this feature, the
remaining time indicator will show in its place.
9. Click OK to save the new settings.
The Show all Methods and Protocols in list view option displays all methods and
protocols in black, and those not available are grayed out (Figure 2-15).When
deselected, unavailable methods and protocols are not shown in the Protocol
Selection List or Detection Method List (Figure 2-16).
Figure 2-15 Protocol Selection List with Show all Methods and Protocols in list
view selected
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Figure 2-16 Protocol Selection List View with Show all Methods and Protocols in
list view deselected
Note: Select multiple items by clicking them and holding down the SHIFT or
CTRL keys.
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The Show enabled state icon in list view for methods and protocols option when
selected displays an enabled column in the Detection Methods list view and the
Protocols list view (Figure 2-17 and Figure 2-18). This allows the user to easily
view if the detection method or protocol is currently enabled.
Figure 2-17 Protocol Selection List View with Show enabled state icon in list
view for methods and protocols selected
Figure 2-18 Protocol Selection List View with Show enabled state icon in list
view for methods and protocols deselected
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Configuring the Data Format
Measurement results may be saved in Excel or .dat (data) file formats. Data
Format (Figure 2-19) provides options to specify how data files are formatted,
such as the delimiter character in .dat files and how to display cycle data for
kinetic measurements in Excel files.
Note: When using Microsoft Excel 2002 or higher, the Multi-Mode Analysis
Software will format the Excel worksheets with the appropriate column width
and apply formatting to display the status of a measurement value (such as
bold and colors).
Figure 2-19 Configuring Data Format
To configure data file formats:
1. In the Delimiter reading / writing data files field, select the character to
use to separate each column when reading and writing .dat files.
Available delimiters are:
 Tab
 Comma ( , )
 Semicolon ( ; )
 Pipe ( | )
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2. In the Export Excel format field, select the desired option:
 List: Results from each cycle are displayed side-by-side adjacent to
the well in a column layout (Well, Cycle1, Cycle2, Cycle3, etc.) on
one Excel spreadsheet.
Note: Area Scan and Wavelength Scan (when the Wavelength Scan
points exceeds 250) cannot be exported in List format due to column
limitations in Excel.
Figure 2-20 Excel Format - List
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
All Cycles on one Sheet: Cycles are displayed in a plate layout format,
with each subsequent cycle displayed below the data for the
previous cycle.
Figure 2-21 Excel Format - All Cycles On One Sheet
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
One Sheet per Cycle: cycles are displayed in a plate layout format,
with each cycle displayed separately on a new worksheet labeled
with the cycle number.
Figure 2-22 Excel Format - One Sheet Per Cycle
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Configuring Database Settings
The current database size and audit log for the database can be viewed using
the Database settings (Figure 2-23). Database settings also provides options
for shrinking the database.
Note: Compressing a database does not affect items in the Trash Selection
list.
Figure 2-23 Configuring Database Settings
To configure database settings:
1. Select the Database menu. Database Settings appear (Figure 2-23).
2. To compress the size of the database containing labware types,
detection methods, and protocols click Shrink for Size Database
Definition. Once the database is compressed, click OK.
3. To compress the size of the database containing results click Shrink for
Size Database Result. Once the database is compressed, click OK.
4. To view the audit log for the database click Show. The Audit Viewer
appears the audit log for the database (Figure 2-24).
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Figure 2-24 Database Audit Log
Deleting and Restoring Items
The Trash Selection List contains labware, detection methods and protocols
that are pending permanently deletion from the database. Items may be
restored for use or permanently removed from the database using this
window.
To restore an item pending deletion:
1. From the navigation pane, select Trash. The Trash List appears.
2. Select the item to restore.
OR
Click Restore All Items to restore all items in the Trash List for use in the
software. All items in the Trash List are restored.
3. Click Restore Item. The selected item in the Trash List is restored.
Note: Select multiple items by clicking them and holding down the
SHIFT or CTRL keys.
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To permanently remove an item from the database:
1. From the navigation pane, select Trash. The Trash List appears.
2. Select the item to permanently remove from the database.
OR
Click Delete All to permanently delete all items in the Trash List from the
database. All items in the Trash List are permanently removed from the
database.
3. Click Delete. The selected item in the Trash List is permanently removed
from the database.
4. To compress the database after items are removed from the database
see Configuring Database Settings on page 47.
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3
Overview
Before defining measurement protocols, detection methods, and labware, or
running protocols on an instrument using Multi-Mode Analysis Software, the
instrument must be configured.
The Instrument Selection List provides access for configuring instrument
settings and performing common instrument actions, such as loading and
ejecting the plate carrier, and for configuring instrument settings.
Use the Instrument Selection List for:
• Managing Instruments on page 52
• Controlling Instrument Actions on page 54
• Configuring the FilterMax Multi-Mode Microplate Readers Instrument
Settings on page 57
• Configuring SpectraMax Paradigm Multi-Mode Detection Platform
Instrument Settings on page 64
• Configuring SpectraMax Paradigm Multi-Mode Detection Platform
System Information Settings on page 65
To configure and manually control instruments:
• From the navigation pane, select Instruments. The Instrument Selection
List appears (Figure 3-1).
Figure 3-1 Instrument Selection List
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All instruments that have been connected to the host computer and configured
in the software are displayed in the Instrument Selection List. When an
instrument is not currently connected to the computer that is selected, the
software automatically enters simulation mode. See Enabling Simulation Mode
on page 56. This allows protocols, detection methods, and labware to be
defined, edited, and tested for the selected instrument even though it is not
physically connected to the host computer.
Note: Select the current instrument for the software. The labware, detection
methods, protocols, and results are specific to each instrument. To
configuring the current instrument see Configuring the Current Instrument on
page 54.
Managing Instruments
Adding a New Instrument
When an instrument is connected to the PC and turned on it is automatically
installed and added to the Instrument Selection list for use.
Note: If a simulated instrument already exists in the Instrument Selection List
and the actual instrument of the same type is connected to the PC and turned
on, all detection methods and protocols for the simulated instrument will be
associated with the connected instrument.
Adding an instrument adds a new simulated instrument to the Instrument
Selection list for use in building and creating methods, labware, and protocols.
Two instruments of the same type may be added and are identified by their
serial number and instrument name. Two simulated instruments of the same
type may not be added.
To manually add an instrument:
1. From the tool bar, click Add a new Instrument to the list.
OR
From the menu bar select Actions > Add a new Instrument to the list.
OR
Right-click on the Instrument Selection list and select Add a new
Instrument to the list from the menu that appears.
2. The Add Instrument Wizard dialog appears (Figure 3-2).
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Figure 3-2 Add Instrument Wizard Dialog
3. Using the Instrument Type field, select the instrument to be added.
4. Click the Install button.
5. The instrument is added to the instrument selection list. To configure
the Instrument Settings, see Configuring the FilterMax Multi-Mode
Microplate Readers Instrument Settings on page 57 or Configuring
SpectraMax Paradigm Multi-Mode Detection Platform Instrument
Settings on page 64.
Deleting an Instrument
Deleting an instrument removes the instrument from the Instrument Selection
list and all associated methods and protocols are disabled. Protocols and
methods from a deleted instrument are automatically associated with an
instrument of the same type and configuration (detection cartridges or filter
slides).
Note: If an instrument is connected and on, the instrument cannot be
deleted. It will be temporarily removed from the Instrument Selection List,
and when the list is refreshed the software will retrieve all defined and
connected instruments. Only simulated instruments can be permanently
removed from the Instrument Selection List.
To delete an instrument:
1. Select the instrument to be deleted.
2. From the tool bar, click Delete the currently selected instrument.
OR
From the menu bar select Actions > Delete the currently selected
instrument.
OR
Right-click on the instrument and select Delete the currently selected
instrument from the menu that appears.
3. The Instrument Delete dialog appears, click Yes to delete the
instrument.
4. The instrument is deleted from the Instrument Selection list, along with
disabling all associated detection methods and protocols.
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Configuring the Current Instrument
Configuring the current instrument readies the instrument for use. It displays
the available detection methods and protocols for the instrument, and disables
other instruments’ detection methods and protocols. Detection methods and
protocols can only be created for the current instrument.
To configure the current instrument:
1. On the Multi-Mode Analysis Software main window, select the
instrument for configuration.
2. From the tool bar, click the Set Current button.
OR
From the menu bar select Actions > Sets the selected Instrument to
Current Instrument.
OR
Right-click on the instrument and from the menu that appears select
Sets the selected Instrument to Current Instrument.
3. The instrument is now configured as the current instrument.
Controlling Instrument Actions
Instrument actions, such as ejecting or loading the plate carrier and initializing
the instrument, can be performed directly from the Instrument Selection List
using the buttons on the tool bar.
Actions that may be controlled include:
• Connecting to the Instrument on page 55
• Connecting to the Instrument on page 55
• Loading the Plate Carrier on page 55
• Initializing the Instrument on page 56
• Enabling Simulation Mode on page 56
Note: Before connecting to any instrument, ensure all connections are secure
and that the instrument is unlocked and powered up.
Note: Only the current instrument can be controlled. Set the desired
instrument to the current instrument. See Configuring the Current
Instrument on page 54.
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Connecting to the Instrument
When started, the Multi-Mode Analysis Software automatically establishes
communication with the instrument or enters simulation mode when no
instrument is detected. A connection to an instrument may be established
manually after physically connecting a different instrument to the computer, or
when switching from simulation mode. See Enabling Simulation Mode on
page 56.
To connect to the current instrument:
• From the tool bar, click the Connect button. The button remains
depressed while the selected instrument is connected and not in
simulation mode.
OR
From the menu bar select Actions > Connect to the instrument.
OR
Right-click on the instrument and from the menu that appears select
Connect to the instrument.
Ejecting the Plate Carrier
Ejecting the plate carrier moves the plate carrier outside the instrument to
allow access for placement or removal of a microplate.
To eject the plate carrier from the current instrument:
• From the tool bar, click the Eject button.
OR
From the menu bar select Actions > Eject the plate carrier.
OR
Right-click on the instrument and from the menu that appears select
Eject the plate carrier.
Loading the Plate Carrier
Loading the plate carrier retracts the plate carrier and microplate back into the
instrument in preparation of performing a measurement.
To load the plate carrier on the current instrument:
• From the tool bar, click the Load button.
OR
From the menu bar select Actions > Load the plate carrier.
OR
Right-click on the instrument and from the menu that appears select
Load the plate carrier.
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Initializing the Instrument
Initializing the instrument moves the optics and microplate transports to home
positions. The instrument is initialized automatically each time it turned on. If
necessary, the instrument may be initialized manually; for example, after an
emergency stop has been performed.
Note: When a hardware error occurs, turning the instrument off and on is the
recommended initialization method.
To manually initialize the current instrument:
• From the tool bar, click the Init button.
OR
From the menu bar select Actions > Initialize the instrument.
OR
Right-click on the instrument and from the menu that appears select
Initialize the instrument.
Enabling Simulation Mode
The Multi-Mode Analysis Software can operate in simulation mode whether or
not an instrument is connected. Simulation mode enables all features
supported by the instrument currently selected in the Instrument Selection
List, but measurement results are generated randomly or read from a file. See
Selecting Simulated Data Files on page 35 for more information about
selecting simulated data files.
Note: Only the current instrument can be controlled, set the desired
instrument to the current instrument. See Configuring the Current
Instrument on page 54.
To enable simulation mode:
• From the tool bar, click Simulate the current instrument. The button
remains depressed while the instrument is in simulation mode.
OR
From the menu bar select Actions > Simulate the current instrument.
OR
Right-click on the current instrument and from the menu that appears
select Simulate the current instrument.
To exit simulation mode, reconnect to the instrument. See Connecting to the
Instrument on page 55.
Note: If no instrument is connected to the controlling PC, then Multi-Mode
Analysis Software may only run in simulation mode.
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Configuring the FilterMax Multi-Mode Microplate Readers
Instrument Settings
Filter slides used by the FilterMax Multi-Mode Microplate Readers are
configured in Instrument Settings. Configuring Instrument Settings informs
Multi-Mode Analysis Software about the instrument and the configuration of
filter slides and individual filters. Instrument activities – such as microplate
shaking and the ejection or loading of filter slides – may also be controlled
manually.
Note: To configure instrument settings for the SpectraMax Paradigm MultiMode Detection Platform see Configuring SpectraMax Paradigm Multi-Mode
Detection Platform Instrument Settings on page 64.
Note: Only the current instrument can be controlled. Set the desired
instrument to the current instrument. See Configuring the Current
Instrument on page 54.
Note: When GxP Permissions is enabled on the system, only users assigned a
role supported by the Instrument Settings permission may configure
instrument settings. See Configuring Roles for Multi-Mode Analysis Software
User Accounts on page 76 for more information about roles and permissions.
To configure current instrument settings:
1. From the tool bar, click the Settings button.
OR
From the menu bar select Actions > Instrument Settings.
OR
Right-click on the current instrument and select Instrument Settings
from the menu that appears.
2. The Instrument Settings window appears.
3. Configure instrument settings on the three tabs as described in the
following sections:
 Configuring the FilterMax Multi-Mode Microplate Readers
Instrument Settings on page 57
 Defining and Editing Filter Slides on page 58
 Manually Controlling the FilterMax Multi-Mode Microplate Readers
on page 62
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Modifying and Viewing System Information
The System Information tab (Figure 3-3) contains information about the
instrument.
Figure 3-3 FilterMax Multi-Mode Microplate Readers Instrument Settings
To configure basic instrument settings:
1. In the Instrument Settings window, select the System Information tab.
2. In the Instrument Name field, modify the alias for the instrument’s
name as desired.
Other fields are read-only (grayed out) and thus cannot be modified.
Table 3-1 Instrument Settings fields
Field
Description
Instrument Name
The alias for the instrument name.
Instrument Type
The model of the instrument
Serial Number
The serial number of the instrument.
Device Number
The device number of the instrument.
Firmware Version
The firmware version loaded for the instrument.
PIC FW Version
The instrument PIC processor firmware version.
Features
The types of measurements the instrument is capable of
performing.
Defining and Editing Filter Slides
The Filter Slides tab (Figure 3-4) is used to add, remove, and configure filter
slides and the filters installed on a filter slide. Slide definitions may also be
imported and exported.
Filters used to perform measurements are mounted on two types of
interchangeable slides. One slide is reserved for excitation filters used in
absorbance and fluorescence measurements; the other is used for emission
filters used in fluorescence and some luminescence measurements. Each slide
can hold up to six filters.
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Note: Excitation and emission filter slides are different sizes to prevent them
from being installed in the incorrect position.
When exchanging slides, an identification code built into the slide allows MultiMode Analysis Software to recognize the new slide and filter configuration.
When a slide with a new configuration is inserted, or the filters on a slide
change, the slide must be configured in the Filter Slides tab. Up to 31 excitation
filter slides and 31 emission filter slides may be stored in Multi-Mode Analysis
Software at one time.
Note: For FilterMax Multi-Mode Microplate Readers to create or run
quantitation protocols, a genomic filter slide, which contains narrow
bandwidth 260 nm and 280 nm filters) must be installed and configured.
Figure 3-4 Instrument Settings - Filter Slides
This section covers:
• Adding Filter Slides on page 59
• Configuring Filter Slides on page 60
• Removing Filter Slides on page 61
• Exporting and Importing All Filter Slide Configurations on page 61
• Exporting and Importing Single Filter Slide Configurations on page 61
Adding Filter Slides
When a new filter slide is used with the instrument for the first time, it must be
added so that the Multi-Mode Analysis Software may identify the slide and
filter configuration.
To add filter slides:
1. Select the type of filter slide to add: Excitation or Emission. The list of
filter slides displays all slides of the selected type currently stored in
memory.
2. Click Add Slide. A new filter slide appears on the list of slides in the
central pane.
3. Configure the slide following the steps in Configuring Filter Slides on
page 60.
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Configuring Filter Slides
The Filter Slide Properties pane shows filter name and ID for the currently
selected slide, and displays information about the filters installed on the slide.
When a new slide is added, or the filter configuration on a slide changes, the
slide must be configured.
CAUTION! It is recommended not to reconfigure standard filter slides.
To configure a filter slide:
1. Select the type of filter slide to configure: Excitation or Emission. The list
of filter slides displays all configured slides of the selected type.
2. Select the desired filter slide to configure from the list. The he Filter
Slide Properties pane displays information about the selected slide
(Figure 3-4).
3. In the Slide ID field, enter the identification number printed on the slide.
4. In the Slide Name field, enter a name by which to identify the filter
slide.
5. In the list of filter slides, click the + to the left of the filter slide name to
display the list of filters installed on the slide.
6. Select a filter to configure. Filter properties for the selected filter is
displayed on the Filter Properties pane (Figure 3-5).
Figure 3-5 Configuring Filter Properties
7. In the Wavelength field, enter the wavelength of the filter.
8. Click in the Techniques field and then click the down arrow to display a
list of the available detection techniques.
9. Select all techniques for which the filter applies. The filter can be used
only for measurements of the selected technique types. When
techniques are selected, the read-only Installed field appears Yes. When
No is appears, no techniques are selected and the filter may not
execute any techniques.
Note: FilterMax 5 Multi-Mode Microplate Reader only: Select Polarization
only for filter positions where a polarization filter is installed.
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10. In the Name field, enter a name for the selected filter. Filter names
default to the wavelength entered, but may be renamed as desired.
11. In the Bandwidth field, enter the bandwidth (in nanometers) of the
selected filter.
12. Repeat steps 6 through 11 to configure additional filters on the slide.
Removing Filter Slides
If a filter slide is no longer used with an instrument, it can be removed from
the Multi-Mode Analysis Software.
To remove a filter slide:
1. Select the type of filter slide to remove: Excitation or Emission. The list
of filter slides displays all slides of the selected type.
2. Select the desired filter slide to remove from the list. The Filter Slide
Properties window displays information about the selected slide.
3. Click Remove Slide. The selected filter slide is removed from the list.
Exporting and Importing All Filter Slide Configurations
Information for all excitation and emission filter slides configured for the
instrument may be exported to an XML file and imported at a later time to
restore that configuration or share the filter slide configuration with another
instrument. Importing the filter slide configuration from an XML file replaces
the current configuration for all filter slides with the configuration from the file.
Note: If necessary, the default filter slide configuration may be restored by
importing the file for the type of instrument in use located in Documents and
Settings\All Users\Application Data\Multi-Mode\Detection Software\Filters.
To export all filter slides:
1. Select Export Slides. The Save As dialog appears.
2. In the Save As window, select the desired directory and enter a file
name.
3. Click Save. Slide information is saved as an XML file with the specified
path and file name.
To import all filter slides from a previously exported file:
1. Select Import Slides. The Open dialog appears.
2. In the Open dialog, browse to and select the desired XML file to import.
3. Click Open. The filter slides defined in the XML file are imported into the
filter slide list and replace all existing filter slides.
Exporting and Importing Single Filter Slide Configurations
Configuration information for a single filter slide may be exported to an XML
file and imported to restore that configuration or share the configuration with
another instrument.
To export a single filter slide configuration:
1. In the list of filter slides, select the slide desired to export.
2. Select Export This Slide. The Save As dialog appears.
3. In the Save As dialog, select the desired directory and enter a file
name.
4. Click Save. Slide information is saved as an XML file with the specified
path and file name.
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To import a single filter slide configuration:
1. If the list of filter slides currently loaded contains a slide with the same
ID as a slide configuration for import, delete that currently loaded slide.
Every filter slide ID stored in the software must be unique.
2. Select Import Single Slide. The Open dialog appears.
3. In the Open dialog, browse to and select the desired XML file to import.
4. Click Open. The selected filter slide is imported and added to the list of
filter slides for the current instrument.
Manually Controlling the FilterMax Multi-Mode
Microplate Readers
The Manual Control tab (Figure 3-6) provides options to control the actions of
the connected instrument. These actions include microplate shaking and
ejecting or loading filter slides.
Figure 3-6 FilterMax Multi-Mode Microplate Readers Instrument Settings Manual Control Tab
Manual Control is divided into five subsections:
• Temperature Control (FilterMax 5 Multi-Mode Microplate Reader only)
on page 63
• Shake Control on page 63
• Plate Carrier Control on page 64
• Excitation Filter and Emission Filter Slide Control on page 64
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Temperature Control (FilterMax 5 Multi-Mode
Microplate Reader only)
Temperature Control is used to set the microplate chamber temperature. The
temperature is set by heating the microplate chamber; cooling the chamber is
not supported. Depending on the light source used to perform measurements
configured in the protocol, the temperature may range from 3°C (5.4°F) or
4°C (7.2°F) above ambient to 45°C (113°F). The Actual field displays the
current temperature of the instrument.
To set the temperature:
1. In the Set Point field, enter the desired temperature in Celsius.
2. Click Set. Temperature control is activated for the instrument and
begins to heat to the desired temperature. The set temperature is
maintained until it is changed or the instrument is powered off.
Note: A minimum of 15 minutes is required for the instrument to reach the
desired temperature from ambient. The actual time required depends on the
relative change in temperature.
The FilterMax 3 Multi-Mode Microplate Reader does not support heating to a
set temperature.
To turn off temperature control:
• In the Set Point field, enter 0, then click Set.
OR
Turn the power to the instrument off and on.
Shake Control
Shake Control is used to manually shake the microplate loaded in the
instrument.
To manually perform a shaking operation:
1. In the Mode field, select the desired shaking mode:
 Linear: shakes from side to side.
 Orbital: shakes in a circular pattern.
 Squared: shakes in a square pattern, moving clockwise or counterclockwise at right angles.
CAUTION! Shake low-density plates, such as 6- or 48-well plates, at Low speed
only. Shaking low density plates at higher speeds may cause liquid in wells to
spill.
2. In the Intensity field, select the desired shaking intensity: Low, Medium,
or High.
3. In the Duration field, enter the length of time (in seconds) for shaking.
4. Click Shake. The instrument immediately shakes the microplate
according to these settings.
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Plate Carrier Control
Plate Carrier Control provides options to eject or load the plate carrier. It also
features an option to sense that a microplate is in the plate carrier before
starting a measurement.
To manually control the plate carrier:
• Click Eject to extend the plate carrier outside the instrument.
• Click Load to retract the plate carrier into the instrument.
• Select Check if plate is inserted before each read to sense if a microplate is
in the plate carrier before starting measurement.
Excitation Filter and Emission Filter Slide Control
Excitation Filter Slide Control and Emission Filter Slide Control are used to
manually eject or load the excitation or emission filter slides.
To manually eject or load the excitation or emission filter slide:
• Click Eject from the desired filter slide control section to unload the
filter slide from the filter compartment and partially open the
compartment door.
Note: To remove the filter slide, it is still necessary to grasp it by the
tab and pull it until it is free of the geared track. Store the removed
filter slide in a protected, dust-free area, preferably in the original
packaging.
•
Click Load from the desired filter slide control section to retract the filter
slide into position.
Configuring SpectraMax Paradigm Multi-Mode
Detection Platform Instrument Settings
Instrument settings and detection cartridges used by the SpectraMax
Paradigm Multi-Mode Detection Platform are configured in Instrument Settings.
Configuring Instrument Settings informs Multi-Mode Analysis Software about
the instrument, such as the configuration of detection cartridges. Instrument
activities – such as microplate shaking and the ejection or loading of filter
slides – may also be controlled manually.
Note: To configure the FilterMax Multi-Mode Microplate Readers, see
Configuring the FilterMax Multi-Mode Microplate Readers Instrument Settings
on page 57.
Note: Only the current instrument can be controlled, set the desired
instrument to the current instrument. See Configuring the Current
Instrument on page 54.
Note: When GxP Permissions is enabled on the system, only users assigned a
role supported by the Instrument Settings permission may configure
instrument settings. See Configuring Roles for Multi-Mode Analysis Software
User Accounts on page 76 for more information about roles and permissions.
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To configure current instrument settings:
1. From the tool bar, click Settings.
OR
From the menu bar select Actions > Instrument Settings.
OR
Right-click on the current instrument and select Instrument Settings
from the menu that appears.
2. The Instrument Settings window appears.
3. Configure instrument settings on the four tabs as described in the
following sections:
 Configuring SpectraMax Paradigm Multi-Mode Detection Platform
System Information Settings on page 65
 Viewing Installed Detection Cartridges on page 66
 Defining and Editing the Available Detection Cartridges on page 66
 Manually Controlling the SpectraMax Paradigm Multi-Mode
Detection Platform Instrument on page 69
Configuring SpectraMax Paradigm Multi-Mode
Detection Platform System Information Settings
The System Information tab (Figure 3-7) contains information about the
instrument.
Figure 3-7 Instrument Settings - System Information Settings
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To configure System Information settings:
1. In the Instrument Settings dialog, select the System Information tab.
2. In the Instrument Name field, modify the alias for the instrument’s
name as desired.
3. Click Apply. The instrument information fields are automatically
populated with information about the connected instrument. Refer to
Table 3-2 for more information about each field.
Table 3-2 Instrument Settings fields
Field
Description
Instrument Name
The alias for the instrument name.
Instrument Type
The model of the instrument
Serial Number
The serial number of the instrument.
Device Number
The device number of the instrument.
Firmware Version
The firmware version loaded for the instrument.
PIC FW Version
The instrument PIC processor firmware version.
Viewing Installed Detection Cartridges
The Installed Detection Cartridges tab appears detection cartridges currently
installed in the instrument. Detection Cartridges are automatically detected
and added to the Installed Detection Cartridge tab and Available Detection
Cartridges tab when they are inserted into the instrument.
Defining and Editing the Available Detection Cartridges
The Available Detection Cartridges tab (Figure 3-8) is used to add detection
cartridges to My Detection Cartridges for convenient configuration of methods
and protocols. The detection cartridges do not need to be installed in the
instrument, however to configure a detection cartridge it is necessary to add it
to My Detection Cartridges.
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Figure 3-8 Instrument Settings - Available Detection Cartridges
This section covers:
• Adding Detection Cartridges to the list of Available Detection Cartridges
on page 67
• Removing Detection Cartridges from the list of Available Detection
Cartridges on page 68
Adding Detection Cartridges to the list of Available
Detection Cartridges
To use a detection cartridge with the instrument, the detection cartridge must
be added to My Detection Cartridges so that it can be used in protocols. Only the
detection cartridges contained within the My Detection Cartridges will be
available for creating Detection Methods and Protocols.
Note: When a detection cartridge is installed in the instrument the software
automatically adds the detection cartridge to My Detection Cartridges.
Note: Any available detection cartridge can be added to My Detection
Cartridges for use in creating detection methods and protocols. The detection
cartridge can be placed in the instrument at a later point in time.
Fluorescence Intensity detection methods are based upon a Top Read or
Bottom Read, it is important to install the cartridge in the proper Top Read or
Bottom Read detection cartridge transport according to the created protocol.
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To manually add detection cartridges to My Detection Cartridges:
1. Click on the Available Detection Cartridges tab.
2. A list of all detection cartridges available is displayed in All Detection
Cartridges. The list of installed detection cartridges is displayed within
My Detection Cartridges. Select the detection cartridges to add from All
Detection Cartridges.
3. Click Add. The selected detection cartridges are added to My Detection
Cartridges. They are now available for use in a detection method, see
Creating Detection Methods (SpectraMax Paradigm Multi-Mode
Detection Platform) on page 99.
Removing Detection Cartridges from the list of
Available Detection Cartridges
In simulation mode, removing a detection cartridge from My Detection
Cartridges disables its use. All Detection Methods and Protocols associated with
the detection cartridge will become unavailable for use in simulation mode.
Associated Detection Methods and Protocols are not deleted, they are simply
removed from the view. If the detection cartridge is added to My Detection
Cartridges again, all Detection Methods and Protocols associated with it will
become available again.
Note: When an instrument is connected and not in simulation mode,
removing a detection cartridge from My Detection Cartridges is only temporary.
As soon as the connection is refreshed the detection cartridge will be added
to My Detection Cartridges and it will become available again.
To remove detection cartridges from My Detection Cartridges:
1. Click on the Available Detection Cartridges tab.
2. A list of all detection cartridges available is displayed in All Detection
Cartridges. The list of installed detection cartridges is displayed within
My Detection Cartridges. Select the detection cartridges to remove from
My Detection Cartridges.
3. Click Remove. The detection cartridges are removed from My Detection
Cartridges. All detection methods and protocols that use this detection
cartridge are now unavailable.
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Manually Controlling the SpectraMax Paradigm Multi-Mode
Detection Platform Instrument
The Manual Control tab (Figure 3-9) provides options to control the actions of
the connected instrument, such as shaking microplates and ejecting or loading
detection cartridges.
Figure 3-9 SpectraMax Paradigm Multi-Mode Detection Platform Instrument
Settings - Manual Control
Manual Control is divided into five subsections:
• Temperature Control on page 70
• Shake Control on page 70
• Plate Control on page 71
• Top Read Detection Cartridge Transport Control on page 71
• Bottom Read Detection Cartridge Transport Control on page 71
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Temperature Control
Temperature Control is used to adjust microplate chamber temperature. The
temperature is set by heating the microplate chamber; cooling the chamber is
not supported. Depending on the light source used to perform measurements
configured in the protocol, the temperature may range from 3°C (5.4°F) or
4°C (7.2°F) above ambient to 45°C (113°F). The Actual field displays the
current temperature of the instrument.
To set the temperature:
1. In the Set Point field, enter the desired temperature in Celsius.
2. Click Set. Temperature control is activated for the instrument and
begins to heat to the desired temperature. The set temperature is
maintained until it is changed or the instrument is powered off.
Note: A minimum of 15 minutes is required for the instrument to reach the
desired temperature from ambient. The actual time required depends on the
relative change in temperature.
To turn off temperature control:
• In the Set Point field, enter 0, then click Set.
OR
Turn the power to the instrument off and on.
Shake Control
Shake Control is used to manually shake the microplate loaded in the
instrument.
To manually perform a shaking operation:
1. In the Mode field, select the desired shaking mode:
 Linear: shakes from side to side.
 Orbital: shakes in a circular pattern.
Note: Squared shaking (available in FilterMax Multi-Mode Microplate
Readers) is not supported on the SpectraMax Paradigm Multi-Mode
Detection Platform.
CAUTION! Shake low-density plates, such as 6-well or 48-well plates, at low
speed only. Shaking low density plates at higher speeds may cause liquid in
wells to spill.
2. In the Intensity field, select the desired shaking intensity: Low, Medium,
or High.
3. In the Duration field, enter the length of time (in seconds) for shaking.
4. Click Shake. The instrument immediately shakes the microplate
according to these settings.
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Plate Control
Plate Control provides options to eject or load the plate carrier. It also features
an option to sense that a microplate is in the plate carrier before starting a
measurement.
To manually control the plate carrier:
• Click Eject to extend the plate carrier outside the instrument.
• Click Load to retract the plate carrier inside the instrument.
• Select Check if plate is inserted before each read to sense if a microplate is
in the plate carrier before starting each measurement.
Top Read Detection Cartridge Transport Control
The Top Read Detection Cartridge Transport Control is used to manually eject
or load detection cartridges into the Top Read detection cartridge transport.
To manually eject or load the Top Read detection cartridge transport:
• Click Eject from the Top Read Detection Cartridge Transport Control
section to unload a detection cartridge from the Top Read
compartment.
• Click Load from the Top Read Detection Cartridge Transport Control
section to retract the detection cartridge into position. If a detection
cartridge is inserted into the instrument it will automatically be
detected.
Bottom Read Detection Cartridge Transport Control
The Bottom Read Detection Cartridge Transport Control is used to manually
eject or load detection cartridges into the Bottom Read detection cartridge
transport.
To manually eject or load the Bottom Read detection cartridge transport:
• Click Eject from the Bottom Read Detection Cartridge Transport Control
section to unload a detection cartridge from the Bottom Read transport
compartment.
• Click Load from the Bottom Read Detection Cartridge Transport Control
section to retract the detection cartridge into position. If a detection
cartridge is inserted into the instrument it will automatically be
detected.
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4
Overview
To assist users in complying with electronic signature regulations, such as 21
CFR Part 11, the optional GxP Permissions module for Multi-Mode Analysis
Software may be purchased from Molecular Devices. When GxP Permissions is
enabled for Multi-Mode Analysis Software, users must have a valid user
account and password on the system to access the software. Each user is
assigned roles that contain specific permissions which determine the software
actions the user may perform.
GxP Permissions provides support for closed systems only; access over a
network is not supported. In a location where several systems are present,
GxP Permissions must be installed and enabled separately for each system
where compliance is desired. Users require separate accounts on each system
they need to access.
Note: Compliance with regulations, such as 21 CFR Part 11, requires
implementing site processes beyond the control of the software.
A single system administrator sets up the level of support provided by GxP
Permissions, creates and manages roles assigned to user accounts, and
configures GxP Permissions system parameters.
This section covers:
• Enabling GxP Permissions on page 73
• Performing System Administration Tasks on page 75
Enabling GxP Permissions
A single system administrator account may be configured for GxP Permissions.
The system administrator enables the system by setting the desired support
level. Three support levels are available:
• No Support: GxP Permissions is disabled; user accounts are not
required.
• GxP Permissions: User accounts are required to log into the software,
but passwords are not required to sign items.
Note: GxP Permissions without password checks may not provide
adequate support to comply with 21 CFR Part 11 or other regulations.
Each site must evaluate the level of support required for a given
system.
•
GxP Permissions, with password checks for signing and check-in: User
accounts are required to log into the software, and passwords must be
entered for confirmation when prompted.
Note: Compliance with regulations, such as 21 CFR Part 11, requires
implementing site processes beyond the control of the software.
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Setting Up and Using GxP Permissions
To enable GxP Permissions by setting a support level:
1. Log off and close all Molecular Devices applications.
2. Place the GxP Permissions CD in the drive, and browse to the contents
of the CD.
3. Double-click GxP Permissions -- Support Options.exe. The
Administrator Login appears.
4. If GxP Permissions is being enabled for the first time, in Administrator
Login, enter Password. A message explaining that the password must
be changed appears.
OR
If GxP Permissions has been enabled previously, in Administrator Login,
enter the administrator password and click OK. Support Options appear.
Proceed to step 5.
Note: If the Administration Password is lost, forgotten, or not known,
follow the steps in Restoring the Administrator Password on page 79.
5. In the message box, click OK. The Change Password dialog appears.
6. In the upper field, enter a new password.
7. In the lower field, re-enter the new password and click OK to confirm.
The Support Options dialog appears (Figure 4-1).
Figure 4-1 Support Options Dialog
8. Select the Multi-Mode Analysis Software tab, as necessary. Multiple tabs
appear only when several software applications with GxP Permissions
support are installed on the system.
9. Select the level of support:
 No support: User accounts are not required to access Multi-Mode
Analysis Software. Users have access to all software operations and
functionality. System activity is logged in the audit trail and may be
viewed in the Audit Log. See Viewing the System Activity Audit Log
on page 79.
 GxP Permissions: Enables the use of user accounts and permissions
for Multi-Mode Analysis Software. Users must log in to use the
software and may access only features and actions for which they
have permission. Actions performed in the software, such as signing
a labware type or protocol, do not require password confirmation.
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Note: GxP Permissions without password checks may not provide
adequate support to comply with 21 CFR Part 11 or other regulations.
Each site must evaluate the level of support required for a given
system.

GxP Permissions, with password checks for signing and check-in:
Enables the use of user accounts and permissions and electronic
signatures for Multi-Mode Analysis Software. Users must log in to
use the software and may access only features and operations for
which they have permission. Support for 21 CFR Part 11 or other
regulations is provided by requiring password checks for operations
such as signing a detection method.
Note: When other applications that support GxP Permissions are
installed on the system, each must be configured with the same
support level as Multi-Mode Analysis Software.
Note: Regulations, such as 21 CFR Part 11, contain additional
requirements for account management beyond the control of this
software.
10. Click OK to activate the support level chosen and close Support
Options.
Note: After GxP Permissions is enabled for the first time, the administrator
must create at least one user account to access Multi-Mode Analysis
Software. See Administering User Accounts and Roles on page 75 for detailed
instructions.
Performing System Administration Tasks
On a system with GxP Permissions enabled, a single administrator account
provides the ability to perform GxP Permissions system administration tasks,
including:
• Administering User Accounts and Roles on page 75
• Restoring the Administrator Password on page 79
• Viewing the System Activity Audit Log on page 79
Administering User Accounts and Roles
GxP Permissions system administration tasks are performed in the Account
Management application included as part of the GxP Permissions installation.
The system administrator sets up and configures user accounts, passwords,
and roles, and configures system settings, such as automatic password
expiration and system logout time.
A single system administrator password is used on a controlling system.
System administration tasks may be performed only on the computer where
Account Management is installed; access to Account Management over a
network is not supported.
Note: If the administrator requires access to Multi-Mode Analysis Software, a
separate user account must be created.
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Note: Regulations, such as 21 CFR Part 11, contain additional requirements
for account management beyond the control of this software.
This section covers accessing Account Management and configuring roles that
are assigned to user accounts. See Configuring Roles for Multi-Mode Analysis
Software User Accounts on page 76. Refer to the Account Management online
help for detailed information about GxP Permissions system administration
tasks.
To open Account Management:
1. Close all Molecular Devices applications.
2. In the Windows Start menu, select Settings > Control Panel. the Control
Panel appears.
3. In Control Panel, double-click on Administrative Tools. The Administrative
Tools window appears.
4. In the Administrative Tools window, double-click on Account
Management. The Administrator Login window appears.
5. Enter the administrator password and click OK. The Account
Management window appears (Figure 4-2).
Figure 4-2 Account Management
Configuring Roles for Multi-Mode Analysis Software
User Accounts
Multi-Mode Analysis Software permissions, which control access to software
actions, are installed as a part of Multi-Mode Analysis Software as the GxP
Permissions module. Permissions are not assigned directly to user accounts.
Instead the system administrator assigns permissions to roles, which are then
assigned to accounts as desired.
Roles may be assigned multiple permissions. When several software
applications that support GxP Permissions are installed on the same system,
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permissions from different applications may be assigned to the same role. A
permission may be assigned to as many roles as desired.
Three preconfigured roles are installed with the GxP Permissions module (refer
to Table 4-3). These roles may be assigned to user accounts as is, or edited,
renamed, or deleted as desired.
Note: Refer to the Account Management online help for more detailed
information. To access online help, press F1 or click the Help (question mark)
button in the lower right corner of the Account Management window.
To configure roles:
1. In the Account Management window, select the Roles tab (Figure4.3).
Figure 4-3 Configuring Roles
2. In the Roles section, click the Create Role button or select an existing
role to edit. Table 4-1 describes the default roles provided with the
software.
3. While ensuring the appropriate role is highlighted in the Roles pane, in
the Permissions pane select the permissions to match the selected role.
Table 4-2 describes the permissions available for Multi-Mode Analysis
Software.
4. Repeat steps 2 and 3 for each role being configured.
5. When all roles are configured as desired, select the Accounts tab.
6. In the Accounts tab, click the Create Account button or select an existing
user account.
7. While ensuring the appropriate role is highlighted in the Accounts pane,
in the Roles pane, select the desired roles to assign to the account
(Figure 4-3).
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Table 4-1 Multi-Mode Analysis Software Default Roles
Role
Description
Lab Administrator
Contains all Multi-Mode Analysis Software permissions. Users
assigned this role may perform all software actions.
Protocol Developer
Contains the Multi-Mode Analysis Software Copy, Create, and
Edit permissions. Users assigned this role may create and edit
protocols, labware, and detection methods, but may not sign
or delete items.
Lab Technician
No Multi-Mode Analysis Software permissions are assigned.
Users assigned this role may run protocols and view
measurement results, but not create, edit, delete, or sign
items or change instrument settings.
Table 4-2 Multi-Mode Analysis Software Permissions
Permission
Description
Add Instruments
Allows users to manually add new simulated instruments to the
Software.
Note: Auto-detected instruments are added to the list
automatically when they are connected.
Add, edit, delete
License Code
Allows users to add, edit, or delete license codes.
Change current
Instrument
Allows user to set the current instrument. See Configuring the
Current Instrument on page 54.
Copy Protocol,
Labware, Method
Allows users to make copies of protocols, labware types, and
detection methods.
Create Protocol,
Labware, Method
Allows users to create protocols, labware types, and detection
methods.
Delete all Items from Allows users to permanently remove all items in the Trash
Trash
Selection List from the database.
78
Delete Protocol,
Labware, Method,
Result, Trash
Allows users to delete protocols, labware types, detection
methods, results, and permanently remove individual items in
the Trash Selection List from the database.
Edit Instrument
Setting
Allows users to edit Instrument Settings. See Configuring and
Controlling Instruments.
Edit Protocol,
Labware, Method,
Result
Allows users to edit protocols, labware types, detection
methods, and results.
Optimize Labware
Allows users to optimize labware. See Optimizing Labware on
page 137.
Sign Protocol,
Labware, Method,
Result
Allows users to electronically sign protocols labware types,
detection methods, and results. See Adding Electronic
Signatures and Comments to Items on page 84.
View Audit Entry
Allows users to view the Multi-Mode Analysis Software audit log
using the Audit Viewer. See Viewing and Searching the MultiMode Analysis Software Audit Log on page 83.
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Restoring the Administrator Password
Only one GxP Permissions administrator account exists on a system with GxP
Permissions installed. If the administrator password is lost or forgotten,
technical support must be contacted to restore access to the Account
Management application.
To restore the administrator password:
1. Place the GxP Permissions CD in the drive, and browse to the contents
of the CD.
2. Double-click on Administrator Password Restore.exe. The Administrator
Password Restore dialog appears (Figure 4-4).
Figure 4-4 Administrator Password Restore Dialog
3. Contact technical support and provide the code displayed in the upper
field of the Administrator Password Restore dialog.
CAUTION! Leave the Administrator Password Restore dialog open until technical
support supplies a new code. The new code is based on the code displayed in
the upper field, which changes each time the Administrator Password Restore
dialog is opened.
4. In the lower field of the Administrator Password Restore dialog, enter
the new code provided by technical support.
5. Click OK to close the Administrator Password Restore dialog and accept
the new code.
6. Follow any additional instructions provided by technical support.
Viewing the System Activity Audit Log
The system administrator may view the Audit Log, which displays the audit
trail for all user activity in software applications that support GxP Permissions.
System activity is logged, even when GxP Permissions is set to No Support. See
Enabling GxP Permissions on page 73.
Note: Other than changing the level of support for GxP Permissions,
Administrator activity is not saved in the Audit Log. Administrator activity is
viewed in the Audit tab of the Account Management application.
Note: User activity within Multi-Mode Analysis Software may be viewed in the
Audit Viewer. See Viewing and Searching the Multi-Mode Analysis Software
Audit Log on page 83.
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Setting Up and Using GxP Permissions
To view the Audit Log:
1. In the Windows Start menu, select Settings > Control Panel. the Control
Panel window appears.
2. In the Control Panel, double-click on Administrative Tools. The
Administrative Tools window appears.
3. In the Administrative Tools window, double-click on Audit Log. The Audit
Log appears (Figure 4-5).
Figure 4-5 GxP Permissions Audit Log
4. As desired, click Export to export the entire audit log to a text file. The
exported file may be opened, read, and printed in any application that
supports text files.
Note: When the Audit Log is open while applications that support GxP
Permissions are open, system activity is logged, but not refreshed on the
screen automatically.
Performing GxP Permissions User Actions in
Multi-Mode Analysis Software
When GxP Permissions is enabled, users are required to log in to Multi-Mode
Analysis Software. Permissions configured in the roles assigned to accounts
determine which actions are available to users. The User Selection List
provides access to GxP Permissions actions (Figure 4-6).
GxP Permissions user actions include:
• Logging On and Off the System on page 81
• Changing the Current User Password on page 82
• Viewing and Searching the Multi-Mode Analysis Software Audit Log on
page 83
• Reactivating Disabled Message Boxes on page 83
• Adding Electronic Signatures and Comments to Items on page 84
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Figure 4-6 Accessing User Actions
Logging On and Off the System
When GxP Permissions is enabled, users must log on before Multi-Mode
Analysis Software or other installed applications that support GxP Permissions
may be accessed. Only one user may be logged onto the system at time. Once
logged in, the current user may access all applications installed on the system
supported by GxP Permissions.
This section covers:
• Logging On the System on page 81
• Logging Off the System on page 82
• Handling Disabled Accounts on page 82
Logging On the System
When the software launches or is idle with no user logged on, the Logon dialog
appears.
To log on the system:
1. Enter the desired account User Name and Password.
Note: The first time a user logs on using a new account, or after having
the password changed by the administrator, the Multi-Mode Analysis
Software prompts for the password to be changed.
The new password must be different from the original and may include
alphanumeric characters and spaces up to 250 characters in length.
Passwords are not case sensitive.
2. Click OK. The user is logged on to the Multi-Mode Analysis Software and
any other supported software applications installed on the system. The
current user’s full name appears in the title bar next to instrument
status (Figure 4-6).
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Logging Off the System
The current user must log off the system before another user may log on.
Logging off automatically logs the user off all installed applications that
support GxP Permissions.
To log off the system and close the software:
• Select File > Exit.
To log off the system and leave the software open for the next user:
1. In the navigation pane, click Users to access the User Selection List.
2. From the tool bar, click Log out current user. The user is logged out of the
Multi-Mode Analysis Software and any other supported software
applications installed on the system.
OR
From the menu bar select Actions > Log out current user.
OR
Right-click in the User Selection List and select Log out current user.
Handling Disabled Accounts
The administrator may manually disable user accounts in Account
Management, or configure accounts to be automatically disabled after a
number of logon attempts for the account fail.
When an account is automatically disabled, an Administrator Notification
appears. The administrator password must be entered before Multi-Mode
Analysis Software may be accessed by the disabled account.
Changing the Current User Password
The user currently logged into the system may change their password.
To change the password:
1. In the navigation pane, click Users to access the User Selection List.
2. From the tool bar, click Change password of user currently logged in. The
Change Password dialog appears.
OR
From the menu bar select Actions > Change password of user currently
logged in.
OR
Right-click in the User Selection List and select Change password of user
currently logged in.
3. In the upper field, enter the new password desired.
4. In the lower field, re-enter the new password to confirm.
5. Click OK to change the password.
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Viewing and Searching the Multi-Mode Analysis
Software Audit Log
Users assigned a role with the View Audit Entry permission may view or search
the audit log of user activity within Multi-Mode Analysis Software. Refer to
Table 4-2 for more information about the permissions available to users.
The Multi-Mode Analysis Software audit log lists actions performed within the
software only. To view a log of system-wide GxP Permissions activity, use the
system Audit Log. See Viewing the System Activity Audit Log on page 79.
To view records in the log or search for specific records:
1. In the navigation pane, click Users to access the User Selection List.
2. From the tool bar, click View the audit log for this software. The Audit
Viewer appears.
OR
From the menu bar select Actions > View the audit log for this software.
OR
Right-click in the User Selection List and select View the audit log for this
software.
3. In Audit Viewer, perform the action desired. Table 4-3 describes the
actions available.
Table 4-3 Audit Log Actions
Action
Description
Close
Close the Audit Viewer.
Export
Export records currently displayed in the Audit Viewer to an XML
file.
Search Criteria
Enter the desired search terms and click Go. All records containing
matching terms are listed. Searching for terms within records may
also be limited to specific dates configured in Date from...to.
Date from...to
Limit the records displayed to those falling between the specified
dates. Searching for records by date may also be combined with
terms entered in Search Criteria.
Reactivating Disabled Message Boxes
Message boxes that have been disabled by users may be reactivated.
Note: Message boxes are disabled by selecting Don't show this message again
when the message box is displayed.
To reactivate disabled dialog boxes:
1. In the navigation pane, click Users to access the User Selection List.
2. From the tool bar, click Reactivate Disabled Message Boxes.
OR
From the menu bar select Actions > Reactivate Disabled Message Boxes.
OR
Right-click in the User Selection List and select Reactivate Disabled
Message Boxes.
3. The Message dialog appears, confirming that the message boxes are
reactivated.
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Adding Electronic Signatures and Comments to Items
Protocols, measurement results, detection methods, and labware types may
signed be by users assigned a role with the Sign permission. Signing an item
adds a user's comments and electronic signature to the audit trail and
prevents the item from being edited or deleted. An item may be signed
multiple times by multiple users.
Users assigned a role with the Sign permission may also view existing
signatures for signed items and unlock any signature attached to an item. An
unlocked signature is deactivated and moved from Signatures to History;
signatures are never permanently removed from the system. When all
signatures for an item are unlocked, the item is no longer signed and may be
edited again.
To sign an item or view or unlock an existing electronic signature:
1. From the desired Selection List, select the item to sign.
2. From the tool bar, click Sign the selected <item>.
OR
From the menu bar select Actions > Sign the selected <item>.
OR
Right-click on the selected item and select Sign the selected <item>.
3. The Sign the Selected Item dialog appears (Figure 4-7).
Figure 4-7 Signing an Item
4. Select the desired action:
 Sign the item. See Signing Items on page 85.
 View or unlock an existing signature. See Viewing or Unlocking
Signatures for an Item on page 85.
 View unlocked signatures. See Viewing Unlocked Signatures on
page 86.
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Signing Items
To sign an item:
1. In the Sign tab, enter a Comment. A comment is required to complete
an electronic signature.
2. Select the type of signature: Sign or Approved. The selected type is
saved in the audit trail.
3. If the Password field is visible, enter the password for the user account.
Note: Passwords are required only when GxP Permissions, with
password checks for signing and check-in is the selected support level.
See Enabling GxP Permissions on page 73.
4. Click OK to sign the item.
Viewing or Unlocking Signatures for an Item
Users assigned a role with the Sign permission may view active signatures for
an item in the Signatures tab. Users with the Sign permission may also unlock
any signature attached to an item. An unlocked signature is deactivated and
moved from Signatures to History. Signatures are never permanently removed
from the system. Unlocking all signatures attached to an item allows the item
to be edited again.
To view existing signatures:
1. Select the desired item and open Sign the Selected Item following the
steps in Adding Electronic Signatures and Comments to Items on
page 84.
2. Select the Signatures tab (Figure 4-8).
Figure 4-8 Viewing Active Signatures
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3. Click on the + or - to the left of a signature to expand or collapse
details about the signature. Details for each signature are listed on four
lines:
 date and time signature was entered
 the full name of the user signing the item
 user comments
 version of the item
4. If the Password field is visible, enter the password for the user account.
Note: Passwords are required only when GxP Permissions, with
password checks for signing and check-in is the selected support level.
See Enabling GxP Permissions on page 73.
5. To unlock the selected signature, click Unlock. Unlocked signatures can
be viewed in the History tab.
Viewing Unlocked Signatures
Unlocked signatures are never permanently removed from the system. Users
assigned a role with Sign permission may view unlocked signatures for an item
in the History tab.
1. Select the desired item and open the Sign the Selected Item dialog
following the steps in Adding Electronic Signatures and Comments to
Items on page 84.
2. Select the History tab.
3. Click on the + or - to the left of a signature to expand or collapse
details about the signature. Details for each signature are listed on four
lines:
 date and time the signature was created
 date and time the signature was unlocked
 the full name of the user signing the method
 comments entered by the use
 version of the item
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Creating and Editing Detection Methods
5
Overview
Multi-Mode Analysis Software stores measurement configuration parameters in
detection methods. Stored parameters include the method technique (for
example, absorbance), FilterMax Filters or SpectraMax Paradigm Detection
Cartridges used, and parameters specific to the selected method, such as
integration time. The software supports absorbance, luminescence, and
fluorescence method techniques. The method techniques available for
configuration depend on the capabilities of the instrument being controlled.
Detection methods are created and edited using the Method Editor. Configured
detection methods are listed in the Detection Method Selection List and are
available for use in measurement protocols. See Creating and Running
Protocols on page 145.
Note: When GxP Permissions is enabled on the system, only users assigned
with Sign, Copy, Create, Delete, and Edit permissions may perform all of the
actions covered in this section. See Configuring Roles for Multi-Mode Analysis
Software User Accounts on page 76 for more information about roles and
permissions.
Viewing Available Detection Methods
To view available detection methods and access the Method Editor:
From the navigation pane, select Detection Methods. The Detection Method
Selection List appears (Figure 5-1) containing detection methods for the
currently selected instrument. To change the current instrument see
Configuring the Current Instrument on page 54.
Figure 5-1 Accessing Detection Method Actions
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Note: For the SpectraMax Paradigm Multi-Mode Detection Platform, detection
methods will only display as enabled if the detection cartridge is listed within
My Detection Cartridges. See Defining and Editing the Available Detection
Cartridges on page 66.
All detection method functions are accessed from the Detection Method
Selection List. Available detection method functions are:
• Creating Detection Methods (FilterMax Multi-Mode Microplate Readers)
on page 88
• Creating Detection Methods (SpectraMax Paradigm Multi-Mode
Detection Platform) on page 99
• Editing Detection Methods on page 123
• Copying Detection Methods on page 124
• Deleting Detection Methods on page 124
• Exporting and Importing Detection Methods on page 125
Creating Detection Methods (FilterMax Multi-Mode
Microplate Readers)
Detection methods are created in the Method Editor, which guides the creation
process with a wizard-type interface. Creating a new detection method
requires:
• Selecting a Method Technique (FilterMax Multi-Mode Microplate
Readers) on page 89
• Selecting the Method Type (FilterMax Multi-Mode Microplate Readers)
on page 90
The Method Type is configured for absorbance detection methods only
• Defining Method Parameters (FilterMax Multi-Mode Microplate Readers)
on page 91
• Signing a Detection Method (FilterMax Multi-Mode Microplate Readers)
on page 98 (Optional)
This is used to prevent methods from being edited or deleted. Methods
can be signed only when GxP Permissions is enabled on the system.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Create permission may create new detection methods.
To sign detection methods, users must be assigned a role containing the Sign
permission. See Configuring Roles for Multi-Mode Analysis Software User
Accounts on page 76 for more information about roles and permissions.
To create and define a new detection method:
1. Click the Detection Methods selection list button.
2. From the tool bar, click Create.
OR
From the menu bar select Actions > Create a new method.
OR
Right-click in the Detection Method Selection List and select Create a
new method.
3. The Method Editor appears (Figure 5-2).
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Selecting a Method Technique (FilterMax
Multi-Mode Microplate Readers)
In the Method Editor, the type of detection method to create is selected in
Method Technique (Figure 5-2). Only techniques supported by the instrument
currently selected in the Instrument Selection List are available for
configuration. See Configuring and Controlling Instruments on page 51.
Figure 5-2 Selecting a Method Technique
To select a method technique:
1. In Supported techniques, select the desired detection method.
2. If defining an absorbance method, click Next to select the Method Type.
See Selecting the Method Type (FilterMax Multi-Mode Microplate
Readers) on page 90.
OR
If defining a luminescence or fluorescence method, click Next to define
Method Parameters. See Defining Method Parameters (FilterMax MultiMode Microplate Readers) on page 91.
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Selecting the Method Type (FilterMax
Multi-Mode Microplate Readers)
When defining an absorbance detection method, use Method Type to select
whether a monochromatic or bichromatic method will be defined (Figure 5-3).
Note: Method Type appears only when defining absorbance methods.
Figure 5-3 Selecting an Absorbance Method Type
To select a method type:
1. In the Method Editor, click on Method Type.
2. Select the desired method: Monochromatic or Bichromatic.
If you want to use PathCheck® Pathlength Measurement Technology,
select Monochromatic. See PathCheck® Pathlength Measurement
Technology on page 245.
Note: Monochromatic methods perform a single-wavelength
measurement.
Bichromatic methods perform a second measurement at a reference
wavelength, which is subtracted from the first to calculate the final
result.
3. Click Next to define Method Parameters. See Defining Method
Parameters (FilterMax Multi-Mode Microplate Readers) on page 91.
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Defining Method Parameters (FilterMax
Multi-Mode Microplate Readers)
Detection method parameters, such as filters and integration time, are defined
in Method Parameters. The parameters available for configuration depend on
the technique selected in Method Technique. See Selecting a Method Technique
(FilterMax Multi-Mode Microplate Readers) on page 89.
Use Method Parameters for:
• Defining Absorbance Method Parameters on page 91
• Defining Luminescence Method Parameters on page 92
• Defining Fluorescence Intensity Top Method Parameters on page 93
• Defining Fluorescence Intensity Bottom Method Parameters (FilterMax
5 Multi-Mode Microplate Reader only) on page 95
• Defining Fluorescence Polarization Method Parameters (FilterMax 5
Multi-Mode Microplate Reader only) on page 96
• Defining Time-Resolved Fluorescence Method Parameters (FilterMax 5
Multi-Mode Microplate Reader only) on page 97
Defining Absorbance Method Parameters
A monochromatic absorbance method performs an absorbance measurement
at a single wavelength. A bichromatic method performs a second
measurement at a reference wavelength. This measurement is subtracted
from the first to calculate the final result.
Figure 5-4 Defining Absorbance Method Parameters
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Creating and Editing Detection Methods
To define absorbance method parameters:
1. Enter a Method Name (Figure 5-4).
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example an
absorbance measurement @ 260 ms might read ABS_260.
2. In the Excitation Wavelength (nm) field, select the measurement filter.
The PathCheck Pathlength Measurement Technology requires a filter
of 900 nm and 998 nm. See Defining and Editing Filter Slides on
page 58.
3. If a bichromatic measurement is being defined, in the Reference
Excitation Filter (nm) field, select the reference filter.
Note: The filters available are those installed on the excitation filter
slide loaded in the instrument and configured for absorbance
techniques in Instrument Settings. See Defining and Editing Filter
Slides on page 58.
4. To enable PathCheck Pathlength Measurement Technology, select the
PathCheck Enabled check box. See PathCheck® Pathlength
Measurement Technology on page 245.
5. Click Save to save the new absorbance detection method. The new
method appears in the Detection Method Selection List.
Defining Luminescence Method Parameters
A luminescence method performs glow luminescence measurements on
samples. Generally, luminescence measurements do not require a filter;
however, cutoff filtration using an emission filter may be specified to eliminate
photoluminescence generated by the microplate itself, if desired.
Figure 5-5 Defining Luminescence Method Parameters
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To define luminescence method parameters:
1. Enter a Method Name (Figure 5-5).
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example a
luminescence measurement @ 400 ms might read LUM_400.
2. In the Emission Filter (nm) field, select 0 when no cutoff filtration is
desired. Most luminescence measurements do not require cutoff
filtration.
OR
In the Emission Filter (nm) field, select the cutoff filter.
Note: The filters available are those installed on the emission filter slide
loaded in the instrument and configured for luminescence techniques in
Instrument Settings. See Defining and Editing Filter Slides on
page 58.
3. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) the signal is collected from samples. Set
the integration time within the range of 50 µseconds to 3600 seconds.
4. Click Save to save the new luminescence detection method. The new
method appears in the Detection Method Selection List.
Defining Fluorescence Intensity Top Method Parameters
In a fluorescence intensity top method, the source light is focused by an
objective lens and directed through an excitation filter above the plate. The
filter passes only the wavelength necessary to excite samples. The objective
lens collects the resulting fluorescence and directs it through an emission filter
to separate background light from the specific wavelengths generated by
samples. This signal is detected by the photo multiplier tube. When performing
a fluorescence intensity top method on a FilterMax 5 Multi-Mode Microplate
Reader, excitation of samples from below the plate is stopped.
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Creating and Editing Detection Methods
Figure 5-6 Defining Fluorescence Intensity Top Method Parameters
To define fluorescence intensity top method parameters:
1. Enter a Method Name (Figure 5-5).
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example a
fluorescence intensity top measurement @ 400 ms might read
FI_T_400.
2. Select the Excitation Filter (nm).
3. Select the Emission Filter (nm).
Note: The filters available are those installed on the slides loaded in the
instrument and configured for fluorescence techniques in Instrument
Settings. See Defining and Editing Filter Slides on page 58.
4. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) the signal is collected from samples. Set
the integration time within the range of 50 µseconds to 3600 seconds.
5. Click Save to save the new fluorescence intensity top detection method.
The new method appears in the Detection Method Selection List.
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Defining Fluorescence Intensity Bottom Method Parameters
(FilterMax 5 Multi-Mode Microplate Reader only)
In a fluorescence intensity bottom method, the source light is directed through
an excitation filter, which passes only the wavelengths necessary to excite
samples, and focused by an objective lens below the plate. The objective lens
collects the resulting fluorescence from below the plate and directs it through
an emission filter to separate background light from the specific wavelengths
generated by samples. This signal is detected by the photo multiplier tube.
When performing a fluorescence intensity bottom method on a FilterMax 5
Multi-Mode Microplate Reader, excitation of samples from above the plate is
stopped.
Figure 5-7 Defining Fluorescence Intensity Bottom Method Parameters
To define fluorescence intensity bottom method parameters:
1. Enter a Method Name (Figure 5-7).
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example a
fluorescence intensity bottom measurement @ 400 ms might read
FI_B_400.
2. Select the Excitation Filter (nm).
3. Select the Emission Filter (nm).
Note: The filters available are those installed on the slides loaded in the
instrument and configured for fluorescence techniques in Instrument
Settings. See Defining and Editing Filter Slides on page 58.
4. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) the signal is collected from samples. Set
the integration time within the range of 50 µseconds to 3600 seconds.
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5. Click Save to save the new fluorescence intensity bottom detection
method. The new method appears in the Detection Method Selection
List.
Defining Fluorescence Polarization Method Parameters
(FilterMax 5 Multi-Mode Microplate Reader only)
A fluorescence polarization method measures two orthogonal (perpendicular)
polarization states by performing two sequential fluorescence intensity
measurements from above the plate.
Light is directed through an excitation filter (which passes only the wavelength
necessary for excitation) and a polarizing filter. The fluorescence resulting from
the excitation of the sample is passed through two emission filters equipped
with polarizing filters to distinguish the parallel and perpendicular polarization
states.
The polarized signals are then detected sequentially by the photo multiplier
tube.
Note: The read direction settings configured in a protocol determine when
polarization states are measured during a run. See Configuring Labware
Layout Settings on page 151.
When Read by well is selected, both states are measured for each sample
before proceeding to the next sample. When Read by row or Read by column is
selected, the parallel states are measured for all samples in a row or column
before measuring the perpendicular states of the same group of samples.
Figure 5-8 Defining Fluorescence Polarization Method Parameters
To define fluorescence polarization parameters:
1. Enter a Method Name (Figure 5-8).
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Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example an
fluorescence polarization measurement @ 400 ms might read FP_400.
2. Select the Excitation Wavelength (nm).
3. Select the Emission Wavelength (nm).
Note: The wavelength filters available are those installed on the
excitation and emission wavelength filter slides loaded in the
instrument and configured for fluorescence polarization techniques in
Instrument Settings. See Defining and Editing Filter Slides on
page 58.
4. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) the signal is collected from samples. Set
the integration time within the range of 50 µseconds to 3600 seconds.
5. Click Save to save the new fluorescence polarization detection method.
The new method appears in the Detection Method Selection List.
Defining Time-Resolved Fluorescence Method Parameters
(FilterMax 5 Multi-Mode Microplate Reader only)
In a time-resolved fluorescence measurement, the excitation light source is
turned off and the measurement is performed from above the plate after a
specified delay. Several of these excitation/measurement cycles may be
performed on each sample. When multiple excitation/measurement cycles are
performed, the results from all cycles are used to calculate a single
measurement result for each sample.
Figure 5-9 Defining Time-Resolved Fluorescence Method Parameters
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To define time-resolved fluorescence parameters:
1. Enter a Method Name (Figure 5-9).
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example a timeresolved fluorescence measurement @ 0.89 ms might read TRF_0.89.
2. Select the Excitation Wavelength (nm).
3. Select the Emission Wavelength (nm).
Note: The wavelength filters available are those installed on the
excitation and emission wavelength filter slides loaded in the
instrument and configured for time-resolved fluorescence techniques in
Instrument Settings. See Defining and Editing Filter Slides on
page 58.
4. In the Pulse Length field, enter the length of time (in seconds,
milliseconds, or microseconds) that the LED light source remains
turned on.
5. In the Number of Pulses field, enter the number of
excitation/measurement cycles performed for each well in the
measurement. The number of pulses sets the exposure received by
samples during measurements.
6. In the Measurement Delay field, enter the interval (in seconds,
milliseconds, or microseconds) between switching off the light source
and performing the measurement. Set the delay within the range of
1 µs to 7.5 ms.
7. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) each sample is measured. Set the
integration time within the range of 50 µs to 7.5 ms.
8. Click Save to save the new time-resolved fluorescence detection
method. The new method appears in the Detection Method Selection
List.
Signing a Detection Method (FilterMax
Multi-Mode Microplate Readers)
When GxP Permissions is enabled on the controlling computer system,
detection methods may be signed to prevent methods from being edited or
deleted. Detection methods may be signed at any time after the configuration
is complete.
Detection methods may be signed by users who are assigned a role containing
the Sign permission. See Configuring Roles for Multi-Mode Analysis Software
User Accounts on page 76 for more information about roles and permissions.
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To sign labware:
1. In the Detection Method Selection List, select the detection method to
sign.
2. From the tool bar, click Sign the selected method.
OR
From the menu bar select Actions > Sign the selected method.
OR
Right click on the selected labware and select Sign the selected method.
3. The Sign the Selected Item dialog appears.
4. In the Sign the Selected Item dialog, add comments and an electronic
signature by following the instructions in Adding Electronic Signatures
and Comments to Items on page 84.
Creating Detection Methods (SpectraMax Paradigm
Multi-Mode Detection Platform)
Detection methods are created in the Method Editor, which guides the creation
process with a wizard-type interface. Creating a new detection method
requires:
• Selecting a Detection Cartridge (SpectraMax Paradigm Multi-Mode
Detection Platform) on page 100
• Selecting the method technique, configuring the method type
(absorbance detection methods only), and defining method parameters
based upon the selected cartridge:
 Absorbance (ABS) Detection Cartridge on page 101
 Fluorescence Polarization (FP) Detection Cartridge on page 102
 Multi-Mode (MULTI) Detection Cartridge on page 104
 Fluorescence Intensity (FI) Detection Cartridge on page 109
 Fluorescence Intensity Dual Label (FI-DL) (MultiTox-Fluor) Detection
Cartridge on page 110
 Time Resolved Fluorescence (TRF) Detection Cartridge on page 112
 Cisbio HTRF® Detection Cartridge on page 116
 Luminescence (LUM) Detection Cartridge on page 118
 AlphaScreen Detection Cartridge on page 121
• Signing a Detection Method (SpectraMax Paradigm Multi-Mode
Detection Platform) on page 122 (Optional)
This is used to prevent methods from being edited or deleted. Methods
can only be signed when GxP Permissions is enabled on the system
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Create permission may create new detection methods.
To sign detection methods, users must be assigned a role containing the Sign
permission. See Configuring Roles for Multi-Mode Analysis Software User
Accounts on page 76 for more information about roles and permissions.
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To create and define a new detection method:
1. From the tool bar, click Create.
OR
From the menu bar select Actions > Create a new method.
OR
Right-click in the Detection Method Selection List and select Create a
new method.
2. The Method Editor appears (Selecting a Detection Cartridge
(SpectraMax Paradigm Multi-Mode Detection Platform) on page 100).
Selecting a Detection Cartridge (SpectraMax Paradigm
Multi-Mode Detection Platform)
In the Method Editor, the detection cartridges contained within My Detection
Cartridges display in the detection cartridge list (Figure 5-10). Detection
cartridges installed on the machine, but not within My Detection Cartridges are
not displayed in the detection cartridge list. See Defining and Editing the
Available Detection Cartridges on page 66.
Figure 5-10 Selecting a Detection Cartridge
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To select a detection cartridge:
1. In the Detection Cartridge field, select the desired detection cartridge.
2. Define the Method Technique, Method Type (for absorbance detection
cartridges), and Method Parameters based upon the selected cartridge:
 Absorbance (ABS) Detection Cartridge on page 101
 Fluorescence Polarization (FP) Detection Cartridge on page 102
 Multi-Mode (MULTI) Detection Cartridge on page 104
 Fluorescence Intensity (FI) Detection Cartridge on page 109
 Fluorescence Intensity Dual Label (FI-DL) (MultiTox-Fluor) Detection
Cartridge on page 110
 Time Resolved Fluorescence (TRF) Detection Cartridge on page 112
 Cisbio HTRF® Detection Cartridge on page 116
 Luminescence (LUM) Detection Cartridge on page 118
 AlphaScreen Detection Cartridge on page 121
Absorbance (ABS) Detection Cartridge
Note: For additional information regarding absorbance detection cartridges
please see the detection cartridge’s user guide.
To create an absorbance detection method using an absorbance detection
cartridge:
1. The only supported method technique using an absorbance detection
cartridge is absorbance. Click Next in Method Technique to define the
Method Type.
2. When defining an absorbance detection method, use Method Type to
select whether a Monochromatic or WavelengthScan method will be
defined (Figure 5-11).
 A Monochromatic absorbance method performs an absorbance
measurement at a single wavelength.
 A WavelengthScan absorbance method performs a series of
absorbance measurement scans within a specified range configured
in the protocol.
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Figure 5-11 Absorbance Detection Cartridge Method Type
3. Click Next to define the Method Parameters.
4. In the Method Name field, enter a name for the method.
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example a
monochromatic measurement @ 260 might read ABS_260, while an
Absorbance scan measurement between 260 -360 might read
ABS_260-350 Scan.
5. For a Monochromatic absorbance method, in the Excitation Wavelength
(nm) field, specify the wavelength.
OR
For a Wavelength Scan absorbance method, in the Minimum Wavelength
(nm) and Maximum Wavelength (nm) fields, specify the wavelength.
6. To enable PathCheck Pathlength Measurement Technology, select the
PathCheck Enabled check box. See PathCheck® Pathlength
Measurement Technology on page 245.
7. Click Save to save the new absorbance detection method. The new
method appears in the Detection Method Selection List.
Fluorescence Polarization (FP) Detection Cartridge
A fluorescence polarization method measures two orthogonal (perpendicular)
polarization states by performing two simultaneous fluorescence intensity
measurements from above the plate.
Light is directed through an excitation filter, which passes only the wavelength
necessary for excitation, and a polarizing filter. The fluorescence resulting from
the excitation of the sample is passed through two emission filters equipped
with polarizing filters to distinguish the parallel and perpendicular polarization
states.
The polarized signals are then detected simultaneously by the photo multiplier
tubes.
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Note: For additional information regarding the fluorescence polarization
detection cartridges please see the detection cartridge’s user guide.
To create a fluorescence polarization detection method using a fluorescence
polarization detection cartridge:
1. The only supported method technique using a fluorescence polarization
detection cartridge is fluorescence polarization. Click Next to define the
Method Parameters (Figure 5-12).
Figure 5-12 Fluorescence Polarization Detection Cartridge Method
Parameters
2. In the Method Name field, enter a name for the method.
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example an
fluorescence polarization measurement @ 400 ms might read FP_400.
3. Optionally, to use on-the-fly detection select On the Fly Detection.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
4. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
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Note: Selecting Speed results in the fastest possible read time per
plate. However there is a trade-off between the data quality (for
example, CVs vs. dynamic range) and read speed because each well is
sampled for shorter integration times. Selecting Performance results in
a faster read time than not using On the Fly Detection, but not as fast as
the Speed mode. Performance provides considerably better results than
Speed for demanding assays.
OR
Specify the measurement time per well (in seconds, milliseconds, or
microseconds) using the Integration Time field.
5. Click Save to save the new fluorescence polarization detection method.
The new method appears in the Detection Method Selection List.
Multi-Mode (MULTI) Detection Cartridge
The Multi-Mode detection cartridge allows for three detection techniques:
• Luminescence: A luminescence method performs glow luminescence
measurements on samples.
• Fluorescence Intensity: In a fluorescence intensity method, the source
light is focused by an objective lens and directed through an excitation
filter above or below the plate. The filter passes only the wavelength
necessary to excite samples. The objective lens collects the resulting
fluorescence and directs it through an emission filter to separate
background light from the specific wavelengths generated by samples.
This signal is detected by the photo multiplier tubes. When performing
a fluorescence intensity method on a SpectraMax Paradigm Multi-Mode
Detection Platform, excitation of samples from below the plate may be
stopped depending on the mounting position of the Multi-Mode
detection cartridge.
• Time Resolved Fluorescence: In a time-resolved fluorescence
measurement, the excitation light source is turned off and the
measurement is performed from above the plate after a specified delay.
Several of these excitation/measurement cycles may be performed on
each sample. When multiple excitation/measurement cycles are
performed, the results from all cycles are used to calculate a single
measurement result for each sample.
Note: It is necessary for the detection cartridge to be installed in the Upper
Read Detection Cartridge Transport for Fluorescence Intensity Top Detection
Methods and in the Lower Read Detection Cartridge Transport for
Fluorescence Intensity Bottom Detection Methods.
Note: For additional information regarding the Multi-Mode detection cartridge
please see the detection cartridge’s user guide.
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To create a detection method using the Multi-Mode detection cartridge:
• In the supported technique select from Luminescence, Fluorescence
Intensity Top, Fluorescence Intensity Bottom, or Time Resolved
Fluorescence (Figure 5-13).
Figure 5-13 Multi-Mode Detection Cartridge Method Technique
For Luminescence (Figure 5-14):
1. Before using the Luminescence technique, determine whether to take
measurements using the On the Fly Detection feature.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
2. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
Note: Selecting Speed results in the fastest possible read time per
plate. However there is trade-off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
3. If not using on-the-fly detection, specify the measurement time per
well (in seconds, milliseconds, or microseconds) using the Integration
Time field.
4. Click Save to save the new luminescence detection method. The new
method appears in the Detection Method Selection List.
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Figure 5-14 Luminescence Method Parameters
For Fluorescence Intensity Top or Fluorescence Intensity Bottom (Figure 5-15):
1. Before using the Fluorescence Intensity Top or Fluorescence Intensity
Bottom techniques, determine whether to take measurements using
the On the Fly Detection feature.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
2. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
Note: Selecting Speed results in the fastest possible read time per
plate. However there is trade-off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
3. If not using on-the-fly detection, specify the measurement time per
well (in seconds, milliseconds, or microseconds) using the Integration
Time field.
4. Click Save to save the new fluorescence intensity detection method.
The new method appears in the Detection Method Selection List.
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Figure 5-15 Fluorescence Intensity Bottom Method Parameters
For Time Resolved Fluorescence (Figure 5-17):
1. Before using the Time Resolved Fluorescence technique, determine
whether to take measurements using the On the Fly Detection feature.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
2. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
Note: Selecting Speed results in the fastest possible read time per
plate. However there is trade-off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
3. In the Method Name field, enter a name for the method.
4. In the Pulse Length field, enter the length of time (in seconds,
milliseconds, or microseconds) that the LED light source remains
turned on (t1 on Figure 5-16).
5. If On the Fly Detection is not selected, in the Number of Pulses field, enter
the number of excitation/measurement cycles performed in the
measurement. The number of pulses sets the exposure received by
samples during measurements.
6. In the Measurement Delay field, enter the interval between (in seconds,
milliseconds, or microseconds) switching off the light source and
performing the measurement (t2 on Figure 5-16).
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7. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) each sample is measured. Set the
integration time within the range of 50 µs to 7.5 ms (t3 on
Figure 5-16).
Note: Measurement Delay + Integration Time + Pulse Delay => Minimum
Pulse Period (t2 + t3 + t4 => t5)
Figure 5-16 Time Resolved Fluorescence
8. Click Save to save the new time resolved fluorescence detection
method. The new method appears in the Detection Method Selection
List.
Figure 5-17 Time Resolved Fluorescence Method Parameters
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Fluorescence Intensity (FI) Detection Cartridge
In a fluorescence intensity detection method, the source light is focused by an
objective lens and directed through an excitation filter above or below the
plate, depending upon the mounting position of the cartridge. Reading of the
plate is determined by the method type, fluorescence intensity top methods
read above the plate and fluorescence intensity top methods read below the
plate. The filter passes only the wavelength necessary to excite samples. The
objective lens collects the resulting fluorescence and directs it through an
emission filter to separate background light from the specific wavelengths
generated by samples. This signal is detected by the photo multiplier tube.
Note: It is necessary for the Fluorescence Intensity detection cartridge to be
installed in the Upper Read Detection Cartridge Transport for the
Fluorescence Intensity Top Detection Method. It is necessary for the
Fluorescence Intensity detection cartridge to be installed in the Bottom Read
Detection Cartridge Transport for the Fluorescence Intensity Bottom detection
method.
Note: For additional information regarding the fluorescence intensity
detection cartridge please see the detection cartridge’s user guide.
To create a fluorescence intensity detection method using a fluorescence
intensity detection cartridge:
1. In the Supported technique field select Fluorescence Intensity Dual-Label,
FRET, Fluorescence Intensity Top, or Fluorescence Intensity Bottom.
2. Click Next to define the Method Parameters (Figure 5-18).
Figure 5-18 Fluorescence Intensity Detection Cartridge Method
Parameters
3. In the Method Name field, enter a name for the method.
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Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example, an
absorbance measurement @ 260 might read ABS_260.
4. To use on-the-fly detection select On the Fly Detection.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
5. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
Note: Selecting Speed results in the fastest possible read time per
plate. However, there is trade off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
6. Specify the measurement time per well (in seconds, milliseconds, or
microseconds) using the Integration Time field.
7. Click Save to save the new fluorescence intensity detection method.
The new method appears in the Detection Method Selection List.
Fluorescence Intensity Dual Label (FI-DL)
(MultiTox-Fluor) Detection Cartridge
In a fluorescence intensity dual-label detection method, the source light is
focused by an objective lens and directed through an excitation filter above or
below the plate, depending upon the mounting position of the cartridge. The
filter passes only the wavelength necessary to excite samples. The objective
lens collects the resulting fluorescence and directs it through an emission filter
to separate background light from the specific wavelengths generated by
samples. This signal is detected by the photo multiplier tubes.
Note: It is necessary for the Fluorescence Intensity Dual Label (FI-DL)
(MultiTox-Fluor) Detection Cartridge to be installed in the Upper Read
Detection Cartridge Transport for reading from above the plate. It is
necessary for the Fluorescence Intensity Dual Label (FI-DL) (MultiTox-Fluor)
Detection Cartridge to be installed in the Bottom Read Detection Cartridge
Transport for reading from the below plate.
Note: For additional information regarding the Fluorescence Intensity Dual
Label (FI-DL) (MultiTox-Fluor) Detection Cartridge, please see the detection
cartridge user guide.
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To create a fluorescence intensity dual-label detection method using a
Fluorescence Intensity Dual Label (FI-DL) (MultiTox-Fluor) Detection
Cartridge:
1. In the Supported technique field, select Fluorescence Dual-Label. Other
detection methods might be available also, such as FRET, Fluorescence
Intensity Top, or Fluorescence Intensity Bottom.
2. Click Next to define the Method Parameters (Figure 5-19).
Figure 5-19 Fluorescence Intensity Dual Label (FI-DL) (MultiTox-Fluor)
Detection Cartridge Method Parameters
3. In the Method Name field, enter a name for the method.
Note: When naming detection methods, it is important to use a
consistent and informative naming convention. For example, an
absorbance measurement @ 260 might read ABS_260.
4. To use on-the-fly detection select On the Fly Detection.
Note: On the Fly Detection yields considerably faster read times since
the plate moves continuously as each well is measured, as opposed to
the stop and go mode where the plate stops moving for each read.
5. If using on-the-fly detection, specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
Note: Selecting Speed results in the fastest possible read time per
plate; however, there is trade off between the data quality (that is, CVs
or dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
6. Specify the measurement time per well (in seconds, milliseconds, or
microseconds) using the Integration Time field.
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7. Click Save to save the new fluorescence intensity dual-label detection
method. The new method appears in the Detection Method Selection
List.
Time Resolved Fluorescence (TRF) Detection Cartridge
In a time resolved fluorescence measurement, the excitation light source is
turned off and the measurement is performed from above the plate after a
specified delay. Several of these excitation/measurement cycles may be
performed on each sample. When multiple excitation/measurement cycles are
performed, the results from all cycles are used to calculate a single
measurement result for each sample.
The time resolved fluorescence measurement cycle consists of five parts:
• Pulse Length: the time that the excitation light source is turned on (t1
on Figure 5-19).
• Measurement Delay: the time between the excitation light source being
turned off and when the measurement begins (t2 on Figure 5-19).
• Integration Time: the measurement time (t3 on Figure 5-19).
• Pulse Delay: the time between the measurement stopping (integration
time) and when the excitation light source is turned on for the next
measurement (t4 on Figure 5-19). This value is read only and is
adjusted based upon the Minimum Pulse Period, Measurement Delay,
and Integration time.
• Minimum Pulse Period: The minimum time required between the
excitation light source being turned off and when the excitation light
source is turned on again (t5 on Figure 5-19). This value is based upon
each detection cartridge and is not editable.
Note: Measurement Delay + Integration Time + Pulse Delay  Minimum
Pulse Period (t2 + t3 + t4  t5)
Figure 5-20 Time Resolved Fluorescence
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The dual-time resolved fluorescence measurement cycle consists of seven
parts:
• Pulse Length: the time that the excitation light source is turned on (t1
on Figure 5-20).
• Measurement Delay (First Window): the time between the excitation light
source being turned off and when the first measurement begins (t2 on
Figure 5-20).
• Integration Time (First Window): the measurement time (t3 on
Figure 5-20) that each sample is measured for the first time.
• Measurement Delay (Second Window): the time between the excitation
light source being turned off and when the second measurement begins
(t2+t3+t6 on Figure 5-20).
• Integration Time (Second Window): the measurement time (t7 on
Figure 5-20) each sample is measured the second time.
• Pulse Delay: the time between the measurement stopping (integration
time) and when the excitation light source is turned on for the next
measurement (t4 on Figure 5-20). This value is read only and is
adjusted based upon the Minimum Pulse Period, Measurement Delay,
and Integration time.
• Minimum Pulse Period: The minimum time required between the
excitation light source being turned off and when the excitation light
source is turned on again (t5 on Figure 5-20). This value is based upon
each detection cartridge and is not editable.
Note: First Measurement Delay + First Integration Time + Second
Measurement Delay + Second Integration Time + Pulse Delay 
Minimum Pulse Period (t2 + t3 + t6 + t7 + t4  t5)
Figure 5-21 Dual-Time Resolved Fluorescence
Note: For additional information regarding the time resolved fluorescence
detection cartridge please see the detection cartridge’s user guide.
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To create a time resolved fluorescence detection method using a time resolved
fluorescence enabled detection cartridge:
1. If applicable, in the Supported Technique field select Time Resolved
Fluorescence or Time Resolved Fluorescence Dual.
2. If applicable, in the Wavelengths field specify the Excitation and
Emission Wavelength.
3. Click Next to define the Method Parameters (Figure 5-21).
Figure 5-22 Time Resolved Fluorescence Method Parameters - Time
Resolved Fluorescence
4. In the Method Name field, enter a name for the method.
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example an
absorbance measurement @ 260 might read ABS_260, while an
Absorbance scan measurement between 260 -360 might read
ABS_260-350 Scan.
5. To use on-the-fly detection select On the Fly Detection.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
6. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
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Note: Selecting Speed results in the fastest possible read time per
plate. However, there is trade off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
7. In the Pulse Length field, enter the length of time (in seconds,
milliseconds, or microseconds) that the light source remains turned on
(t1 in Figure 5-19 and Figure 5-20).
8. If On the Fly Detection is not selected, in the Number of Pulses field, enter
the number of excitation/measurement cycles performed in the
measurement. The number of pulses sets the exposure received by
samples during measurements.
9. In the Measurement Delay field, enter the time interval (in seconds,
milliseconds, or microseconds) between switching off the light source
and performing the measurement (t2 in Figure 5-19 and Figure 5-20).
10. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) each sample is measured. Set the
integration time within the range of 10 µs to 10 ms (t3 in Figure 5-19
and Figure 5-20).
11. For dual time resolved fluorescence, in the second Measurement Delay
field, enter the time interval (in seconds, milliseconds, or
microseconds) between switching off the light source and performing
the second measurement (t2+t3+t6 in Figure 5-20).
12. For dual time resolved fluorescence, in the second Integration Time
field, enter the length of time (in seconds, milliseconds, or
microseconds) each sample is measured the second time. Set the
integration time within the range of 10 µs to 10 ms (t7 in Figure 5-20).
13. Click Save to save the new time resolved fluorescence detection
method. The new method appears in the Detection Method Selection
List.
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Cisbio HTRF® Detection Cartridge
HTRF (homogeneous time resolved fluorescence) is a measurement technique
based upon fluorescence resonance energy transfer (FRET) using the
advantage of time resolved florescence.
The homogeneous time resolved fluorescence measurement cycle consists of
five parts:
1. Pulse Length: the time that the excitation light source is turned on (t1
on Figure 5-22).
2. Measurement Delay: the time between the excitation light source being
turned off and when the measurement begins (t2 on Figure 5-22).
3. Integration Time: the measurement time (t3 on Figure 5-22).
• Pulse Delay: the time between the measurement stopping (integration
time) and when the excitation light source is turned on for the next
measurement (t4 on Figure 5-22). This value is read only and is
adjusted based upon the Minimum Pulse Period, Measurement Delay,
and Integration time.
• Minimum Pulse Period: The minimum time required between the
excitation light source being turned off and when the excitation light
source is turned on again (t5 on Figure 5-22). This value is based upon
each detection cartridge and is not editable.
Note: Measurement Delay + Integration Time + Pulse Delay =>
Minimum Pulse Period (t2 + t3 + t4 => t5)
Figure 5-23 Homogeneous Time Resolved Fluorescence
Note: For additional information regarding the homogeneous time
resolved fluorescence detection cartridge please see the detection
cartridge’s user guide.
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To create a homogeneous time resolved fluorescence detection method using a
homogeneous time resolved fluorescence enabled detection cartridge:
1. The only supported method technique using a homogeneous time
resolved fluorescence detection cartridge is homogeneous time
resolved fluorescence. Click Next to define the Method Parameters
(Figure 5-23).
Figure 5-24 Homogeneous Time Resolved Fluorescence Method
Parameters
2. In the Method Name field, enter a name for the method.
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example an
absorbance measurement @ 260 might read ABS_260, while an
Absorbance scan measurement between 260 -360 might read
ABS_260-350 Scan.
3. To use on-the-fly detection select On the Fly Detection.
Note: On the Fly Detection yields considerably faster read times while
the plate moves continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
4. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
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Note: Selecting Speed results in the fastest possible read time per
plate. However, there is trade off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
5. If On the Fly Detection is not selected, in the Number of Pulses field, enter
the number of excitation/measurement cycles performed in the
measurement. The number of pulses sets the exposure received by
samples during measurements.
6. In the Measurement Delay field, enter the interval (in seconds,
milliseconds, or microseconds) between switching off the light source
and performing the measurement (t2 in Figure 5-22).
7. In the Integration Time field, enter the length of time (in seconds,
milliseconds, or microseconds) each sample is measured. Set the
integration time within the range of 10 µs to 10 ms (t3 in Figure 5-22).
8. Click Save to save the new homogeneous time resolved fluorescence
detection method. The new method appears in the Detection Method
Selection List.
Luminescence (LUM) Detection Cartridge
In a luminescence method, the intensity at which light is emitted from a
chemiluminescent or bioluminescent reaction is measured. The light output is
measured as the rate of photons per time and is expressed as counts per
second. In glow luminescence reactions, the light output decays slowly with
time. Since the light is emitted as a result of a chemical reaction, no excitation
light and no excitation filters are required to measure luminescence. In a dual
glow luminescence method, different wavelength bands at the same time are
measured.
Note: There are different types of Luminescence detection cartridges available
for the SpectraMax Paradigm Multi-Mode Detection Platform. All are designed
and optimized for different applications and microplate formats (for more
details, refer to the respective detection cartridge manuals).
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To create a detection method using the Luminescence detection cartridge:
1. In the supported technique select Luminescence or Dual Luminescence
(Figure 5-25).
Figure 5-25 Luminescence Detection Cartridge Method Technique
2. As required, select the detection wavelengths using the Wavelengths
field.
3. Click Next to define the Method Parameters (Figure 5-26).
4. In the Method Name field, enter a name for the method.
Note: When naming detection methods it is important to use a
consistent and informative naming convention. For example
Absorbance measurement @ 260 might read ABS_260, while an
Absorbance scan measurement between 260 -360 might read
ABS_260-350 Scan.
5. To use on-the-fly detection select On the Fly Detection.
Note: On the Fly Detection yields considerably faster read times due to
the plate moving continuously as each well is measured, as opposed to
stop and go mode where the plate stops moving for each read.
6. If using on-the-fly detection specify whether the detection method
should be optimized for Speed or Performance using the On the Fly
Optimization field.
Note: Selecting Speed results in the fastest possible read time per
plate. However, there is trade off between the data quality (i.e. CVs or
dynamic range) and read speed because each well is sampled for
shorter integration times. Selecting Performance results in a faster read
time than not using On the Fly Detection, but not as fast as the Speed
mode. Performance provides considerably better results than Speed for
demanding assays.
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OR
If not using on-the-fly detection, specify the measurement time per
well (in seconds, milliseconds, or microseconds) using the Integration
Time field.
7. Select Attenuation to apply a neutral density optical filter to the reading,
which will reduce the intensity of all samples.
Note: Using attenuation will shift the linear dynamic range to higher
sample concentrations. A similar effect can be achieved by using black
plates instead of white plates. Samples appearing even stronger in
signal although attenuation is applied are outside the measurement
range.
Note: The attenuation option is available only for luminescence top
reading.
CAUTION! Luminescence light levels visible to the human eye may cause
damage to the detection system.
8. Click Save to save the new luminescence detection method. The new
method appears in the Detection Method Selection List.
Figure 5-26 Dual Luminescence Method Parameters
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AlphaScreen Detection Cartridge
In an AlphaScreen method, the intensity at which light is emitted from the
bead-based AlphaScreen assay is measured. The light output is measured as
the rate of photons per time and can be normalized to counts per second. In
AlphaScreen reactions, the light output decays slowly with time. Since the light
is emitted as a result of a photochemical reaction, excitation light is exposed to
the sample once, before signal is integrated for a specified time.
Note: There are different types of AlphaScreen detection cartridges available
for the SpectraMax Paradigm Multi-Mode Detection Platform. All are designed
and optimized for different microplate formats (for more details, refer to the
AlphaScreen Detection Cartridge user guide).
To create a detection method using the AlphaScreen detection cartridge:
1. In the Supported technique, select AlphaScreen (Figure 5-27).
Figure 5-27 AlphaScreen Detection Cartridge Method Technique
2. As required, select the detection wavelengths using the Wavelengths
field.
3. Click Next to define the Method Parameters (Figure 5-28).
4. In the Method Name field, enter a name for the method.
Note: When naming detection methods, it is important to use a
consistent and informative naming convention. For example,
Absorbance measurement @ 260 might read ABS_260, while an
Absorbance scan measurement between 260 and 350 might read
ABS_260-350 Scan.
5. In the Excitation Time field, type the length of time in milliseconds that
you want the laser beam to be on.
6. In the Integration Time field, type the elapsed time in milliseconds from
when the laser beam is turned off to when you want the signal to be
detected.
7. To normalize raw data from counts into counts per second, select
Normalization.
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8. Select Interlaced Reading when you expect a high assay dynamic range
in white plates.
Note: Interlaced Reading processes every other well in a checkerboard
fashion and adds another plate run to cover the wells left from the first
run. Using this process minimizes crosstalk from the possible afterglow
of an adjacent well that may have a strong emission when the critical
well is read. Interlaced Reading is the suggested read mode when
expecting high assay dynamic range in white plates.
9. Click Save to save the new AlphaScreen detection method. The new
method appears in the Detection Method Selection List.
Figure 5-28 AlphaScreen Method Parameters
Signing a Detection Method (SpectraMax Paradigm
Multi-Mode Detection Platform)
When GxP Permissions is enabled on the system, detection methods may be
signed to prevent method properties from being edited or methods from being
deleted. Detection methods may be signed at any time after the configuration
is complete.
Detection methods may be signed by users who are assigned a role containing
the Sign permission. See Configuring Roles for Multi-Mode Analysis Software
User Accounts on page 76 for more information about roles and permissions.
To sign a detection method:
1. In the Detection Method Selection List, select the detection method to
sign.
2. From the tool bar, click Sign the selected method.
OR
From the menu bar select Actions > Sign the selected method.
OR
Right click on the selected labware and select Sign the selected method.
3. The Sign the Selected Item dialog appears.
4. In the Sign the Selected Item dialog, add comments and an electronic
signature by following the instructions in Adding Electronic Signatures
and Comments to Items on page 84.
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Editing Detection Methods
Parameters configured in user-defined detection methods may be edited;
however, the method technique may not be changed. Default methods
installed with the software and methods used in protocols may be edited, but
not renamed.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Delete permission may delete user-defined detection
methods. Signed methods may not be deleted. See Configuring Roles for
Multi-Mode Analysis Software User Accounts on page 76 for more information
about roles and permissions.
To edit a detection method:
1. In the Detection Method Selection List, select the detection method to
edit.
2. From the tool bar, click Edit.
OR
From the menu bar select Actions > Edit the selected method.
OR
Right-click on the selected detection method and select Edit the selected
method.
3. The Method Editor appears.
4. Edit the method parameters as desired. For more information about the
parameters for a specific detection method, refer to the section that
covers defining the desired detection method:
 Creating Detection Methods (FilterMax Multi-Mode Microplate
Readers) on page 88
 Creating Detection Methods (SpectraMax Paradigm Multi-Mode
Detection Platform) on page 99
5. Click Save to close the Method Editor and save the changes.
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Copying Detection Methods
Copies may be made of existing detection methods. After a copy has been
created, it may be used as a template for a new detection method using the
same method technique.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Delete permission may delete user-defined detection
methods. Signed methods may not be deleted. See Configuring Roles for
Multi-Mode Analysis Software User Accounts on page 76 for more information
about roles and permissions.
To make a copy of a detection method:
1. In the Detection Method Selection List, select the detection method to
copy.
2. From the tool bar, click Copy.
OR
From the menu bar select Actions > Make a copy of the selected method.
OR
Right-click on the selected detection method and select Make a copy of
the selected method.
Note: The default name format for copied detection methods is Copy of
OriginalName. To change the name, edit the detection method. See Editing
Detection Methods on page 123.
Deleting Detection Methods
User-defined detection methods may be deleted from the Detection Method
Selection List. Some detection methods may not be deleted, including:
• methods used in protocols.
• default methods installed with Multi-Mode Analysis Software.
• methods signed on systems with GxP Permissions enabled.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Delete permission may delete user-defined detection
methods. Signed methods may not be deleted. See Configuring Roles for
Multi-Mode Analysis Software User Accounts on page 76 for more information
about roles and permissions.
When a detection method is deleted it is moved to the trash selection list. To
permanently remove or restore items for deletion see Deleting and Restoring
Items on page 48.
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To delete a detection method:
1. In the Detection Method Selection List, select the detection method to
delete.
2. From the tool bar, click Delete.
OR
From the menu bar select Actions > Delete the selected method.
OR
Right-click on the selected detection method and select Delete the
selected method.
Note: Multiple items may be selected for deletion by holding down the
CTRL or SHIFT key while selecting each item desired.
3. A dialog box appears. Click Yes to delete the selected detection
method.
4. To permanently remove the detection method see Deleting and
Restoring Items on page 48
Exporting and Importing Detection Methods
A user-defined detection method can be exported to an XML file and imported
later to restore that configuration or share it with a copy of Multi-Mode
Analysis Software installed on another system.
Default detection methods installed with Multi-Mode Analysis Software are
present on all systems and may not be deleted or overwritten. For this reason,
importing default detection methods from an XML export file is not permitted.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Delete permission may delete user-defined detection
methods. Signed methods may not be deleted. See Configuring Roles for
Multi-Mode Analysis Software User Accounts on page 76 for more information
about roles and permissions.
To export a detection method:
1. In the Detection Method Selection List, select the detection method to
export.
2. From the File menu, click Export > Detection Method. The Browse for
Folder dialog appears.
3. In the Browse for Folder dialog, browse to the folder where the
exported detection method will be saved.
OR
Click Make New Folder to create a new folder where the exported
detection method will be saved.
4. Click OK to export the detection method. The exported detection
method is saved using the default file name format,
Method_MethodName.xml.
Note: To import the file at a later date, the filename must not be
changed.
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To import a detection method from an exported XML file:
1. From the File menu, click Import > Detection Method. The Open dialog
appears.
Note: For SpectraMax Paradigm Multi-Mode Detection Platform, the
detection cartridge used in the imported detection method must be
contained within the list of available detection cartridges in My
Detection Cartridges configured in instrument settings. To add a
detection cartridge to the list of available detection cartridges see
Adding Detection Cartridges to the list of Available Detection Cartridges
on page 67.
2. In the Open dialog, browse to and select the desired XML file to import.
3. Click Open. The detection method is imported to the Detection Method
Selection List.
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6
Overview
Multi-Mode Analysis Software supports a wide range of labware, with many
common microplate formats already preconfigured and ready for use in
protocols. Configured labware types are listed in the Labware Selection List
and are available for use in protocols.
New labware types may be created at any time using the Labware Editor. The
Labware Editor also provides the ability to edit and delete existing labware
types not used in protocols, make copies of labware types, and optimize
labware dimensions to compensate for slight dimensional variations that may
exist between production lots.
The types of labware supported depend on the capabilities of the instrument:
• FilterMax 3 Multi-Mode Microplate Reader: Supports 96-well and 384well microplates.
• FilterMax 5 Multi-Mode Microplate Reader: Supports 6-well to 384-well
microplates.
• The SpectraMax Paradigm Multi-Mode Detection Platform supports 6well to 1536-well microplates, depending on the installed detection
cartridges.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Create permission may define labware. See Configuring
Roles for Multi-Mode Analysis Software User Accounts on page 76 for more
information about roles and permissions.
Labware actions are accessed from the Labware Selection List (Figure6.1).
Labware actions include:
• Creating Labware on page 128
• Editing Labware on page 133
• Copying Labware on page 136
• Deleting Labware on page 136
• Optimizing Labware on page 137
• Exporting and Importing Labware on page 143
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Creating and Editing Labware
To define and edit labware:
• From the navigation pane, click Labware. The Labware Selection List
appears (Figure 6-1).
Figure 6-1 Accessing Labware Actions
Creating Labware
New types of labware are created in the Labware Editor, which guides the
creation process with a wizard-type interface. Creating labware includes:
• Defining Labware Information on page 129
• Configuring Offsets and Well Dimensions for the Default Labware Lot on
page 131
• Signing Labware on page 133 (Optional)
This is used to prevent labware from being edited or deleted. Labware
may be signed only when GxP Permissions is enabled on the system.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Create permission may create new labware definitions. To
sign labware, users must be assigned a role containing the Sign permission.
See Configuring Roles for Multi-Mode Analysis Software User Accounts on
page 76 for more information about roles and permissions.
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To create and define new labware:
1. From the tool bar, click Create.
OR
From the menu bar select Actions > Create a new labware type.
OR
Right-click in the Labware Selection List and select Create a new labware
type.
2. The Labware Editor display (Figure 6-2).
Note: After installing Multi-Mode Analysis Software, profiles for commonly
used labware load to the system upon start up. Further labware profiles may
be loaded by importing them. For details see Exporting and Importing
Labware on page 143.
Defining Labware Information
Use Labware Information to define labware names, dimensions, well
parameters, and supported measurement techniques (Figure 6-2).
Figure 6-2 Defining Plate Dimensions and Information
To define Labware Information:
1. If necessary, click the + next to Labware Info to display the fields in the
category.
2. Enter the Plate Name. A name must be entered to proceed to the
second configuration screen, Labware Lots.
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3. If necessary, click the + next to Labware Measurements to display the
fields in the category.
Note: More information about the field being defined is displayed below
the property grid (Figure 6-2).
If information text is too long to be displayed entirely, the text box may
be enlarged by dragging the upper border of the Notes box.
CAUTION! The plate height configured must not be less than that of the actual
plate. Doing so may cause the FilterMax Multi-Mode Microplate Readers to
collide with the plate during a Read Height Optimization. The SpectraMax
Paradigm Multi-Mode Detection Platform has an auto-detection to prevent
collision, if an incorrect plate height is entered for the SpectraMax Paradigm
Multi-Mode Detection Platform an error message appears while running
protocols using the defined labware.
4. In the Height field enter the height of the plate without the lid. All
labware dimensions are entered in centimeters.
5. In the Height with lid field enter the height of the plate with lid in
centimeters.
6. In the Length field enter the length of the plate in centimeters.
7. In the Reading height field enter the height from the top of the plate at
which the plate is read.
8. In the Width field enter the width of the plate.
9. If necessary, click the + next to Well Info to display the fields in the
category.
10. In the Columns field enter the number of columns on the plate.
11. In the Row Label field select Alpha or Numeric for the row label.
12. In the Rows field enter the number of rows on the plate.
13. Click in either column of Well bottom shape, then click on the down
arrow and select the shape of well bottoms: Flat, Cone, or Round.
14. Click in either column of Well shape, then click on the down arrow and
select the shape of the wells: Round, Square, or Cone.
15. Enter the maximum Well volume in microliters.
16. In Supported Techniques, select all measurement techniques compatible
with the plate being defined. The labware being configured will only be
available for use in protocols configured with compatible measurement
techniques.
Note: See General Labware Selection Guidelines on page 131 for more
information about selecting the appropriate labware for the desired
techniques.
17. As desired, in Notes, enter information about the labware or
configuration.
18. Click Next to define the default row and column offsets and well
dimensions for the labware type in Labware Lots. See Configuring
Offsets and Well Dimensions for the Default Labware Lot on page 131.
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General Labware Selection Guidelines
When creating labware, select only measurement techniques compatible with
the microplate being defined. Each measurement technique requires labware
of a specific color and/or material be used.
Table 6-1 provides general labware color and material guidelines for each
measurement technique. Along with these basic guidelines, always select
microplates with a surface treatment suitable for the desired application, and
follow any additional guidelines provided by the plate manufacturer.
Table 6-1 General Microplate Selection Guidelines
Measurement
Technique
Supported
Plate Color
Additional Considerations
Absorbance
clear, white with
clear bottom, or
black with clear
bottom
Clear polystyrene or film plates with
transparent bottoms are suitable.
Polypropylene or PVC plates do not
provide sufficient optical quality.
Luminescence Glow
Type
solid black or solid
white
Black plates are recommended unless
the signal is weak enough to require the
higher sensitivity of white plates.
However, with strong signals, white
plates may produce crosstalk.
Fluorescence Intensity
Top
solid black
N/A
Fluorescence Intensity
Bottom
black with clear
bottom
N/A
Fluorescence
Polarization
solid black
Microplates must not be covered with a
lid or plastic film during fluorescence
polarization measurements.
Time-Resolved
Fluorescence
solid white
N/A
Time-Resolved
Fluorescence Dual
solid white
N/A
Configuring Offsets and Well Dimensions for
the Default Labware Lot
Use Labware Lots to define row and column offsets and well dimensions
(Figure 6-3). The offsets and dimensions entered when new labware is created
define the default labware lot (DefaultLot). After the new labware has been
saved, additional lots may be created by optimizing the labware to
compensate for dimensional variations between different production lots. See
Optimizing Labware on page 137.
In Labware Lots, x and y offsets are defined for all four corners of the labware.
An x offset is the distance from the edge of the microplate to the center of
wells on the first row; a y offset is the distance from the edge of plate to the
center of wells in the first column. Well dimensions defined include well depth,
length, and width, as well as distances between rows and columns.
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To configure offsets and well dimensions:
1. If necessary, click the + next to Labware Lot Measurements to display
the fields in the category. More information about the field being
defined is displayed below the property grid (Figure 6-3).
Note: The fields in Labware Lot Info may not be configured when
creating new labware.
2. Enter column and row x and y offsets for each of the four corner wells.
All offsets and well dimensions are entered in millimeters.
Figure 6-3 Defining Offsets and Well Dimensions
3. If necessary, click the + next to Well Measurements to display the fields
in the category.
4. In Column Distance, enter the distance between columns (well center to
well center).
5. In Row Distance, enter the distance between rows (well center to well
center).
6. Enter the Well depth.
7. In Well Width, enter the diameter of the well in the direction of the rows
on the plate.
8. In Notes, enter information about the labware lot or configuration, if
desired.
9. Click Save to save the new labware and close the Labware Editor.
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Signing Labware
When GxP Permissions is enabled on the system, labware may be signed to
prevent labware properties from being edited. Signed labware may not be
optimized to create new labware lots unless all signatures attached to the
labware are unlocked, which changes the labware status to unsigned.
Labware may be signed by users who are assigned a role containing the Sign
permission. See Configuring Roles for Multi-Mode Analysis Software User
Accounts on page 76 for more information about roles and permissions.
To sign labware:
1. In the Labware Selection List, select the labware type to sign.
2. From the tool bar, select Sign the selected labware type.
OR
From the menu bar select Actions > Sign the selected labware type.
OR
Right-click on the selected labware and select Sign the selected labware
type.
3. The Sign the Selected Item dialog appears.
4. In the Sign the Selected Item dialog, add an electronic signature by
following the instructions in Adding Electronic Signatures and
Comments to Items on page 84.
Editing Labware
Dimensions and information for user-defined labware not used in
measurement protocols may be edited. Dimensions and information may be
viewed, but not edited, for:
• default labware installed with Multi-Mode Analysis Software.
• labware used in protocols.
• labware that has been signed on a system with GxP Permissions
enabled.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Edit permission may edit labware definitions. See
Configuring Roles for Multi-Mode Analysis Software User Accounts on page 76
for more information about roles and permissions.
All labware in the Labware Selection List may be optimized to create new
labware lots. See Optimizing Labware on page 137. Labware lots compensate
for dimensional variations between production lots. When multiple lots exist
for a labware type, the active lot may be changed. Labware lot properties may
be edited for all labware types except those that have been signed.
Labware is edited in the Labware Editor (Figure 6-5). Editing includes:
• Viewing and Editing Labware Information on page 134
• Selecting and Editing Labware Lots on page 135
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Creating and Editing Labware
To view and edit labware dimensions and information:
1. In the Labware Selection List, select the labware to edit.
2. From the tool bar, click Edit.
OR
From the menu bar select Actions > Edit the selected labware type.
OR
Right-click on the selected labware and select Edit the selected labware
type.
Viewing and Editing Labware Information
Use Labware Information to view and edit labware dimensions, information,
and supported techniques. Plate information for default labware included in the
software installation and labware used in protocols may be viewed, but not
edited.
Figure 6-4 Editing Labware Dimensions and Well Information
To edit labware information:
1. In the property grid, edit labware dimensions and information as
desired. See Defining Labware Information on page 129 for more
information about the fields available in the property grid.
2. In Supported Techniques, change the measurement techniques
supported by the labware, if desired.
Note: See General Labware Selection Guidelines on page 131 for more
information about labware/technique compatibility.
3. Edit the labware Notes, if desired.
4. Click Next to select and edit labware lots and save changes made to the
labware. See Selecting and Editing Labware Lots on page 135.
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Selecting and Editing Labware Lots
Use Labware Lots to select the active lot and/or edit and save changes made in
the Labware Editor (Figure 6-5). Lots can be selected and edited for all
labware, including labware used in measurement protocols.
Note: Labware Lots are created by optimizing labware. See Optimizing
Labware on page 137.
Figure 6-5 Configuring Offsets and Well Dimensions in Labware Lots
To select and edit lots:
1. From the pull-down menu, select the lot to use or edit. The default lot
created when the labware was defined and all lots configured using
Optimizing Labware are available. See Optimizing Labware on
page 137.
2. Click in Current labware lot and select True, if necessary. True must be
selected to save changes made to the labware lot.
3. In the property grid, edit lot dimensions and information as desired.
See Configuring Offsets and Well Dimensions for the Default Labware
Lot on page 131, for more information about the fields available in the
property grid.
4. Edit the lot Notes, if desired.
5. Click Save to save changes made in the Labware Editor.
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Copying Labware
Labware can be copied and then used as a template for a new labware type by
editing the dimensions and parameters in the Labware Editor. See Editing
Labware on page 133.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Copy permission may create copies of labware definitions.
See Configuring Roles for Multi-Mode Analysis Software User Accounts on
page 76 for more information about roles and permissions.
To make a copy of a labware type:
1. In the Labware Selection List, select the labware type to copy.
2. From the tool bar, click Copy.
OR
From the menu bar select Actions > Make a copy of the selected labware
type.
OR
Right-click on the selected labware type and select Make a copy of the
selected labware type.
Note: The default name format for copied labware types is Copy of
OriginalName. To change the name, edit the labware type. See Editing
Labware on page 133.
Deleting Labware
User-defined labware may be deleted from the Labware Selection List. Some
labware may not be deleted:
• labware used in protocols.
• default labware installed with Multi-Mode Analysis Software.
• labware that has been signed on a system with GxP Permissions
enabled.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Delete permission may delete user-defined labware. See
Configuring Roles for Multi-Mode Analysis Software User Accounts on page 76
for more information about roles and permissions.
When labware is deleted it is moved to the trash selection list. To permanently
remove or restore items for deletion see Deleting and Restoring Items on
page 48.
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To delete labware:
1. In the Labware Selection List, select the labware to delete.
2. From the tool bar, click Delete.
OR
From the menu bar select Actions > Delete the selected labware type.
OR
Right-click on the selected labware and select Delete the selected labware
type.
Note: Multiple items may be selected for deletion by holding down the
CTRL or SHIFT key while selecting each item desired.
3. The Message dialog appears.
4. Click Yes to delete the selected labware.
5. To permanently remove the labware see Deleting and Restoring Items
on page 48.
Optimizing Labware
Microplate dimensions may vary slightly between production lots, which
potentially affects measurement accuracy. Multi-Mode Analysis Software
allows labware dimensions to be optimized by determining the centers of the
four corner wells on the plate. Each time a labware type is optimized, a new
labware lot is created with dimensions specific to that lot.
Note: If a microplate type is to be used in different plate orientations for
measurements, labware optimization must be done for each plate orientation
separately.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Optimize permission may optimize labware to create new
labware lots. See Configuring Roles for Multi-Mode Analysis Software User
Accounts on page 76 for details about permissions.
New labware lots may be created by optimizing labware for labware types
that have been signed. See Signing Labware on page 133.
Labware is optimized in Optimizing Labware, which guides the process with a
wizard-type interface. Optimizing labware includes:
• Creating a Copy of the Labware to be Optimized on page 138
• Start the Optimization Wizard on page 138
• Selecting the Detection Method on page 138
• Preparing and Loading the Labware on page 139
• Performing the Optimization Read on page 140
• Selecting the Centers of the Four Corner Wells on page 141
• Verifying Well Centers on page 142
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Creating and Editing Labware
Creating a Copy of the Labware to be Optimized
To create a copy of the labware to be optimized:
1. In the Labware Selection List, select the labware to optimize.
2. From the tool bar, click Make a copy of the selected labware type.
OR
From the menu bar select Actions > Make a copy of the selected labware
type.
OR
Right-click on the selected labware and select Make a copy of the selected
labware type.
3. As desired, rename the copied labware. See Editing Labware on
page 133.
Start the Optimization Wizard
To start the optimization wizard:
1. In the Labware Selection List, select the copied version of the labware
to optimize.
2. From the tool bar, click Optimize the selected labware type.
OR
From the menu bar select Actions > Optimize the selected labware type.
OR
Right-click on the selected labware and select Optimize the selected
labware type.
Selecting the Detection Method
Labware is optimized by performing area scan measurements of the four
corner wells of the microplate and then defining the well centers using images
of the wells generated by the measurements. To ensure the most accurate
optimization is performed, use Select Detection Method to select the most
appropriate detection method for the optimization (Figure 6-6).
Figure 6-6 Selecting the Detection Method for Labware Optimization
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To select the detection method:
1. To optimize labware for use in absorbance, fluorescence, or
luminescence protocols, select a detection method configured in the
protocol.
2. Click Next to Prepare the Labware. See Preparing and Loading the
Labware on page 139.
Preparing and Loading the Labware
Labware dimensions are optimized by reading the four corner wells of the
plate. Prepare Labware provides controls to load and eject labware from the
instrument and to select the orientation of the plate on the microplate carrier
(Figure 6-7).
Note: If a microplate type is to be used in different plate orientations for
measurements, labware optimization must be done for each plate orientation
separately.
Figure 6-7 Preparing the Labware for Optimization
To prepare labware for optimization:
1. Click Eject Plate Carrier to move the microplate carrier outside the
instrument.
2. Fill the corner wells of the plate with identical samples. To ensure
accuracy, samples must be appropriate for the selected detection
method. Sample concentration and volume must be identical in each
well.
3. Place the microplate to be optimized on the plate carrier.
4. Click Close Plate Carrier to load the microplate into the instrument.
5. In Select Plate Orientation, select the orientation of the plate on the
microplate carrier. The selected orientation is displayed graphically to
the right of the screen, with well A1 highlighted in red.
6. Click Next to start the optimization. See Performing the Optimization
Read on page 140. The optimization read begins automatically.
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Performing the Optimization Read
Optimization in Progress displays the status of the optimization read and
provides the ability to cancel the optimization in progress (Figure 6-8). The
optimization read requires several minutes to complete.
Figure 6-8 Labware Optimization In Progress
To cancel the optimization process and close the Optimizing Labware dialog
without saving the optimization data click the Stop Optimization button.
When the optimization read is complete:
• Click Next to select the centers of the four corner wells. See Selecting
the Centers of the Four Corner Wells on page 141.
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Selecting the Centers of the Four Corner Wells
Use Select Center to precisely define the centers of the corner wells read in the
optimization Figure 6-9. Select Center displays an image of the well generated
by the optimization read. Well centers are defined graphically by dragging
cross hairs to the position visually identified as the center. Select Center is
performed for each corner well individually.
Figure 6-9 Selecting the Well Center
To define the centers of the wells:
1. Place the cursor in the well image.
2. Click-and-drag the cross hairs to the desired center of the well.
Note: The cross hairs will not display if the cursor is not in the well
image.
3. Click Next to define the centers of the remaining well reads.
4. When all four well centers are defined, Verify Well Centers appears. See
Verifying Well Centers on page 142.
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Verifying Well Centers
Use Verify Well Centers to verify that the x and y offsets and distances
between rows and columns are correct (Figure 6-10). The offsets, distances,
and lot name may be edited in Verify Well Centers.
Figure 6-10 Verifying Well Centers
1. If necessary, click the + next to Labware Lot Measurements to display
the fields in the category.
Note: More information about the field being defined is displayed below
the property grid (Figure 6-10).
2. In Column distance, verify the distance between columns and edit the
dimension. All offsets and well dimensions are entered in centimeters,
if desired.
3. Verify the x and y offsets for the lower two wells and edit the
dimensions, if desired.
4. In Row distance, verify the distance between rows and edit the
dimension, if desired.
5. Verify the x and y offsets for the upper two wells and edit the
dimensions, if desired.
6. If necessary, click the + next to Labware Lot Name to display the default
name assigned to the new labware lot.
7. Enter a new Lot ID/Name, if desired.
8. Click Save to save the optimization data and create the new labware lot.
Note: To use the optimized lot in a measurement protocol, open the labware
for editing and select the new Labware Lot. See Selecting and Editing
Labware Lots on page 135.
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Exporting and Importing Labware
User-defined labware can be exported to an XML file and imported later to
restore that configuration or share it with a copy of Multi-Mode Analysis
Software installed on another system.
Default labware installed with Multi-Mode Analysis Software is present on all
systems and may not be edited, deleted, or overwritten. For this reason,
importing default labware from an XML export file is not permitted.
Note: When GxP Permissions is enabled, signed labware may be exported for
use on another system; however, electronic signatures are not retained,
which allows labware to be edited when imported to another system. Because
signed labware may not be deleted or overwritten, importing signed labware
into the system from which it was originally exported is not permitted.
To export labware:
1. In the Labware Selection List, select the labware to export.
2. From the File menu, select Export > Labware. The Browse for Folder
dialog appears.
3. In the Browse for Folder dialog, browse to the folder where the exported
labware will be saved.
OR
Click Make New Folder to create a new folder where the exported
labware will be saved.
4. Click OK to export the labware. The exported labware is saved using the
default file name format, Labware__LabwareName.xml. To import the
file at a later date, the filename must not be changed.
To import labware from an exported XML file:
1. From the File menu, select Import > Labware. The Open dialog appears.
2. In the Open dialog, browse to and select the desired XML file to import.
3. Click Open. The labware is imported to the Labware Selection List.
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7
Overview
A protocol stores all parameters required to perform a measurement, including
technique type, detection methods, labware type, and preparation methods,
such as shaking. Multiple measurements, including kinetic and scan
measurements, may be configured in a single protocol. Protocols also specify
how measurement results are viewed, exported, or printed when a protocol
run completes. This section includes instructions for configuring the analysis
features. Detection methods and labware must be configured before the
protocol is created. See Creating and Editing Detection Methods on page 87
and Creating and Editing Labware on page 127 for additional information.
Note: Always verify the parameters configured in a protocol. Failing to verify
all configured parameters may result in incorrect measurement results.
Protocols are listed in the Protocol Selection List (Figure 7-1), which provides
access to all protocol actions:
• Creating Protocols on page 146
• Creating a Protocol from a Template on page 196
• Running Protocols on page 197
• Editing Protocols on page 211
• Copying Protocols on page 212
• Deleting Protocols on page 212
• Printing Protocol Configuration Information on page 213
• Exporting and Importing Protocols on page 214
To select protocols and access protocol functions:
• From the navigation pane, click Protocols. The Protocol Selection List
appears (Figure 7-1).
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Figure 7-1 Protocol Selection List
Creating Protocols
New protocols are defined in Create Protocol, which guides the creation
process with a wizard-type interface. Creating a new protocol requires:
• Configuring General Settings on page 148
• Selecting the Technique Type on page 149 (for Analysis protocols)
• Selecting the Labware Type Used in the Protocol on page 150
• Configuring Labware Layout Settings on page 151
• Adding Detection and Preparation Methods for Analysis Protocols on
page 155
OR
Configuring Methods for Quantitation Protocols on page 165
• Configuring the Data Reduction on page 172
• Configuring Output Settings on page 187
Several analysis options may be selected and configured to transform
measurement data as desired when configuring Analysis and Quantitation
protocols:
• Configuring Variables on page 170
• Configuring a Transformation Formula on page 177
• Configuring Concentration on page 179
• Configuring Cutoff Values on page 183
• Configuring Validation Rules on page 185
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To create and configure a new protocol:
1. From the tool bar, click Create.
OR
From the menu bar select Actions > Create a new protocol.
OR
Right-click in the Protocol Selection List and select Create a new protocol.
2. The Select Protocol Type dialog appears (Figure 7-2).
Figure 7-2 Selecting the Protocol Type
3. There are two options for creating protocols, from the New Protocol tab
and Template Protocols tab. To create a new (non-template) protocol,
continue to step 4. To create a protocol using a template protocol see
Creating a Protocol from a Template on page 196.
Note: Template protocols are used to create a protocol based upon a
selected template. Pre-defined settings appear as the protocol is
configured.
Note: By disabling the Menu Options > Show Example Protocols, all
example protocols (starting with x_) are hidden from view in the
Protocol Selection List.
4. Select the Protocol Type:
 Analysis: Analysis applications allow measurement data to be
transformed and analyzed using formulas, variables, and
parameters configured in the protocol.
 Quantitation: Quantitation applications measure the purity and/or
concentration of proteins or nucleic acid samples, such as DNA or
RNA.
Note: For the FilterMax Multi-Mode Microplate Readers, to create or run
quantitation protocols a genomic filter slide, which contains narrow
bandwidth 260nm and 280nm filters must be installed and configured.
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5. Click Next to configure the protocol. The Create Protocol dialog
appears, displaying General Settings. See Configuring General Settings
on page 148.
Configuring General Settings
Use General Settings to define the protocol name and enter any related notes
about the protocol (Figure 7-3). Analysis Options to include in the protocol are
available for selection.
Figure 7-3 Defining a Protocol Name and Entering Notes About the Protocol
To configure the general settings for a new protocol:
1. In Protocol name, enter a unique name for the protocol. Duplicate
protocol names are not permitted.
2. In Notes, enter a description for the protocol, if desired.
3. In Run Notes, enter further notes specific to this run, if desired. These
notes will appear when the protocol starts up.
4. Select the desired Analysis Options for configuration in the protocol:
 Variables: define up to ten numeric values that may be used in any
formula configured in the protocol. See Configuring Variables on
page 170.
Note: The Variables option is only available for Analysis applications.

Transformation: configure an algebraic formula to transform
measurement data. See Configuring a Transformation Formula on
page 177.
Note: The Transformation option is only available for Analysis
applications.
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


Concentration: values or formulas for quantitation of sample
concentration with a standard curve. See Configuring Concentration
on page 179.
Cutoff: configure cutoff formulas to classify measured samples
according to defined cutoff values. See Configuring Cutoff Values on
page 183.
Validation: configure up to ten validation formulas to evaluate if a
protocol run meets the specified conditions required to be valid. See
Configuring Validation Rules on page 185.
Note: Only Analysis Options that have been selected appear in the
Create Protocol navigation pane and are available for configuration in
the protocol.
5. Click Next to select the Technique Type. See Selecting the Technique
Type on page 149.
Selecting the Technique Type
Use Technique Type to select the measurement technique to be performed by
the protocol (Figure 7-4). Only techniques supported by the instrument and
for which detection methods have already been defined are available. For more
information about technique types, see Creating and Editing Detection
Methods on page 87.
Note: Technique Type is only configured for Analysis protocols. For
Quantitation protocols see Selecting the Labware Type Used in the Protocol on
page 150.
Figure 7-4 Selecting the Measurement Technique
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To select a technique type:
1. In Technique Type, select the desired measurement techniques. Multiple
techniques may be selected to create protocols using different
detection techniques.
Note: By selecting different technique types following options while
creating a protocol are filtered (such as available labware, detection
methods, etc.).
Note: If editing an existing protocol, selecting a different technique
type removes any detection methods previously configured in Method
Selection. New detection methods must be configured before the
protocol may be used to perform measurements. See Adding Detection
and Preparation Methods for Analysis Protocols on page 155.
2. Click Next to select the Labware Type. See Selecting the Labware Type
Used in the Protocol on page 150.
Selecting the Labware Type Used in the Protocol
Use Labware Selection to select the type of labware used in the protocol
(Figure 7-5). Labware must be configured prior to configuring the protocol.
Only labware configured for the selected protocol and technique type is
available. Labware cannot be edited once it is used in a protocol. See Creating
and Editing Labware on page 127 for detailed information about creating and
configuring labware.
Figure 7-5 Selecting the Type of Labware Used in the Protocol
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To select labware:
1. Select the desired Type of Labware from the list.
Note: If the labware is not optimized a Warning dialog appears. To
continue without optimizing the labware click Yes. To optimize the
labware, click No and then Cancel to exit the Create Protocol Wizard
and optimize the labware first. See Optimizing Labware on page 137.
Labware optimization can be done after the protocol is created. The
protocol always uses the active labware lot.
2. Click Next to configure the Labware Layout Settings. See Configuring
Labware Layout Settings on page 151.
Configuring Labware Layout Settings
Use Layout Settings to configure how wells on the plate are read (Figure 7-6).
Settings include configuring well types and locations, replicates, and the layout
of well identifiers on the plate.
To configure labware layout settings:
1. To import a plate layout from an existing protocol, click Import Layout
and select the desired protocol from the list that appears. Only
protocols with compatible plate layouts are listed.
OR
To create a new or edit an existing plate layout, select the desired wells
to label. To select:
 all wells on the plate: click the small button in the upper left corner of
the plate layout display (Figure 7-6).
 all wells in a single column or row: click the desired column or row
header. Multiple columns or rows may be selected by holding down
the CTRL key while selecting each header desired.
 individual wells: click on the desired well. Multiple wells may be
selected by holding down the CTRL key while clicking on each well
desired.
 groups of wells: click and drag over the desired group of wells.
Multiple groups may be selected by holding down the CTRL key
while dragging over each desired group.
Figure 7-6 Configuring Layout Settings
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2. In Index, select the initial label number for the sequence of selected
wells.
3. In Filling, select the desired direction for labeling the selected wells:
 Vertical: labels wells column by column.
 Horizontal: labels wells row by row.
4. In Flow, select how the index is applied to wells in the selection.
 Constant: all well identifiers in the selection are assigned the current
index number.
 Incremental: increases each well identifier in the selection by one.
5. In Replicates, select the number of replicates for each sample and the
layout orientation on the plate:
 Vertical: replicates are arranged vertically in columns.
 Horizontal: replicates are arranged horizontally in rows.
Note: Replicate parameters are available for configuration only when
Incremental Flow is selected.
6. Select the type of wells to add to the plate layout from the Type field
and clicking Fill or by right-clicking on a selected well:
 Standard: a well with a known concentration used to develop or
correct a standard curve. Up to twelve standards may be configured
on a plate.
 Control: a well with a known, expected signal used to verify the
results of the plate.
 Positive Control: a control well in which a known amount of target
reagent generates a signal to verify positive results measured in
sample wells.
• Negative Control: a control well lacking the target reagent that
generates little to no signal; verifies negative results measured in
sample wells.
 Sample: a well containing a sample to measure.
 Blank: a well filled with reagents but no reacting sample. Blank
wells are used to measure background noise. When blanks are
configured, background correction is automatically applied to
measurement results.
 Empty: a well that is left empty.
 Advanced Controls (Blue/Green/Red): For use with wells of a known,
expected color signal to verify the results of the plate.
7. If configuring Blank wells, select the type of Blank Validity desired:
Plate, Row, or Column. The mean value of all blank wells in the selected
validity option is subtracted from sample wells to provide background
correction.
Note: By choosing Blank, Blank Validity replaces Filling, Flow, and
Replicate options in Layout Settings when configuring Blank wells.
8. If necessary, click Delete to delete existing labels from the selected
wells.
9. Repeat steps 1 through 8 to define additional well selections, as
desired.
10. Configure Dilution Factors, if desired. See Configuring Dilution Factors
on page 154.
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11. Select the desired reading direction using the Direction menu:
 Read by row reads plates row-by-row.
 Read by column reads plates column-by-column.
 Read by well reads each well individually before reading the next
well, which is useful for short-interval kinetic, area scan, and
wavelength scan measurements.
Note: If adding a wavelength scan to the protocol, the reading direction
must be set to well mode.
12. To use a multi-plate layout, using the Multi Layout menu select Yes. To
view the multiplate layout click View. A multi-plate layout places all the
controls on the first plate and the following plates only have samples.
The number of plates in a multi-plate layout is specified when the
protocol is run, see Running a Protocol on an Instrument on page 197.
Note: In a multi-plate layout the multiple plates are treated like one
large plate. All controls are on the first plate and the following plates
only have samples. The limit for a multi-plate layout is 100 plates.
13. Click Print Options and select which information about plate layouts will
display in printed reports.
 Print all Wells in List Format: Well label identifiers will display in a list.
 Print all Wells in Layout Format: Well label identifiers appear in a
layout.
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Configuring Dilution Factors
If wells are diluted, the dilution factor can be set for each well. As desired, the
dilution factor can be used in the Data Reduction step.
To configure dilution factors for the wells on a plate:
1. In the View: menu, select Dilutions. The plate map display changes to
show the well identifier and the dilution ratio. Initially, the dilution ratio
for all wells is 1/1, or undiluted.
Figure 7-7 Configuring Dilution Factors for a Plate
2. Select the well or wells for which to set the dilution ratio.
3. In the Dilution Factor field, select the desired dilution ratio.
4. In Filling, select whether to fill across rows first or down columns first.
Options are:
 Vertical: fill the dilution ratio for wells vertically down columns
before filling the dilution ratio in the next column.
 Horizontal: fill the dilution ratio for wells horizontally across rows
before filling the dilution ratio in the next row.
5. In Flow, specify whether to use a constant dilution factor or to
increment each well by the Dilution Factor. Options are:
 Constant: set the dilution ratio of all selected wells to the Dilution
Factor.
 Incremental: increment the dilution ratio for each well by the
Dilution Factor, starting with an undiluted well. For example, if the
Dilution Factor is 1/2, four wells are selected, and the Flow is
incremental, the dilution ratio for those four wells will be 1/1, 1/2,
1/4, and 1/8.
6. Click Fill to set the dilution ratio for the selected wells using the current
Dilution Factor, Filling, and Flow settings.
7. Repeat Step 1 through Step 5 to configure the dilution ratio for all wells
on the plate.
8. Click Next to configure the Detection and Preparation Methods. See
Adding Detection and Preparation Methods for Analysis Protocols on
page 155 or Configuring Methods for Quantitation Protocols on
page 165.
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Adding Detection and Preparation Methods
for Analysis Protocols
Use Method Selection to select and add detection and preparation methods.
The estimated duration time for the protocol is displayed in the Estimated Time
Field of the protocol. Selecting Per Cartridge sorts the detection methods by
cartridge type versus detection method type. Selecting Show only installed
Methods displays only enabled detection methods in the selection list when
connected to an instrument.
Note: If configuring a protocol in Quantitation mode, see Configuring Methods
for Quantitation Protocols on page 165.
To add a method:
1. Select the measurement type using the tabs:
 Single: One read per well (endpoint measurement).
 Kinetic: Kinetic measurements perform a specified series of
measurements on each sample at specified intervals. Final
measurement results are calculated from raw data using a data
reduction method. For more information about data reductions see
Configuring the Data Reduction on page 172.
 Area Scan: Area scans read a number of measurement points
arranged in a grid pattern across each well. Linear scans read a
number of points in a linear axis crossing the center of each well.
 Wavelength Scan: Wavelength scan enables scan measurements
between 230-1000nm in 1nm increments on each well.
Note: If adding a wavelength scan the reading direction must be set to
well mode.
2. Available detection and preparation methods display within the Select
Method section on the left-side of the window. To add a detection or
preparation method, click-and-drag the method to the protocol list in
the center of the window.
OR
Select the detection or preparation method and click the Add a method
to this protocol button (Figure 7-8).
OR
Select the detection or preparation method and press Enter or Space to
add the method.
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Figure 7-8 Adding a Single Detection Method
3. Select the method in the protocol and as required configure it using the
Method Info section in the right pane.
OR
If adding a preparation method, in the protocol pane select the
preparation method. The preparation info replaces the Method Info in
the right pane. Configure the preparation method properties, as
applicable:
 Shake: See Configuring Shake Properties on page 163 to configure the
Method Properties for the Shake preparation method.
 Set Temperature: See Configuring Set Temperature Properties
(FilterMax 5 Multi-Mode Microplate Reader and SpectraMax
Paradigm Multi-Mode Detection Platform only) on page 163 to
configure the Method Properties for the Set Temperature
preparation method.
 Wait: halts operations on the instrument for a specified length of
time before continuing to the next action in the method sequence.
See Configuring Wait Properties on page 164 to configure the Method
Properties for the Wait preparation method.
 Eject: moves the plate carrier outside the instrument to allow access
for placement or removal of a microplate. Eject has no Method
Properties to configure.
Note: The Eject preparation method should be followed by a Pause
preparation method. If there is no Pause, the next command in the
sequence is executed immediately after completion of the Eject
command.


156
Load: retracts the plate carrier and microplate inside the instrument
in preparation for performing a measurement. Load has no Method
Properties to configure.
Pause: halts operations on the instrument for an indefinite length of
time and displays a message, requiring user interaction to continue
to the next action in the method sequence. See Configuring Pause
Properties on page 164 to configure the Method Properties for the
preparation method.
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Note: A new detection method can be created at this time by clicking
the Create button. The Method Editor appears allowing the creation of a
new detection method for the current instrument. See Creating
Detection Methods (FilterMax Multi-Mode Microplate Readers) on
page 88 or Creating Detection Methods (SpectraMax Paradigm MultiMode Detection Platform) on page 99 for more information regarding
creating a detection method.
Note: To change method parameters, in the Method Information
window select the method and then click the Edit button.
4. If adding a kinetic detection method, in the protocol select Kinetic for
the detection method. Kinetic Info appears in the right pane. Configure
Kinetic Info by following the instructions in Configuring Kinetic Method
Properties on page 159.
OR
If adding an area or linear scan detection method, in the protocol select
Area Scan for the detection method. Area Scan Info appears in the right
pane. Configure Area Scan Info by following the instructions in
Configuring Area Scan Method Properties on page 160 or Configuring Linear Scan
Method Properties on page 161.
OR
If adding a wavelength scan detection method, in the protocol select
Wavelength Scan for the detection method. Wavelength Scan Info
appears in the right pane. Configure Wavelength Scan Info by following
the instructions in Configuring Wavelength Scan Method Properties on page 162.
Note: If adding a wavelength scan the reading direction must be set to
well mode.
5. Add and configure additional detection or preparation methods by
repeating steps 1 through 5, as desired.
Note: Edit selected methods by clicking the Edit button near the top
right corner of the Method Selection window. See Figure 7-9.
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Figure 7-9 Method Selection window Edit button
6. To change the order in which detection and preparation methods are
executed in the sequence, in the protocol, select the method to be
moved and click the blue up or down arrows.
OR
In in the protocol, right-click on the desired method and select Move Up
or Move Down.
OR
In the protocol, click on the desired method and drag the method up or
down into the desired position.
Note: To move a kinetic, area scan, or wavelength scan method, select
Kinetic, Area Scan, or Wavelength Scan above the detection method
desired to move, not the method itself.
7. To remove a detection or preparation method from the protocol, in the
protocol select the method to be removed and click the red delete
button.
OR
In the protocol, right-click on the desired detection or preparation
method and select Remove.
Note: To delete a kinetic, area scan, or wavelength scan method, select
Kinetic, Area Scan, or Wavelength Scan above the detection method
desired to delete, not the method itself.
8. To add a group, select the desired detection or preparation method for
creating a new group. Click on Group, and a new group will be created.
Two or more groups can be created in a protocol, there is no limit to the
number of groups that can be created.
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Note: The group option is used for integration or multi-step analysis
purposes, providing a break in the protocol without ending the
protocol. Data obtained from each group can be used together in the
Analysis.
9. If you are using a method with PathCheck Pathlength Measurement
Technology enabled and you have determined a plate background
constant for your microplate, you can enter the value in the Plate
Background field. See Use Plate Background Constant on page 247.
10. Click on the Print Options button to select the method information and
measurement results data included in printouts:
 Print Method Parameters: details about the configured method,
including technique type and filters used.
 Print Graphical View: kinetic or scan graphs of results for all
measured samples. Available for kinetic and scan measurements
only.
 Raw Data: results from each kinetic cycle or scan point. Available
when kinetic measurements, scan measurements, or multiple
detection methods are configured in the sequence.
 Print Well Status: status indicating whether the well was read
successfully.
11. Click Next to configure the Variables (if selected in the General Settings,
see Configuring Variables on page 170) or to configure the Data
Reduction, see Configuring the Data Reduction on page 172.
Configuring Method Properties
Detection methods and preparation methods that are added to a protocol may
have method properties that need to be configured.
• Configuring Kinetic Method Properties on page 159
• Configuring Area Scan Method Properties on page 160
• Configuring Linear Scan Method Properties on page 161
• Configuring Wavelength Scan Method Properties on page 162
• Configuring Shake Properties on page 163
• Configuring Set Temperature Properties (FilterMax 5 Multi-Mode
Microplate Reader and SpectraMax Paradigm Multi-Mode Detection
Platform only) on page 163
• Configuring Wait Properties on page 164
• Configuring Pause Properties on page 164
Configuring Kinetic Method Properties
Kinetic measurements perform a specified series of measurements on each
sample at specified intervals. Final measurement results are calculated from
raw data using a data reduction method.
• FilterMax Multi-Mode Microplate Readers: Kinetic measurements may be
configured for all FilterMax Multi-Mode Microplate Readers method
types except time-resolved fluorescence, FRET and area scans.
• SpectraMax Paradigm Multi-Mode Detection Platform: Kinetic
measurements may be configured for all SpectraMax Paradigm MultiMode Detection Platform method types except area scans and
absorbance wavelength scans.
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To configure properties for a kinetic measurement:
1. Select Kinetic for the detection method being configured. Kinetic Info
appears in the right pane.
2. In Kinetic Info enter the number of Kinetic Cycles to be performed.
Kinetic measurements may be set to perform 2 to 100 cycles.
3. In Kinetic Info enter the desired Kinetic Interval in seconds. The interval
is the length of time between each measurement of the same well.
Note: The minimum kinetic interval is populated automatically in Kinetic
Interval, and is determined by the labware type and layout settings
configured in the protocol. The maximum interval between
measurement cycles is 65,535 seconds.
Configuring Area Scan Method Properties
Area scan measurements may be configured for absorbance and fluorescence
intensity detection methods. Area scans read a number of measurement points
arranged in a grid pattern across each well.
Note: Properties (Resolution and Point Selection) are fixed when using onthe-fly detection methods.
To configure properties for an area scan:
1. Select Area Scan for the detection method being configured. Area Scan
Info appears in the right pane.
2. To configure the type of scan measurement and the number of points
measured, in Method Properties, click in Scan Points and click the
configuration button. Scan Selection Editor appears (Figure 7-10).
Figure 7-10 Configuring an Area Scan
3. In Resolution (mm), use the up and down arrows to select the proximity
of measurement points. selecting a smaller value increases the number
of measurement points available; selecting a larger value decreases the
number of points available. Available resolutions are determined by the
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type of labware selected for use in the protocol. Detection methods
with “On the fly” detection selected have fixed resolution and scan
points. See Selecting the Labware Type Used in the Protocol on
page 150 and Configuring Labware Layout Settings on page 151 for
more information.
4. Click anywhere inside the well boundary, except the center row, and
drag until the desired number of measurement points is selected
(Figure 7-10).
5. Click OK to save the scan configuration and close the Scan Selection
Editor.
Configuring Linear Scan Method Properties
Linear scan measurements may be configured for absorbance and fluorescence
intensity detection methods. Linear scans read a number of points in a linear
axis crossing the center of each well.
To configure properties for a linear scan:
1. Select Area Scan for the detection method being configured. Area Scan
Info appears in the right pane.
2. To configure the type of scan measurement and the number of points
measured, in Method Properties, click in Scan Points and click the
configuration button. Scan Selection Editor appears (Figure 7-11).
Figure 7-11 Configuring a Linear Scan
3. In Resolution (mm), use the up and down arrows to select the proximity
of measurement points. selecting a smaller value increases the number
of measurement points available; selecting a larger value decreases the
number of points available. Available resolutions are determined by the
type of labware selected for use in the protocol. Detection methods
with “On the fly” detection selected have fixed resolution and scan
points. See Selecting the Labware Type Used in the Protocol on
page 150 and Configuring Labware Layout Settings on page 151 for
more information.
4. To configure a linear scan, click anywhere on the center row or column
inside the well boundary and drag towards the boundary until the
desired number of measurement points is selected (Figure 7-11).
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Note: The type of scan that may be configured is determined by the
reading direction settings in Layout Settings. See Configuring Labware
Layout Settings on page 151. Horizontal linear scans along the center
row may be configured only when Read by row is selected, while
vertical linear scans along the center column may be configured only
when Read by column or Read by well is selected.
5. Click OK to save the scan configuration and close the Scan Selection
Editor.
Configuring Wavelength Scan Method Properties
Wavelength scan measurements enables scans between the defined start
wavelength and end wavelength in user configurable increments on each well.
Note: If adding a wavelength scan the reading direction must be set to well
mode.
To configure properties for a wavelength scan:
1. Select the wavelength scan detection method to configure. Wavelength
Scan Info appears in the right pane (Figure 7-12).
Figure 7-12 Wavelength Scan Detection Method Properties
2. In Method Info enter the number of wavelength ranges in Number of
Ranges, Up to three wavelength ranges can be defined so that the
spectrum can be divided into separate parts (such as 230-300 and 9001000).
3. In Method Info enter the Wavelength Increment in nm. The wavelength
step interval is the increment between each wavelength measurement
of the same well.
4. In Method Info enter the Start Wavelength in nm. The starting
wavelength must me smaller than the end wavelength.
5. In Method Info enter the End Wavelength in nm.
6. As required for multiple wavelength ranges, repeat Step 4 through
Step 5.
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Configuring Shake Properties
A Shake preparation method may be placed in the desired location in the
sequence, or attached to a kinetic measurement when interval shaking
between each measurement cycle is desired.
To configure properties for a Shake preparation method:
1. Select the desired Shake preparation method in the protocol. Shake
Info appears in the right pane.
CAUTION! Shake low density plates, such as 6- or 48-well plates, at low speed
only. Shaking low density plates at higher speeds may cause liquid in wells to
spill.
2. In Shake Intensity, select the desired intensity of shaking: Low, Medium,
or High.
3. In Shake Interval, enter the length of time in seconds (0-18000) to
shake the microplate.
Note: Shaking efficiency for 24- to 384-well plates has been improved
in Multi-Mode Analysis Software version 2.0 and above. The Shake
Interval for protocols originally created for use with version 1.0 may
need to be reduced.
4. In



Shake Mode, select the desired shaking pattern.
Linear: shakes from side to side.
Orbital: shakes labware in a circular pattern.
Squared: shakes labware in a square pattern, moving at right angles
(FilterMax Multi-Mode Microplate Readers only).
Configuring Set Temperature Properties (FilterMax 5 Multi-Mode Microplate
Reader and SpectraMax Paradigm Multi-Mode Detection Platform only)
A Set Temperature preparation method sets the temperature inside the
microplate chamber by heating the chamber; cooling the chamber is not
supported. Depending on the light source used in the protocol, the set
temperature may range from 3°C (5.4°F) or 4°C (7.2°F) above ambient to
45°C (113°F). A minimum of 15 minutes is required for the instrument to
reach the desired temperature. The actual time required depends on the
relative change in temperature. The instrument may be configured to wait for
it to reach the desired temperature or continue immediately to the next
command in the method sequence.
Note: Set Temperature preparation methods are useful for kinetic
measurements intended to measure the effects of temperature changes on
samples.
The FilterMax 5 Multi-Mode Microplate Reader does not support heating to a
set temperature.
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To configure properties for a Set Temperature preparation method:
1. Select the Set Temperature preparation method in the protocol.
Temperature Info appears in the right pane.
2. In Set Temperature, enter the desired microplate chamber temperature
in degrees Celsius. In protocols that perform measurements only at
visible wavelengths (>359 nm), the minimum temperature that may be
set is 3°C (5.4°F) above ambient. When the protocol performs
measurements in the UV range the minimum temperature is 4°C
(7.2°F) above ambient. The maximum temperature that may be set is
45°C (113°F).
Note: The temperature remains at the current setting until overridden
by another Set Temperature preparation method, by changing the
temperature in Manual Control, or by turning the instrument off and
on.
3. In Wait for Temperature, select the desired option:
 True: wait until the FilterMax 5Multi-Mode Microplate Reader or
SpectraMax Paradigm Multi-Mode Detection Platform reaches the
Set Temperature before executing the next command.
 False: immediately execute the next command.
Configuring Wait Properties
A Wait preparation method halts actions on the instrument for a specified
length of time prior to executing the next command. Properties for a Wait
preparation method include the length of time to wait before continuing with
the protocol.
To configure properties for a Wait preparation method:
1. In Method Selection, select the desired Wait preparation method.
Method Properties for the selected method appear.
2. In Wait Time, enter the length of time in seconds the instrument should
wait before executing the next command.
Note: Wait Time must be between 1 and 3600 seconds.
Configuring Pause Properties
A Pause preparation method halts actions on the instrument for an indefinite
length of time and display a message, requiring user interaction to continue to
the next action in the method sequence. Properties for a Pause preparation
method include the message to display during the pause.
To configure properties for a Pause preparation method:
1. Select the desired Pause preparation method in the protocol. Pause Info
appears in the right pane.
2. In Comment, enter the text for the message to display when the Pause
is executed during the protocol run.
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Configuring Methods for Quantitation Protocols
In a Quantitation protocol, Method Selection (Figure 7-13) is used to select the
quantitation methods to perform as part of the measurement. Configuring a
quantitation method includes selecting the desired applications to run and
configuring the parameters for the selected applications. Parameters may
include a Normalization Factor, or effective sample height, which transforms
the microplate OD values to a comparable value for the same sample in a 1cm
cuvette. This Normalization Factor is applied as a divisor of the sample
reading.
Note: To create or run quantitation protocols for a FilterMax Multi-Mode
Microplate Reader, a genomic filter slide, which contains narrow bandwidth
260nm and 280nm filters must be installed and configured.
Figure 7-13 Configuring a Quantitation Method in Method Selection
To select and configure a quantitation method:
1. In Method Selection, select the Applications tab (Figure 7-13).
2. In Select Methods, select the desired quantitation applications to run:
 260 Abs Value: net absorbance value at 260 nm. This selection is
required when the Analysis option Concentration is selected in
General Settings and samples are quantified against standards
supplied in the plate layout. See Configuring Labware Layout
Settings on page 151.
 DNA Purity: measures absorbance at both 260 nm and 280 nm and
determines the ratio as an indicator of nucleic acid purity. Pure DNA
has a ratio around 1.8, while pure RNA has a ratio around 2.0.
 Pure dsDNA Concentration (260): measures absorbance at 260 nm
and determines the concentration of pure dsDNA by normalizing the
measurement values to equivalent 1cm cuvette measurements and
transforming the equivalent values into concentrations. Requires
input of a normalization factor and reciprocal coefficient of
extinction.
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Pure RNA Concentration (260): measures absorbance at 260 nm and
determines the concentration of pure RNA by normalizing the
measurement values to equivalent 1 cm cuvette measurements and
transforming the equivalent values into concentrations. Requires
the input of a normalization factor and reciprocal coefficient of
extinction.
 Pure ssDNA Concentration (260): measures absorbance at 260 nm
and determines the concentration of pure ssDNA by normalizing the
measurement values to equivalent 1cm cuvette measurements and
transforming the equivalent values into concentrations. Requires
the input of a normalization factor and reciprocal coefficient of
extinction.
3. If no blank wells were added in Layout Settings, alternative Blank
Correction options are available. Select Blank Correction to enable it for
the protocol and select the desired type of correction to use:

Note: Reliable results require blank subtraction prior to performing
further calculations. If the plate layout does not include blank wells, it
is recommended that Blank Correction is selected.

Pre read high: requires a pre read plate filled with blanks that is read
prior to the measurement plate; subtracts the buffer measurement
value of a well from the analyte measurement value of the same
well for each well read. Use this option when blank variability from
well to well is high.
Note: The blank plate should come from the same batch as the
measurement plate with blank replicates dispensed into all wells. A
blank replicate should contain all components common to all samples
except for the analyte. Leaving blank wells empty may be an
approximation and should be validated for each assay.
Note: When running a quantitation protocol with a pre read, the blank
plate is measured first. After reading the blank plate, the plate carrier
opens and the protocol pauses to allow the blank plate to be removed
and the measurement plate to be loaded.

Pre read low: requires a pre read plate filled with blanks that is read
prior to the measurement plate; averages the buffer measurement
values from all wells read and subtract the average from the analyte
measurement value for each well. Use this option when blank
variability from well to well is low, or relatively constant.
Note: The blank plate should come from the same batch as the
measurement plate with blank replicates dispensed into all wells. A
blank replicate should contain all components common to all samples
except for the analyte. Leaving blank wells empty may be an
approximation and should be validated for each assay.
Note: When running a quantitation protocol with a pre read, the blank
plate is measured first. After reading the blank plate, the plate carrier
opens and the protocol pauses to allow the blank plate to be removed
and the measurement plate to be loaded.
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
Fixed Constant: subtracts a fixed constant for 260 nm, 280 nm, and
320 nm (if 320 nm Background Correction is selected)
measurements from each well. Use this option when the average
blank value is stable for the given set of assay conditions. Enter the
desired constants for 260 and 280, and 320. Default values are
displayed in Table 7-1.
Table 7-1 Default blank values for Fixed Constanta
Wavelength
Blank Value
260
0.065
280
0.047
320
0.035
a
Values are based on using TE buffer in a Costar 96-well microplate.
4. Select 320 nm Background Correction to subtract the blanked
measurement value at 320 nm from the value of each well. This
background correction partially compensates for the turbidity of
samples and is in addition to blank subtraction. Selection of this option
results in an additional measurement being made at 320 nm.
Note: Reading background at 320nm does not substitute for blank
correction, as the 320nm sample read is typically different from the
blank reads at 260 nm and 280nm.
5. Select the Parameters tab to display the parameter information. Only
the parameters for the methods selected on the Applications tab are
displayed.
6. Configure the Parameters as appropriate. The application each
parameter is associated with is identified in the front of each parameter
name. See Table 7-2.
Table 7-2 Quantitation Parameters by Application Type
Application
Parameter
Default
Value
260 Abs Value
Has no
parameters.
N/A
Normalization
Factor [cm] (also
called effective
sample height)
Default:
0.29aValid
range: 0.01
to 1
Pure dsDNA Conc (260)
Normalization
Factor [cm] (also
called effective
sample height)
Default:
0.29a Valid
range: 0.01
to 1
abs = absorbance value at 260 nm, as
defined in 260 Abs Value above
norm = normalization factor
1/E = reciprocal coefficient of extinction
dilution = dilution factor
Reciprocal
Coefficient of
Extinction
[(µg/mL) /
(OD/cm)]
Default: 50
Valid range:
1 to 100
A[xxx] = sample measurement at xxx nm
B[xxx] = blank measurement at xxx nm
DNA Purity
A[xxx] = sample measurement at xxx nm
B[xxx] = blank measurement at xxx nm
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Table 7-2 Quantitation Parameters by Application Type (cont’d)
a
Application
Parameter
Default
Value
Pure RNA Conc (260)
Normalization
Factor [cm] (also
called effective
sample height)
Default:
0.29aValid
range: 0.01
to 1
abs = absorbance value at 260 nm, as
defined in 260 Abs Value above
norm = normalization factor
1/E = reciprocal coefficient of extinction
dilution = dilution factor
Reciprocal
Coefficient of
Extinction
[(µg/mL) /
(OD/cm)]
Default: 40
Valid range:
1 to 100
Pure ssDNA Conc (260)
Normalization
Factor [cm] (also
called effective
sample height)
Default:
0.29aValid
range: 0.01
to 1
abs = absorbance value at 260 nm, as
defined in 260 Abs Value above
norm = normalization factor
1/E = reciprocal coefficient of extinction
dilution = dilution factor
Reciprocal
Coefficient of
Extinction
[(µg/mL) /
(OD/cm)]
Default: 37
Valid range:
1 to 100
Default value for normalization factor is based on 100 µL of DNA in a 96-well plate. This
value is dependent on a number of factors, including volume of DNA, buffer viscosity,
plate type, and well shape, and should be determined empirically and modified for the
specific application. See Determining the Normalization Factor. See Table 7-3 for typical
values for DNA in a 96-well plate.
Table 7-3 Typical Values for Normalization Factora
a
Volume of DNA
Normalization Factor
(Effective Sample Height)
100 µL
0.29 cm
150 µL
0.44 cm
200 µL
0.59 cm
Values are based on volume of DNA in TE buffer in a Costar 96-well microplate. See
Determining the Normalization Factor for instructions on determining normalization
factors for different labware types.
7. As desired, in Options select Temperature to set the temperature of the
instrument before reading. Properties for Temperature appears.
8. As necessary, in Set Temperature, enter the desired microplate
chamber temperature in degrees Celsius. In protocols that perform
measurements only at visible wavelengths (>359 nm), the minimum
temperature that may be set is 3°C (5.4°F) above ambient. When the
protocol performs measurements in the UV range the minimum
temperature is 4°C (7.2°F) above ambient. The maximum temperature
that may be set is 45°C (113°F).
Note: The temperature remains at the current setting until overridden
by another Set Temperature preparation method, by changing the
temperature in Manual Control, or by turning the instrument off and
on.
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9. As necessary, in Wait for Temperature, select the desired option:
 True: wait until instrument reaches the Set Temperature before
reading the plate.
 False: immediately read the plate.
10. As desired, in Options select Shake Before Read to shake the microplate
before reading, if desired.
CAUTION! Shake low density plates, such as 6-well or 48-well plates, at low
speed only. Shaking low density plates at higher speeds may cause liquid in
wells to spill.
11. As necessary, in Shake Intensity, select the desired intensity of shaking:
Low, Medium, or High.
12. As necessary, in Shake Interval, enter the length of time in seconds (018000) to shake the microplate.
Note: Shaking efficiency for 24-well to 384-well plates has been
improved in versions 2.0 and above. The Shake Interval for protocols
originally created for use with version 1.0 of the software may need to
be reduced.
13. As



necessary, in Shake Mode, select the desired shaking pattern.
Linear: shakes from side to side.
Orbital: shakes labware in a circular pattern.
Squared (FilterMax Multi-Mode Microplate Readers only): shakes
labware in a square pattern, moving at right angles.
14. Click Report Options and select the method information and
measurement results data included in printouts:
 Method Information: details about the configured method, including
technique type and filters used.
 Raw Data: results from each kinetic cycle or scan point. Available for
kinetic and scan measurements only.
 Print Status: status indicating whether or not the well was read
successfully.
15. Click Next to configure the Variables (if selected in the General Settings,
see Configuring Variables on page 170) or to configure the Data
Reduction, see Configuring the Data Reduction on page 172.
Determining the Normalization Factor
The normalization factor is a value that relates the measurement value of a
microplate well to its equivalent value in a 1cm cuvette. This normalization
factor depends on the microplate type, well shape and dimensions, sample
volume and viscosity, and other factors, and can be determined experimentally
by comparing the value of a sample in a cuvette to the same sample measured
in a microplate.
Note: It is recommended for best results that the assay conditions for the
microplate are replicated as closely as possible when determining the
normalization factor. Therefore, use a DNA standard diluted in assay buffer
with UV-transparent microplates and quartz glass cuvettes. The microplate
used with the instrument should be optimized (see Performing the
Optimization Read on page 140) and measurements made using the 260 nm
filter on the genomic filter slide.
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To experimentally determine the normalization factor:
1. Aliquot a sample and a sample blank into separate 1cm pathlength
cuvettes.
Note: Select a sample concentration within the dynamic range of the
spectrophotometer at 1cm pathlength and in the instrument.
2. Measure the sample and the sample blank in a spectrophotometer.
Record the blanked value (absorbance of the sample minus absorbance
of the blank) as the Absorbance value per 1cm.
3. Aliquot a volume of the same sample and sample blank equal to the
volume that will be read with unknown samples into several wells of the
microplate which will be used for measurements. This enables
replicates to be performed and yields a more accurate result.
4. Measure the microplate on the instrument. Record the blanked value
(absorbance of the sample minus absorbance of the blank) as the
Absorbance value of the plate.
5. Calculate the normalization factor by dividing the Absorbance value of
the plate (step 4) by the Absorbance value per 1 cm (step 2). For
example:
Table 7-4 Example Calculation of Normalization Factor
Blank
Sample
Absorbance
(Sample Blank)
1 cm cuvette
0.066
0.816
0.750 (step 2)
microplate
0.064
0.314
0.250 (step 4)
Normalization
Factor
0.250/0.750 = 0.333
(step 5)
Configuring Variables
Up to ten variables may be defined for use in formulas configured in the
protocol (Figure 7-14). Variables are typically used with test kits that have
cutoff values or standard correction values based on lot number.
Note: Variables appear only when selected in General Settings for an Analysis
protocol. See Configuring General Settings on page 148.
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Figure 7-14 Configuring Variables in an Analysis Protocol
To configure variables:
1. Select the Number of variables to be configured. Up to ten variables may
be configured. Entry fields for each variable appear.
2. For each variable, enter the desired numeric Value.
3. For each variable, enter the desired Name to be used in reports.
4. Click Report Options and select Definition to include all variable names,
values, and names used in reports in printouts, if desired.
5. Click Next to configure the Data Reduction. See Configuring the Data
Reduction on page 172.
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Configuring the Data Reduction
Data reduction allows for multiple data calculations of measurement results
from the detection methods in the protocol. Raw data results can be
summarized to a single value. Results from the data reduction are used in
analysis. Passes allow for additional data reduction using a previous data
reduction. Results from the data reduction are displayed in the results and can
be used for transformation, concentration, cutoff values, or for validation.
The raw data from each detection method is assigned a character that is listed
besides the detection method in the Select Methods pane (For example, the
first detection method is labeled “A”, the second “B”, and so on). The formula
A+B+C would add the raw data from the three detection methods represented
by A, B, and C. Detection methods that include multi-point data results can be
expanded to view the additional labels (Figure 7-15).
Multipoint methods should have a data reduction (kinetic, area scan,
wavelength scan). If the user does not enter a data reduction, the software
creates a standard data reduction once the protocol is saved.
Figure 7-15 Data Reduction Page with Labels
To configure the data reductions:
1. In Data Reduction Method click Add new to use a data reduction
method.
2. Select either the Functions tab or the Formula tab. The Functions tab
provides access to predefined data reduction methods. The Formula tab
allows for a manually creating a data reduction formula.
Note: The Functions tab is accessible for certain types of detection
methods and only on the first pass of the data reduction.
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3. If using the Functions tab (Figure 7-16):
 Select the desired Basis of Evaluation using the selection box.
Note: Only detection methods that can be used as a basis of evaluation
are available for selection.





As necessary, select a Pre-Read Method. The Pre-Read method will
subtract the measurement values of the Pre-Read method from the
measurement values of the method selected in Basis of Evaluation.
When necessary, using the Pre-Read Method menu select whether
the Pre-Read method will subtract the average for all wells in the
Pre-Read method (Mean), or subtract on a well-by well basis.
(Well).
Enter a name for the Data using the Name of Data field. This
information is used later during data output in the reduced data
results.
As necessary, enter any notes about the data reduction using the
Notes field.
In the Reduction Properties section, using the Function field select
the predefined data reduction method to use.
Note: Each type of read mode has its own set of predefined data
reduction functions. See Table A-1 on page 241 for details about the
data reduction methods available for sequence measurements.

As necessary, configure the function’s parameters using the fields
displaying below the Function field.
Figure 7-16 Functions Tab
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OR
4. If using the Formula tab (Figure 7-17):
 Enter a formula for the desired data reduction using any of the
mathematical operators (except for <, >, or =) or mathematical
functions listed in Mathematical Operators and Functions on
page 249.
Note: The Formula field can be used to create ratios, such as A/B, or
corrected ratios, such as (A–C)/(B–C).




Enter a name for the Data using the Name of Data field. This
information is used later during data output in the reduced data
results.
Enter the units for the data using the Name of Units field. This
information is used for information purposes only during data
output.
As necessary, enter any notes about the formula using the Notes
field.
Select the wells to apply the data reduction formula to using the
Calculate Formula for Controls section. Only the selected well types
will be used in the current data reduction formula.
Figure 7-17 Formula Tab
5. To add an additional data reduction click Add new.
OR
To add an additional pass of data reduction formulas click Add new Pass.
OR
To add an additional pass of data reduction formulas click Add new Pass.
Note: Up to twenty-six data reductions may be added for each pass. Up
to twenty-six passes can be added.
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6. Optionally, click the Syntax Helper button, and the Syntax Helper window
(Figure 7-18) appears. Syntax Helper helps in the creation of the
correct syntax for accessing advanced data values. Access raw
measurement data, blanked data (if blanks are used) or data resulting
from any previous data reduction.
Note: Select the insertion point inside of the formula before starting
Syntax Helper.
Figure 7-18 Syntax Helper window
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Available mathematical functions (Figure 7-19) included in Syntax
Helper are minimum, maximum, mean, median, standard deviation or
coefficient of variation.
Figure 7-19 Syntax Helper mathematical functions selection
Select attributes from the drop-down menus (Figure 7-20) to combine
data with mathematical functions and validity constraints to render a
desired configuration.
Figure 7-20 Syntax Helper Validity
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Note: Depending on the type of the data and mathematical function,
validity can be plate-wide (valid for the whole plate), cycle wide (valid
for the selected cycle), identifier (for example, maximum value of the
specified control). Depending on function type and selected validity
there are additional parameters available to specify a cycle for which
the function should be applied.
Figure 7-21 Syntax Helper parameters
Conclude by clicking on the Insert Syntax button to apply the syntax to
the formula at the point of insertion.
7. Add and configure additional passes by repeating steps 2 through 6.
8. Click Next.
Configuring a Transformation Formula
Use Transformation to configure an algebraic formula (X' =) that is applied to
every well in a set of reduced data (X) (Figure 7-22). The transformation
formula must include X, and may include mathematical operators, but not
relational or logical operators. See Mathematical Operators and Functions on
page 249 for more information about supported mathematical operators.
Note: X represents the result value of a data reduction selected in the Basis of
Evaluation field.
Note: Transformation is available for configuration only when selected in
General Settings for an Analysis protocol. See Configuring General Settings
on page 148.
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Figure 7-22 Configuring a Transformation Formula
To configure a transformation formula:
1. In the Basis of Evaluation field, select the desired data reduction to use
for the transformation.
2. In X' =, enter the desired transformation formula. See Mathematical
Operators and Functions on page 249 for detailed information about
mathematical operators supported by the software.
3. In Name of X', enter a new name for the transformation formula. The
name appears in printed reports and in protocol configuration screens
where a basis for evaluation must be selected.
4. Click Report Options and select the transformation information included
in printouts:
 Definition: the transformation formula and name are listed.
 Print in Matrix: the transformed result calculated for each sample will
display in a measurement results matrix corresponding to the plate
layout.
 Print in List: the transformed result calculated for each sample will
display in a list of measurement results.
 Print Status: status indicating whether or not the well was read
successfully.
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Configuring Concentration
Use Concentration to select a curve fitting method and configure concentration
and response formulas for standards (Figure 7-23).
Note: Concentration is available for configuration only when selected in
General Settings for an Analysis or Quantitation protocol. See Configuring
General Settings on page 148.
Figure 7-23 Configuring Concentration Parameters
Note: Standards may be deleted or inserted with a special key stroke
combination. Use CTRL+Y to delete a standard and CTRL+N to insert a
standard.
To configure a standard curve and standards:
1. To use a stored Standard Curve select Use stored Standard Curve. Click
Select to select the standard curve. Using the Standard Curve Record
Selection Form dialog select the specific record to use as the standard
curve or Always use the most recent record from the Database. Click Next
to continue.
OR
To use the standard curve definition from another protocol select Copy
Standard curve definition from another protocol to this protocol. Click Select
to select the protocol to copy the standard curve from. Click Next to
continue.
OR
Select a Curve Type: Point to Point, Linear Regression, Cubic Spline, Four
Parameter Fit, or Polynomial. See Table 7-5 more information about
curve fitting methods.
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Table 7-5 Curve Fitting Methods
Method
Description
Linear regression
Construction of a straight line using the least
squares method with the highest possible
approximation to all standard points. Requires a
minimum of 3 standard points.
Point to Point
Direct connection of all standard points. Requires
a minimum of 3 standard points.
Cubic Spline
All standard points are connected by the best
fitting curve.
Can only be used for nonlinear and nonsigmoid
functions.
Requires a minimum of 3 standard points.
4 Parameter Fit
This procedure can be used only to characterize
sigmoid curves. The curve is calculated according
to the formula:
Example
a = zero dose response (upper asymptote)
d = infinite dose response (lower asymptote)
c = dose level which results in a response
midway between a and d
b = slope factor
Requires a minimum of 3 standard points.
The X and Y axes are fixed:
X = logarithm
Y = linear
Polynomial
Calculates the least squares fit through points
using the formula:
Requires a minimum of n+1 standard points,
where n is the order of the polynomial.
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2. Select the Number of standards to configure. Up to 12 standards may be
configured in a protocol. Standards configured in the labware layout are
automatically added to Concentration.
3. In Extrapolation, enter a percentage value to extrapolate the standard
curve above and below the highest and lowest standard points in the
curve, if desired. Extrapolation may be configured for all curve fitting
methods.
4. In Y-Axis, select the Base for the axis.
 Reduction: the reduced data from the protocol run.
 Transformation: the value calculated using the transformation
formula configured in Transformation. This option is available only
when Transformation is configured in the protocol. See Configuring
a Transformation Formula on page 177.
Note: Transformation is the default name for transformation formulas.
If a different name is entered in Transformation, that name appears in
Base. See Configuring a Transformation Formula on page 177.
5. In Y-Axis, select the Type of scale for the Y-Axis: linear or logarithmic.
Note: Type is not available when configuring a four parameter fit curve.
6. In X-Axis, enter a Name for the axis, if desired.
7. In X-Axis, select the Type of scale for the X-Axis: linear or logarithmic.
Note: Type is not available when configuring a four parameter fit curve.
8. Click Report Options and select the concentration information and data
included in printouts:
 Definition: curve type, parameters, and statistics, such as intercept
and slope.
 Graph: the standard curve.
 Print in Matrix: the transformed result calculated for each sample will
display in a measurement results matrix corresponding to the plate
layout.
 Print in List: the transformed result calculated for each sample will
display in a list of measurement results.
 Print Status: status indicating whether or not the well was read
successfully.
9. In the Graph Setup tab, edit each Response Formula and the
corresponding Concentration. Response formulas may contain any
controls, standards, or variables defined in the test, as well as
numerical constants and mathematical operators. A response formula is
often simply the value of a measured standard, which is expressed as
STD1, STD2, or STD3.
Note: See Mathematical Operators and Functions on page 249 for
detailed information about mathematical operators supported by the
software.
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10. If configuring a linear regression curve fitting method, select the
Validation tab to validate the protocol based on acceptable coefficient of
correlation, if desired (Concentration Options Tab on page 183).
Note: The Validation tab appears only when configuring a linear
regression curve fitting method.
Figure 7-24 Configuring Standard Curve Validation Parameters
11. Select Linear Regression Check Correlation to enable validation.
12. In Linear Regression Min Correlation, enter the minimum correlation
percentage value for the test to be valid.
13. In the Options tab, it is possible to configure an algebraic formula that is
applied to the calculated concentration of every well (Figure 7-28). The
formula shall include X, and may include mathematical operators, but
not relational or logical operators. For detailed information about
mathematical operators supported by the software, see Mathematical
Operators and Functions on page 249.
Note: X represents the result value of the concentration calculation. For
example: X/DF => divides the concentration values of every well by
the dilution factor (DF), which is entered in the plate layout settings.
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Figure 7-25 Concentration Options Tab
Configuring Cutoff Values
Use Cutoff to configure qualitative evaluations that classify measured samples
into groups according to defined cutoff formulas or values (Figure 7-26). Up to
ten cutoff groups may be configured.
Note: Cutoff is available for configuration only when selected in General
Settings for an Analysis or Quantitation protocol. See Configuring General
Settings on page 148.
Figure 7-26 Configuring Cutoff Values
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To configure cutoff groups and formulas:
1. Select the Basis of Evaluation:
 Concentration: the value calculated using the standard curve
configured in Concentration. This option is available only when
Concentration is configured in the protocol. See Configuring
Concentration on page 179.
 Transformation: the value calculated using the transformation
formula configured in Transformation. This option is available only
when Transformation is configured in the protocol. See Configuring
a Transformation Formula on page 177.
 Reduction: reduced data from the protocol run. See Configuring the
Data Reduction on page 172.
Note: Transformation is the default name for transformation formulas.
If a different name is entered in Transformation, that name appears in
Basis of Evaluation. See Configuring a Transformation Formula on
page 177.
2. Select the Number of groups to configure.
3. Enter a Name for each group.
4. Enter the formulas and/or values used to classify samples into groups.
The cutoff formula or value entered represents the maximum value
included the group being configured.
Note: The results calculated from the formulas or the values entered
must ascend. Results or values that do not ascend will generate an
error during protocol runs.
5. Click Report Options and select the cutoff information and data included
in printouts:
 Definition: the basis for measurement, group names, and cutoff
values and/or formulas configured.
 Print in Matrix: the cutoff group classification for each sample
appears in a measurement results matrix corresponding to the plate
layout.
 Print in List: the cutoff group classification for each sample appears
in a list of measurement results.
 Print Status: status indicating whether or not the well was read
successfully.
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Configuring Validation Rules
Use Validation to configure up to ten validation rules (Figure 7-27). Protocol
runs that do not meet the conditions specified in the rules are marked as
invalid.
Note: Validation is available for configuration only when selected in General
Settings for an Analysis or Quantitation protocol. See Configuring General
Settings on page 148.
Figure 7-27 Configuring Validation Rules
To configure validation rules:
1. Select the Number of formulas to configure. Up to ten formulas may be
configured.
2. Select the Basis of Evaluation for the first formula:
 Concentration: the value calculated using the standard curve
configured in Concentration. This option is available only when
Concentration is configured in the protocol. See Configuring
Concentration on page 179.
 Transformation: the value calculated using the transformation
formula configured in Transformation. This option is available only
when Transformation is configured in the protocol. See Configuring
a Transformation Formula on page 177.
 Data Reduction Results: reduced data from the protocol run. See
Configuring the Data Reduction on page 172.
Note: Transformation is the default name for transformation formulas.
If a different name is entered in Transformation, that name appears in
Basis of Evaluation. See Configuring a Transformation Formula on
page 177.
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3. Enter the first formula. Formulas may contain:
 any controls, standards, or variables defined in the protocol. For
controls and standards, use the same labels displayed in Layout
Settings; for example, STD1 for standard 1, C2 for control 2, P5 for
positive control 5, or N2 for negative control 1.
 numeric constants.
 mathematical operators and functions and logical operators. See
Mathematical Operators and Functions on page 249 for a complete
list of supported operators and functions.
Table 7-6 Example Test Validation Formulas
Application
Validation Formula
The results from a protocol run are valid only if the
mean absorption value of the positive control wells
P2 is less than or equal to 0.8 OD.
P2<=0.8
The results from a protocol run are valid only if both 0.1<=C1 AND
controls are within the linear range of the
C1<=3.0 AND
instrument.
0.1<=C2 AND
C2<=3.0
4. Repeat steps 2 through 3 for any additional formulas.
5. Click Report Options and select Definition to include the validation
configuration and state (pass/fail) for all rules in printouts.
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Configuring Output Settings
Use Output Settings to specify which measurement result export, view, and
print actions are performed automatically when a protocol run completes
(Figure 7-28). An external software application, such as a notification utility,
may also be configured to execute when a run completes.
Figure 7-28 Configuring Output Settings
To configure Output Settings:
1. Select export, view, and print output options as desired. Table 7-7
describes the options available. Further output options are described in
Table 7-8, Table 7-9, and Table 7-10.
2. Click Execute a program after protocol executes to display options for
configuring an external software application to run after the protocol
run is completed. See Configuring a Program to Execute after a Protocol
Run Completes on page 195 for more information.
3. Click Run protocol now to run the protocol. See Running Protocols on
page 197 for more information about running protocols.
Note: When creating or editing a protocol, the protocol must be saved
before it can be run. After saving the protocol, Run Protocol appears for
protocols that were edited; new protocols must be selected in the
Protocol Selection List before they may be run.
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Table 7-7 Output Options
Output Option
Description
Export to Microsoft
Excel
Saves results in a format compatible with Microsoft Excel
according to the Data Format configuration in Software Settings.
See Configuring the Data Format on page 43, and automatically
opens Excel after completing a protocol run.
Note: Versions of Excel prior to Office 2000 are not
supported by the Export to Microsoft Excel function, but
can open measurement results stored in tab-delimited
data .dat files.
Note: When using Microsoft Excel 2002 or higher, the
Multi-Mode Analysis Software will format the Excel
worksheets with the appropriate column width and apply
formatting to display the status of a measurement value
(such as bold and colors).
User Defined Excel
Export
Saves results in a format compatible with Microsoft Excel with
customizable output attributes. Upon clicking the User Defined
Excel Export checkbox, click the Define button to invoke the
Excel Export Definition Dialog. Within this dialog designate more
specific output attributes as needed. For more details, see User
Defined Excel Export on page 189.
Show Result Viewer Automatically opens the measurement results in the Result
Viewer after completing a protocol run. See Viewing
Measurement Results in the Result Viewer on page 217.
Create XML and
DAT data files
Automatically exports measurement results to a tab-delimited
data (*.dat) file and an XML file. These files may be opened by
software applications compatible with tab-delimited data or XML
files.
Note: The directory where the data files are saved is
configured in System Settings. See Selecting a Directory
for Saving Exported Measurement Results on page 37.
Export Data to
SoftMax Pro File
Format
Automatically exports measurement results to a text file in a
format that can be used to import the data into SoftMax Pro
Software. See Exporting Data to SoftMax Pro File Format on
page 193.
Note: The directory where the data file is saved is
configured in System Settings. See Selecting a Directory
for Saving Exported Measurement Results on page 37.
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Start SoftMax Pro
Software and
Import Data
Automatically exports measurement results to a formatted text
file, and then opens SoftMax Pro Software and imports the data
from the text file after completing a protocol run. See Starting
SoftMax Pro Software and Importing Data on page 194.
Print options
Automatically prints the results after completing a protocol run.
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User Defined Excel Export
Upon completion of a protocol run, results may be exported into a user-defined
format for viewing in Microsoft Excel. A preview of the exported results may be
seen in the Preview window at the lower left portion of the Export Option
Dialog window (Figure 7-29).
To configure User Defined Excel Export:
1. In Output Settings, click the Define button. The Excel Export Definitions
Dialog window appears (Figure 7-29).
Figure 7-29 Export Option Dialog window
The Options list to the left of the Excel Export Definitions Dialog window
allows for selection of data layout options. These options may be
selected on the left portion of the window:
 General
 List Format
 Matrix Format
 List Format Blanked Data
 Matrix Format Blanked Data
Further options specific to workbook and worksheet export properties
may be combined to meet specific needs. These further export options
are summarized in:
 Workbook Export Options on page 190
 Worksheet Export Options on page 191
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Workbook Export Options
Options (Figure 7-30) specific to workbook export properties are available as
follows:
Table 7-8 Workbook Export Options
Properties
Description
Export Automatic
Multi-Mode Analysis Software automatically determines the file
name and exports data to that file name.
Export to Open
Workbook
Data results are exported to the currently open workbook on the
controlling PC.
New Workbook
Data results are exported to a new workbook on the controlling
PC.
Existing Workbook
Data results are exported to an existing workbook on the
controlling PC.
Export disabled
Data results will not be exported to an Excel file.
Figure 7-30 Workbook options
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Worksheet Export Options
Options (Figure 7-31) specific to worksheet export properties are available as
follows:
Table 7-9 Worksheet Export Options
Properties
Description
Automatic
Multi-Mode Analysis Software automatically determines the
worksheet name and exports data to a sheet with that name.
Active Sheet on
Export
Data results are exported to the currently open worksheet on
the controlling PC.
New Sheet
Data results are exported to a new worksheet on the controlling
PC.
Existing Sheet
Data results are exported to an existing worksheet selected by
the user on the controlling PC.
Figure 7-31 Worksheet options
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New Sheet and Existing Sheet Export Options
Further worksheet options (Figure 7-32) allow for selection of data layout
options for both new and existing sheets.
Table 7-10 Further Worksheet Export Options
Properties
Description
Column
Determines the start column for export.
Row
Determines the start row for export.
Formatting
Allows export of data using user-defined formatting assigned to
a numbered template.
Export data only
Allows export of data without well, horizontal and vertical
labels.
Export Mean Data
Allows export of all mean values of each data reduction step.
Export CV Data
Allows export of CV values of each data reduction step.
Export SD Data
Allows export of Standard Deviation values of each data
reduction step.
Figure 7-32 Further Worksheet Options
Note: New Sheet and Existing Sheet only: A preview of the selected format is
shown in the Preview window.
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Exporting Measurement Data to SoftMax Pro Software
At the conclusion of a read, Multi-Mode Analysis Software can export the raw
data, plate settings, wavelength settings, kinetic parameters, and scan
parameters to a text file that can then be imported into SoftMax Pro Software.
Results, reductions, and template settings are not exported. Certain data
might be altered to match the parameters for the data differ in each program.
For example, in Multi-Mode Analysis Software, you can specify a shorter
interval time for a kinetic read than can be specified in SoftMax Pro Software.
Note: Before importing Multi-Mode Analysis Software data into SoftMax Pro
Software, you must select an instrument in SoftMax Pro Software that
supports the read types, methods, and modes that were used in the
Multi-Mode Analysis Software protocol.
There are two methods of exporting Multi-Mode Analysis Software data to
SoftMax Pro Software:
• Export Data to SoftMax Pro File Format exports measurement results to a
text file in a format that can be used to import the data into SoftMax
Pro Software.
• Start SoftMax Pro Software and Import Data exports measurement results
to a formatted text file, and then opens SoftMax Pro Software and
imports the data from the text file.
Exporting Data to SoftMax Pro File Format
At the conclusion of a read, Multi-Mode Analysis Software can export the data
to a text file that can then be imported into SoftMax Pro Software. To do this,
select the Export Data to SoftMax Pro File Format check box in the Output Settings
window. See Configuring Output Settings on page 187.
The text file is save in the directory where Multi-Mode Analysis Software saves
its measurement results export files. See Selecting a Directory for Saving
Exported Measurement Results on page 37.
The exported text file is given a unique name based on the Result Name and
Protocol Name for the read.
For example, if the Result Name is 20100922-021736 and the Protocol Name is
x_FilterMaxF5_Abs_384well_405_kin, then the text file will have the following
name: 20100922-021736_x_FilterMaxF5_Abs_384well_405nm_kin SMP.txt
When you save the data from the Results Viewer, the raw data is exported
again to a formatted text file. For information about saving data from the
Results Viewer, see Saving Measurement Results on page 228.
For information about importing a text file into SoftMax Pro Software, see the
user guide provided with the program.
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Starting SoftMax Pro Software and Importing Data
If you have SoftMax Pro Software installed on the same computer as
Multi-Mode Analysis Software, then you can export the data at the conclusion
of the read and then start SoftMax Pro Software to automatically import the
data. To do this, select the Start SoftMax Pro Software and Import Data check box
in the Output Settings window. See Configuring Output Settings on page 187.
Before starting SoftMax Pro Software, an export file is generated and saved.
For information about how to locate this export file, see Exporting Data to
SoftMax Pro File Format on page 193.
After Multi-Mode Analysis Software finishes the read and exports the data,
SoftMax Pro Software starts and then automatically imports the data from the
text file.
Figure 7-33 Data imported into SoftMax Pro Software
You can immediately work with the imported data in SoftMax Pro Software, or
save the data to work with it later. For information about working with data in
SoftMax Pro Software, see the user guide provided with the program.
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Configuring a Program to Execute after
a Protocol Run Completes
Output Settings can be configured to open an external software application
after completing a protocol run. If the selected application supports entering
commands using a command line interface, a specific command for the
application may also be configured.
To configure a program to run after a protocol is executed:
1. In Output Settings, click Execute a program after protocol executes. Two
configuration fields appear (Figure 7-34).
Figure 7-34 Configuring an External Software Application in Output
Settings
2. In Execute Program, enter the complete path of the program to run; for
example, C:\Windows\System32\Net.exe. Net.exe is a small utility
supplied with Windows operating systems that sends messages to
computers on the same network.
OR
Select Choose an external program to run at the end of measurement. The
Open dialog appears.
3. In the Open dialog, browse to the location of the desired application
and select it.
4. Click Open to return to Output Settings. The selected path appears in
Execute Program.
5. If the selected application supports command line parameters, in
Command line parameter, enter the desired parameter. For example, if
using Net.exe, entering the parameters “SEND” “Workstation1”
“Finished” instructs the application to send the message, “Finished,” to
a computer named Workstation1 when the protocol run completes.
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Signing a Protocol
When GxP Permissions is enabled on the system, protocols may be signed to
prevent the configured parameters from being edited. Protocols may be signed
at any time after the configuration is complete.
Protocols may be signed by users who are assigned a role containing the Sign
permission. See Configuring Roles for Multi-Mode Analysis Software User
Accounts on page 76 for more information about roles and permissions.
To sign a protocol:
1. In the Protocol Selection List, select the protocol to sign.
2. From the tool bar, click Sign the selected protocol.
OR
From the menu bar select Actions > Sign the selected protocol.
OR
Right-click on the selected labware and select Sign the selected protocol.
3. The Sign the Selected Item dialog appears.
4. In the Sign the Selected Item dialog, add comments and an electronic
signature by following the instructions in Adding Electronic Signatures
and Comments to Items on page 84.
Creating a Protocol from a Template
Template protocols are used to create a protocol based upon the selected
template. Pre-defined settings appear as the protocol is configured.
To create a protocol from a template:
1. From the tool bar, click Create.
OR
From the menu bar select Actions > Create a new protocol.
OR
Right-click in the Protocol Selection List and select Create a new protocol.
2. The Select Application Type dialog appears.
3. Select the Templates tab.
Figure 7-35 Selecting the Application Type - Templates Tab
4. Select the Group and Type for the template. To obtain more information
about the template protocol click on Info.
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5. Click Next to configure the protocol. The Create Protocol dialog
appears, displaying General Settings. See Configuring General Settings
on page 148.
Note: Pre-defined settings appear as the protocol is configured. See
Creating Protocols on page 146 for detailed information about
configuring protocol parameters.
Running Protocols
Saved protocols may be accessed and run at any time, either on an instrument
or in simulation mode. The run options available are different for each mode.
For more information, refer to:
• Running a Protocol on an Instrument on page 197
• Running a Protocol When Simulation Mode is Enabled on page 209
Running a Protocol on an Instrument
Running a protocol on an instrument performs measurements on samples and
outputs results data following the parameters configured in the protocol.
Note: To create or run quantitation protocols for a FilterMax Multi-Mode
Microplate Readers instrument, a genomic filter slide, which contains narrow
bandwidth 260 nm and 280 nm filters, must be installed and configured.
To run a protocol on an instrument:
1. In the Protocol Selection List, select the protocol to run.
2. From the tool bar, click Run.
Note: When running an Analysis protocol with variables configured,
Variables appear as the first screen in Run Protocol. Change the values
of the variables, if desired, and click Next to continue. Prepare to Run
appears.
OR
From the menu bar select Actions > Run the selected protocol.
OR
Right-click on the selected protocol and select Run the selected protocol
from the menu.
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3. The Prepare to Run dialog appears (Figure 7-36).
Figure 7-36 Preparing to Run a Protocol on an Instrument
4. Enter a new unique Result Name, if desired. The name must not match
any previous result names, including those pending deletion.
5. Specify the Number of Samples to measure per plate.
6. Specify the Number of Plates to read. Changing the number of plates to
read will increase or decrease the number of plates to read as specified
in the plate layout of the protocol.
7. Use the Read Sample ID’s button to import .DAT file format samples.
Note: If a multi-plate layout is specified in the plate layout only the first
plate will contain controls and all following plates will contain only
samples. If a multi-plate layout is not selected in the plate layout for
every plate will contain the controls specified in the plate layout. For
more information see Configuring Labware Layout Settings on
page 151.
Note: Clicking on the plate layout icon provides an expanded view of
the microplate in its current configuration. Limited editing of the plate
is allowed from this expanded view.
8. As required, select Plate is lidded.
CAUTION! It is important to select Plate is lidded when the plate has a lid due to
the low reading height.
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9. Use Eject Plate Carrier and Close Plate Carrier to load the microplate into
the instrument, if necessary.
Note: If running a quantitation protocol with either Pre read low or Pre
read high selected for blank correction, insert the blank plate first.
During the protocol run, there will be a pause which requests the
measurement plate be inserted.
10. Select the orientation that matches how the plate is positioned on the
plate carrier:
 Landscape: the long edges of the plate run parallel to the front of
the instrument, with well A1 located in the upper left corner.
 Portrait: the short edges of the plate run parallel to the front of the
instrument, with well A1 located in the upper right corner.
 Opposite Landscape: the edges of the plate run parallel to the front
of the instrument, with well A1 located in the lower right corner.
 Opposite Portrait: the short edges of the plate run parallel to the
front of the instrument, with well A1 located in the lower left corner.
Note: Labware optimization should be performed for the selected plate
orientation.
Note: Well A1 is identified in the plate graphic by a red highlight.
Clicking on the layout preview will zoom the view of the plate layout.
11. When preparing to run a luminescence, fluorescence top, fluorescence
bottom (SpectraMax Paradigm Multi-Mode Detection Platform only),
fluorescence polarization, or time-resolved (TRF) protocol, select
Optimize Read Height to automatically determine and set the optimal
read height used in the protocol run. See Optimizing Read Height
(FilterMax 5 Multi-Mode Microplate Reader) on page 200 or Optimizing
Read Height (SpectraMax Paradigm Multi-Mode Detection Platform) on
page 203.
Note: Optimize Read Height is available for the FilterMax 5 Multi-Mode
Microplate Reader and SpectraMax Paradigm Multi-Mode Detection
Platform only.
Note: SpectraMax Paradigm Multi-Mode Detection Platform only —
Optimize Read Height is not available for Luminescence detection
cartridges. For Luminescence detection cartridges the optimum read
height is the closest distance between the read head and the
microplate, as derived from the labware definition, and confirmed by
the plate height detection.
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12. Click Run to start the protocol run. The Run Protocol runtime window
appears (Figure 7-37).
Figure 7-37 Run Protocol Runtime Display
Optimizing Read Height (FilterMax 5 Multi-Mode
Microplate Reader)
The FilterMax 5 Multi-Mode Microplate Reader features an objective lens that
may be moved up and down to optimize the read height used in luminescence,
fluorescence intensity top, fluorescence polarization, and time-resolved
fluorescence protocols. Read height is the distance between the top or bottom
(using bottom reading) surface of the microplate being read and the surface of
the objective lens. Optimizing read height matches the focus of the optics with
the sample volume. This maximizes the raw signal, which yields the highest
precision and maximum sensitivity.
Read height is optimized using the Read Height Optimization Wizard
(Figure 7-40). A single sample with a known maximum signal and volume is
placed on the same type of microplate used in the protocol. The sample is
measured using the same, or very similar, detection method used in the
protocol.
The optimized read height is saved in the protocol and is used for all
subsequent runs of the protocol until reset by performing a new optimization
or manually selecting a read height option.
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To optimize the read height:
1. In Run Protocol, select Optimize Read Height. When clicking on Run, the
Read Height Optimization Wizard appears (Figure 7-40).
2. Select the well measured to perform the optimization. Prepare Labware
appears (Figure 7-38).
Figure 7-38 Selecting the Well Read in the Read Height Optimization
3. Use a standard or sample position with a good signal or pipette liquid
with a known maximum signal to a single well on the microplate used in
the optimization. The concentration of the optimization sample should
be at least ten times greater than the detection limit. The sample
volume should be the same as that of samples measured in the
protocol. If using a layout with standards, the standard well closest to
the center of the plate is pre-selected. If not using a layout with
standards, the first sample is pre-selected.
Note: When optimizing reading height for a fluorescence protocol,
make sure the optimization sample is the same fluorescent substance
the detection method is configured to detect.
4. Load the plate into the instrument.
5. In Prepare Labware, select the well containing the optimization sample
(Figure 7-38).
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6. Click Next to start the optimization. Optimization in Progress appears
(Figure 7-39). The optimization may take several seconds or up to
several minutes depending on the detection methods used.
Figure 7-39 Read Height Optimization in Progress
7. When the read is finished, Optimization Complete appears, displaying
the Optimized Read Height (Figure 7-40). While the optimization is in
progress, click Cancel to stop the optimization read and close the
wizard, if desired.
Figure 7-40 Read Height Optimization Completed
8. In the Optimization Complete window the Optimized Read Height is
displayed. As desired, modify the Custom Read Height.
9. Click Save to save the optimized read height in the protocol. The
optimized read height is used for all subsequent runs of the protocol
until reset by performing a new optimization or manually selecting a
read height option.
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Optimizing Read Height (SpectraMax Paradigm
Multi-Mode Detection Platform)
The SpectraMax Paradigm Multi-Mode Detection Platform features an objective
lens that may be moved up and down to optimize the read height used in
luminescence, fluorescence intensity top and bottom, fluorescence
polarization, and time-resolved fluorescence protocols. Read height is the
distance between the top or bottom (using bottom reading) surface of the
microplate being read and the surface of the objective lens. Optimizing read
height matches the focus of the optics with the sample volume. This
maximizes the raw signal, which yields the highest precision and maximum
sensitivity.
Read height is optimized using the Read Height Optimization Wizard
(Figure 7-41). A single sample with a known maximum signal is placed on the
same type of microplate used in the protocol. The sample is measured using
the same, or very similar, detection method used in the protocol.
The optimized read height is saved in the protocol and is used for all
subsequent runs of the protocol until reset by performing a new optimization
or manually selecting a read height option.
To optimize read height:
1. In Run Protocol, select Optimize Read Height. When clicking on Run, the
Read Height Optimization Wizard appears.
Note: SpectraMax Paradigm Multi-Mode Detection Platform only —
Optimize Read Height is not available for Luminescence detection
cartridges. For Luminescence detection cartridges the optimum read
height is the closest distance between the read head and the
microplate, as derived from the labware definition, and confirmed by
the plate height detection.
2. Select the well measured to perform the optimization. Prepare Labware
appears (Figure 7-41).
Figure 7-41 Selecting the Well Read in the Read Height Optimization
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3. Use a standard or sample position with a good signal or pipette liquid
with a known maximum signal to a single well on the microplate used in
the optimization. The concentration of the optimization sample should
be at least ten times greater than the detection limit. The sample
volume should be the same as that of samples measured in the
protocol. If using a layout with standards, the middle most standard
well is pre-selected. If not using a layout with standards, the first
sample is pre-selected.
Note: When optimizing reading height for a fluorescence protocol,
make sure the optimization sample is the same fluorescent substance
the detection method is configured to detect.
4. Load the plate into the instrument.
5. In Prepare Labware, select the well containing the optimization sample
(Figure 7-41).
6. Click Next to start the optimization. Optimization in Progress appears
(Figure 7-42). The optimization may take several seconds or up to
several minutes depending on the detection methods used.
Figure 7-42 Read Height Optimization in Progress
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7. When the read is finished, Optimization Complete appears, displaying
the Optimized Read Height (Figure 7-43). While the optimization is in
progress, click Cancel to stop the optimization read and close the
wizard, if desired.
Figure 7-43 Read Height Optimization Completed
8. In Optimization Complete, click Save to save the optimized read height
in the protocol. The optimized read height is used for all subsequent
runs of the protocol until reset by performing a new optimization or
manually selecting a read height option.
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Viewing the Run Protocol Runtime Display
Once a protocol run begins, the Run Protocol runtime display shows
information about the status and results of the current run.
Figure 7-44 Run Protocol Runtime Display
Run Protocol displays the following information:
• Elapsed Time: how much time has elapsed since the protocol started, in
HH:MM:SS format.
• Temperature: the current temperature inside the instrument, in ºC.
• Current Method: the current detection or preparation method that is
being executed.
• Raw Data (tab): dynamically displays the raw data for the selected
detection method as it is read.
• Graph (tab): dynamically graphs the raw data as it is read for Kinetic or
Scan measurements.
The protocol run may be stopped at any time using the Stop button at the
bottom right of the screen.
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During certain preparation methods, such as Wait and Pause, a Continue or
Skip button appears. The Continue button functions as described below
depending on the Current Method:
• Pause: the protocol run pauses and displays a message. The protocol
remains paused until the user selects Continue to resume the protocol
(Figure 7-45).
Note: In Quantitation protocols using Pre read low or Pre read high for
blank correction, Pause is used to exchange the blank plate with the
measurement plate.
Figure 7-45 Pause During a Protocol Run
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•
Wait: the protocols waits a predefined length of time as specified in the
protocol definition before continuing the protocol run. The user may
choose to end the wait and continue before the full length of time
passes by clicking Skip (Figure 7-46).
Figure 7-46 Wait During a Protocol Run
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•
Set Temperature: if the protocol is configured to set the temperature
and Wait is True, the protocol pauses until the Set Temperature is
reached. The user may resume the protocol at any time by clicking
Skip, and the protocol continues at the current temperature; that is, it
does not reach the desired Set Temperature (Figure 7-47).
Figure 7-47 Set Temperature During a Protocol Run
Running a Protocol When Simulation Mode is Enabled
Running a protocol in simulation mode allows the protocol configuration to be
tested using simulated data before performing the protocol on actual samples.
Simulated data is either generated randomly or read from a data file.
Simulation mode is automatically enabled when the host computer is not
connected to an instrument. When an instrument is connected, simulation
mode may be enabled manually in Instruments. See Enabling Simulation Mode
on page 56.
To run a protocol in simulation mode:
1. In the Protocol Selection List, select the protocol to run.
2. From the tool bar, click Run the selected protocol.
Note: When running an Analysis protocol with variables configured,
Variables appears as the first screen in Run Protocol. Change the
values of the variables, if desired, and click Next to continue. Prepare
to Run appears.
OR
From the menu bar select Actions > Run the selected protocol.
OR
Right-click on the selected protocol and select Run the selected protocol.
3. Prepare to Run appears (Figure 7-48).
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Figure 7-48 Preparing to Run a Protocol in Simulation Mode
4. Enter a new unique Result Name, if desired.
5. Select Check to generate random data to run the protocol using random
data generated by the software, if desired.
6. In Use this data simulation file for this read:
 Leave the directory path of the simulated data path as configured to
use the data file selected in Software Settings. See Selecting
Simulated Data Files on page 35.
 Browse to the location where the desired data file is saved and
select it.
Note: Results from prior measurements saved in .dat format may be used as
simulated data files. See Configuring Output Settings. Simulated data files are
used when the number of measurement points in the simulated protocol run
is the same as those present in the data file. When the number of
measurement points is different, the software generates random data.
When a different simulated data file is selected in Prepare to Run Protocol,
the file is used for the current simulated run only. After the simulated run has
finished, the data file defaults to the file selected in Software Settings. See
Selecting Simulated Data Files.
7. Click Run or Next to run the selected protocol.
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Editing Protocols
Parameters configured in a protocol may be edited. When the GxP Permissions
module is enabled on the system, signed protocols may not be edited.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Edit permission may edit protocol definitions. See
Configuring Roles for Multi-Mode Analysis Software User Accounts on page 76
for more information about roles and permissions.
To edit a protocol:
1. In the Protocol Selection List, select the protocol to edit.
2. From the tool bar, click Edit the selected protocol.
OR
From the menu bar select Actions > Edit the selected protocol.
OR
Right-click on the selected protocol and select Edit the selected protocol.
OR
Double-click on the selected protocol.
3. The Edit Protocol window appears (Figure 7-49).
Figure 7-49 Editing an Fluorescence Polarization Protocol
4. Edit the parameters in each Edit Protocol screen as desired. See
Creating Protocols on page 146 for detailed information about
configuring protocol parameters.
5. Click Save to close Edit Protocol and save the changes.
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Copying Protocols
Copies may be made of existing protocols. A copy of an existing protocol may
be used as a template for a new protocol using the same technique.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Copy permission may create copies of protocols. See
Configuring Roles for Multi-Mode Analysis Software User Accounts on page 76
for more information about roles and permissions.
Signed protocols may be copied. Copies of signed protocols are unsigned and
may be edited.
To make a copy of a protocol:
1. In the Protocol Selection List, select the protocol to copy.
2. From the tool bar, click Make a copy of the selected protocol. A copy of the
selected protocol appears in the Protocol Selection List.
OR
From the menu bar select Actions > Make a copy of the selected protocol.
OR
Right-click on the selected protocol and select Make a copy of the selected
protocol.
Note: The default name format for copied protocols is Copy of
OriginalName. To change the name, open the protocol for editing and
enter the new protocol name. See Editing Protocols on page 211.
Deleting Protocols
Protocols that are no longer used to perform measurements may be deleted
from the Protocol Selection List. When the optional GxP Permissions module is
enabled on the system, signed protocols may not be deleted.
Note: When GxP Permissions is enabled on the system, only users assigned a
role containing the Delete permission may delete protocols. See Configuring
Roles for Multi-Mode Analysis Software User Accounts on page 76 for more
information about roles and permissions.
To delete a user-defined protocol:
1. In the Protocol Selection List, select the protocol to delete.
2. From the tool bar, click Delete the selected protocol.
OR
From the menu bar select Actions > Delete the selected protocol.
OR
Right-click on the selected protocol and select Delete the selected
protocol.
3. The delete message dialog appears.
4. Click Yes to delete the selected protocol. The protocol is moved to the
Trash list (to permanently remove the protocol from the database see
Deleting and Restoring Items on page 48.
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Note: Multiple protocols may be selected by holding down the CTRL key
while selecting each protocol desired.
Printing Protocol Configuration Information
Information about the protocol configuration and sample layout may be
printed separately from measurement results.
To print protocol configuration information:
1. In the Protocol Selection List, select the protocol to print.
2. From the tool bar, click Print.
OR
From the menu bar select Actions > Print the selected protocol.
OR
Right-click on the selected protocol and select Print the selected protocol.
Note: Depending on how Print Settings are configured, Print or Print
Preview may display before the protocol configuration prints. See
Configuring Print Settings on page 38 for more information about
enabling and disabling Print and Print Preview.
3. If Show Printer Settings and Print Preview are not enabled in Print
Settings, no additional configuration is required.
OR
If the Print dialog appears, configure printing options as desired and
click OK.
Note: Print is the dialog box that appears when Show Printer Settings is
selected.
OR
If the Print Preview dialog appears, use the tool bar controls to change
the magnification, layout view, or pages displayed, if desired.
4. In the Print Preview dialog, click Print to print out the measurement
results.
5. In the Print Preview dialog, click Close to close the window.
Note: Clicking Close without first clicking Print cancels printing.
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Exporting and Importing Protocols
A protocol can be exported to an XML file, which may be imported at a later
time to restore the configuration saved in the file or shared with a copy of
Multi-Mode Analysis Software installed on another system. Detection methods
and labware configurations used in the protocol are also saved in the export
file.
Protocols that use default detection methods and labware installed with MultiMode Analysis Software may be imported and exported; however, default
methods and labware are not imported with the protocol because these items
are present on all systems and may not be edited, deleted, or overwritten.
Note: When GxP Permissions is enabled, signed protocols may be exported for
use on another system; however, electronic signatures attached to the
protocol are not retained, which allows the protocol to be edited. Importing a
signed method to the system from which it was originally exported is not
permitted because signed methods may not be deleted or overwritten.
To export a protocol:
1. In the Protocol Selection List, select the protocol to export.
2. From the File menu, click Export > Protocol. The Browse for Folder dialog
appears.
3. In the Browse for Folder dialog, browse to the folder where the
exported protocol will be saved.
OR
Click Make New Folder to create a new folder where the exported
protocol will be saved.
4. Click OK to export the protocol. The exported protocol is saved using
the default file name format, Protocol_ProtocolName.xml. To import the
file at a later date, the filename must not be changed.
To import a protocol from an exported XML file:
1. From the File menu, select Import > Protocol. The Open dialog appears.
2. In the Open dialog, browse to and select the desired XML file to import.
3. Click Open. The protocol, as well as detection methods and labware
used in the protocol, are imported. Any default detection methods or
labware used in the protocol are not imported because default methods
and labware may not be edited, deleted, or overwritten. Instead, the
imported protocol uses the same default methods and labware stored in
the software.
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8
Overview
Measurement results from each protocol run are stored in the Multi-Mode
Analysis Software database and are accessed from the Results Selection List
(Figure 8-1), which also provides access to result actions and the ability to
search for specific results based on names and/or dates.
Figure 8-1 Accessing Measurement Result Actions
Measurement results selected from the list are viewed in the Result Viewer,
which, depending on measurement type, displays raw data from each
measurement technique, measurement cycle or point, reduced data, and
graphs. Results calculated using a data reduction method may be reevaluated
using different parameters.
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Results may be reevaluated by editing analysis parameters configured in the
protocol.
Result actions covered in this section include:
• Viewing Measurement Results in the Result Viewer on page 217
• Viewing and Reevaluating Results from an Analysis Application on
page 229
• Viewing Exported Measurement Results on page 235
Note: This section includes viewing measurement results exported to
Microsoft Excel from the Result Viewer and results exported to XML or
data files at the completion of a protocol run.
• Signing Measurement Results on page 238
• Deleting Measurement Results on page 239
• Printing Measurement Results on page 239
To view measurement results:
1. From the navigation pane, click Results. The Results Selection List
appears (Figure 8-1).
2. In the Results Selection List, select the desired results and from the
tool bar, click View. The Result Viewer appears (Figure 8-2).
OR
Use the search options to locate specific results. Table 8-1 describes the
search options available. Results matching the search parameters
appear in the Results Selection List.
Table 8-1 Measurement Results Search Options
216
Search
Option
Description
Result Name
Enter a partial or complete Result Name. Searching for result names
may also be limited to specific dates configured in Date.
Date
Select the desired range option: Less Than or Equal, Equal, Greater
Than or Equal, or Between, then select the desired dates.
Protocol Name
Enter a partial or complete Protocol Name. Searching for protocol
names may also be limited to specific dates configured in Date.
Go
Perform the search. Matching results appear in the Results Selection
List.
Clear
Clear search results and display all measurement results in the
Results Selection List.
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Viewing Measurement Results in the Result Viewer
Measurement results accessed from the Results Selection List are viewed in
the Result Viewer (Figure 8-2). Results are displayed in a series of tabs. The
tabs displayed depend on the measurement types configured in the protocol;
for example, reduced data is not displayed when data reduction is not
configured.
Results may also be printed, saved, or exported to a Microsoft Excel
spreadsheet using the Result Viewer actions. Results calculated using data
reduction may be reevaluated by editing data reduction parameters or
selecting a different method.
Figure 8-2 Viewing Raw Data
This section covers Result Viewer functionality provided in the Data screen,
which is displayed for analysis applications, including:
• Viewing Raw Data on page 218
• Viewing Blanked Data on page 219
• Viewing Reduced Data on page 221
• Viewing Mean Data on page 223
• Viewing Graphs on page 224
• Recalculating Data Reduction on page 227
• Exporting Measurement Results to Microsoft Excel on page 228
• Saving Measurement Results on page 228
Note: The Result Viewer also appears transformed measurement results for
analysis options configured in the protocol. See Viewing and Reevaluating
Results from an Analysis Application on page 229.
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Viewing Raw Data
The Raw Data tab appears all data measured during the protocol run
(Figure 8-3). Depending on the measurement types configured in the protocol,
the left pane lists all detection methods, measurement cycles, or wells in a
tree view. Selecting a method, cycle, or well displays measured values and
status in the right panel. A result may be rejected as an outlier when the value
falls outside of the expected result.
Note: Results for single-point measurements are displayed in Raw Data.
To view raw data:
1. Select the Raw Data tab, if necessary.
Figure 8-3 Viewing Raw Data
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2. From the tree view in the left pane, select the detection method,
measurement cycle, or well desired to view. Results and status appear
in the right pane. Table 8-2 describes the status indicators that may be
displayed.
Table 8-2 Well Status Indicators
Status
Description
OK
The sample was measured successfully.
Error
The sample was not measured because an instrument error
occurred.
Overflow
No result is available because the value exceeds the
indication limit.
Underflow
No result is available because reduced data could not be
calculated.
Extrapolated
The result fell within the extrapolation percentage set for a
standard curve.
Not Evaluated
The measurement result was not evaluated.
Rejected
The sample was rejected as an outlier by a user. Samples
may be rejected in any tab displaying a matrix view of
measurement results.
Unused
The sample was not selected for measurement in the
protocol.
Viewing Blanked Data
The Blanked Data tab displays the well identifier, and the blanked data for each
well measured during the protocol run (Raw Data – Blank Data = Blanked
Data). The Blanked Data tab displays this information in a matrix
corresponding to the plate layout (Figure 8-4). Depending on the
measurement types configured in the protocol, the left pane lists all detection
methods, measurement cycles, or wells in a tree view. Selecting a method,
cycle, or well displays measured values and status in the right panel.
Note: The Blanked Data tab is only available if the plate layout has blank wells
specified in the plate layout.
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To view blanked data:
1. Select the Blanked Data tab, if necessary.
Figure 8-4 Viewing Blanked Data
2. From the tree view in the left pane, select the detection method,
measurement cycle, or well desired to view. Blank results and the well
status appear in the right pane. Table 8-3 describes the status
indicators that may be displayed.
Table 8-3 Well Status Indicators
Status
220
Description
OK
The sample was measured successfully.
Error
The sample was not measured because an instrument error
occurred.
Overflow
No result is available because the value exceeds the
indication limit.
Underflow
No result is available because reduced data could not be
calculated.
Extrapolated
The result fell within the extrapolation percentage set for a
standard curve.
Not Evaluated
The measurement result was not evaluated.
Rejected
The sample was rejected as an outlier by a user. Samples
may be rejected in any tab displaying a matrix view of
measurement results.
Unused
The sample was not selected for measurement in the
protocol.
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Viewing Reduced Data
The Reduced Data tab is displayed when the detection methods configured in
the protocol use data reductions (Figure 8-5). You can view PathCheck®
Pathlength Measurement Technology adjusted results in the Reduced Data tab.
Wells may also be rejected as outliers when the calculated value falls outside
of the expected result. Reduced data for the plate may be recalculated with
outliers removed, if desired.
Figure 8-5 Viewing Reduced Data for a measurement Performed in a
Multiwavelength Protocol
Note: Reduced data may be also shown as 2D or 3D graphic by clicking the
graphic symbol at the top left corner of the plate grid.
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For a Quantitation protocol, each Quantitation application that was performed
as part of the protocol is listed in Reduced Data. Results for each application
type can be viewed by selecting the desired application.
Figure 8-6 Viewing Reduced Data for a Measurement Performed in a
Quantitation protocol
To view reduced data, reject outliers, and recalculate reduced data:
1. Select the Reduced Data tab, if necessary.
2. If multiple detection methods with data reduction techniques are
configured in the protocol, select the desired data reduction technique
from the left pane. Reduced data for selected method appear in the
right pane.
OR
For a Quantitation protocol, if multiple Quantitation applications are
selected for the protocol, select the desired application. Reduced data
for the selected Quantitation application is displayed.
3. To reject a well as an outlier, right-click on the desired well and select
Reject Well. A red X appears over the well and the Reevaluate current
measurement results button appears on the tool bar.
Note: Multiple wells may be rejected as outliers. Rejected wells may be
included in the measurement results again by right-clicking on each
well desired and selecting Accept Well.
4. From the tool bar, click Reevaluate current measurement results to
recalculate the results with outliers removed.
Note: The Reevaluate button appears on the tool bar only when a
parameter in the results, such as data reduction technique, has been
edited.
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Viewing Mean Data
The Mean Data and Mean Data List tabs display the well identifier, mean
(reduced) value, well status, coefficient of variation (CV%), and standard
deviation for replicate groups. The Mean Data tab displays this information in a
matrix corresponding to the plate layout (Figure 8-7); the Mean Data List tab
displays the same information in a list. Mean data are calculated and displayed
for each result of the data reduction.
Note: The Mean Data tab is only available if the protocol has replicates in the
plate layout.
Wells may be rejected as outliers when the calculated value falls outside the
expected result. The results may be recalculated with outliers removed, if
desired.
Figure 8-7 Viewing Mean Data
To view mean data:
1. Select the Mean Data tab, if necessary.
2. Select Show Status to show the measurement status for each well, if
desired. Table 8-2 describes the status indicators that may be
displayed.
3. Select Show Well Identifier to show identifiers for each well, if desired.
4. To reject a well as an outlier, right-click on the desired well and select
Reject Well. A red X appears over the well and the Reevaluate current
measurement results button activates on the tool bar.
Note: Multiple wells may be rejected as outliers. Rejected wells may be
included in the measurement results again by right-clicking on each
well desired and selecting Accept Well.
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5. Click Reevaluate current measurement results to recalculate the results
with outliers removed.
Note: The Reevaluate button appears on the tool bar only when a
parameter in the results, such as an outlier, has been changed.
Note: If Sample-ID was used on the run protocol screen, Sample-ID is
also displayed here.
Viewing Graphs
The Graphs tab displays graphs for all measured wells on a plate (Figure 8-8).
The detection methods configured in the protocol determine the types of
graphs displayed.
Figure 8-8 Viewing Kinetic Measurement Graphs
Detailed graphs for individual samples, all samples in a column or row, or all
samples on the plate may be viewed and printed. To view detailed graphs for:
• an individual sample: click in the desired well. Depending on
measurement type, a two- or three-dimensional graph of the selected
result appears. See Viewing Two-Dimensional Graphs on page 225 or
Viewing Three-Dimensional Graphs on page 226.
Note: Detailed graphs for individual samples may be viewed for all
measurement types, even when the graphs displayed appear to be
empty.
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•
a row or column: click in the desired row or column header. A threedimensional graph of results for the row or column appears. See
Viewing Three-Dimensional Graphs on page 226.
Note: Rows and columns may not be selected for multiwavelength and
area scan measurement results.
•
all samples on the plate: click in the upper left corner of the plate layout
(Figure 8-10). A three-dimensional graph of all results on the plate
appears. See Viewing Three-Dimensional Graphs on page 226.
Note: All samples may not be selected for multiwavelength and area
scan measurement results.
Viewing Two-Dimensional Graphs
Results for individual single-point, kinetic, and linear scan measurements are
displayed in two-dimensional graphs (Figure 8-9). Two-dimensional graphs
may be printed.
Figure 8-9 Viewing a Two-Dimensional Absorbance Graph
To print the graph:
1. From the File menu, select Print.
Note: Depending on how Print Settings are configured, Print and/or
Print Preview may display before the protocol configuration prints. See
Configuring Print Settings on page 38 for more information about
enabling and disabling Print and Print Preview.
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2. If Show Printer Settings and Print Preview are not enabled in Print
Settings, the graph prints automatically.
OR
If the Print dialog appears, configure printing options as desired and
click OK.
Note: Print is the dialog box that appears when Show Printer Settings is
selected.
OR
If Print Preview appears, use the tool bar controls to change the
magnification, layout view, or pages displayed, if desired. See Printing
Measurement Results on page 239 for more information about Print
Preview.
Viewing Three-Dimensional Graphs
Selecting an individual area scan graph, a row, column, or all samples in the
Graph tab displays a three-dimensional graph (Figure 8-10). Threedimensional graphs may be rotated horizontally or vertically and printed.
Figure 8-10 Viewing a Three-Dimensional Area Scan Graph
To rotate the graph:
1. Use the vertical scroll bar to rotate the graph vertically.
2. Use the horizontal scroll bar to rotate the graph horizontally.
3. Double-click on the graph to start and stop a continuous animated
horizontal rotation of the graph.
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To print the graph:
1. From the File menu, click Print.
OR
Right-click on the graph and select Export Dialog and then select Print.
Note: Depending on how Print Settings are configured, Print and/or
Print Preview may display before the protocol configuration prints. See
Configuring Print Settings on page 38 for more information about
enabling and disabling Print and Print Preview.
2. If Show Printer Settings and Print Preview are not enabled in Print
Settings, the graph prints automatically.
OR
If the Print dialog appears, configure printing options as desired and
click OK.
Note: Print is the dialog box that appears when Show Printer Settings is
selected.
OR
If the Print Preview dialog appears, use the tool bar controls to change
the magnification, layout view, or pages displayed, if desired. See
Printing Measurement Results on page 239 for more information about
Print Preview.
Recalculating Data Reduction
The Edit tab allows reduced data to be recalculated by editing the parameters
of the current data reduction method or by selecting a different data reduction
method (Figure 8-11). Data reduction may be recalculated for any detection
method configured with data reduction in the protocol.
Figure 8-11 Changing Data Reduction Parameters in the Results Viewer
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To change parameters:
1. Click the Edit tab, if necessary.
Note: Refer to Data Reduction Techniques on page 241 for details about
the data reduction methods available for different measurement types.
2. In the Edit tab, click Report Options and select the method information
and measurement results data included in printouts:
 Method Information: details about the configured method, including
technique type and filters used.
 Graph: graphs of results for all measured samples.
 Raw Data: results from each detection method, kinetic cycle, or well
scanned.
3. Click Reevaluate current measurement results to recalculate the results
using the new data reduction configuration.
Note: The Reevaluate button appears on the tool bar only when a
parameter in the results, such as a data reduction technique, has been
edited.
Exporting Measurement Results to Microsoft Excel
Results displayed in the Result Viewer may be exported to Microsoft Excel.
Exported results are saved in the directory selected in Directory Settings. See
Selecting a Directory for Saving Exported Measurement Results on page 37.
To export results to Excel:
1. From the tool bar, select Export the current measurement results to Excel.
Excel opens automatically.
2. In Excel, note that exported results appear in multiple workbooks. A
workbook may contain general information and raw data for a single
detection method, or general information and reduced data.
Note: See Exporting Measurement Results to Microsoft Excel on
page 228 for information about viewing exported results in Excel.
Saving Measurement Results
The measurement results currently being viewed may be saved to the
database from within the Result Viewer, which allows results that have been
reevaluated by editing data reduction or analysis parameters to be saved with
a different name. Optionally, parameters edited in the Result Viewer may be
saved in the original protocol definition.
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To save measurement results:
1. From the tool bar, click Save the current measurement results to the
database. The question dialog appears, asking if the existing results
should be overwritten.
2. Click Yes to overwrite existing results. The results are overwritten and a
message dialog appears, asking if parameters edited in the Result
Viewer should also be saved to the protocol definition. Proceed to
Step 3.
Note: When GxP Permissions is enabled on the system, measurement
results that have been signed may not be overwritten. See Signing
Measurement Results for more information about signing results.
OR
Click No to save the results with a different name. Result Name
appears.
3. Enter a new name for the results and click OK. The results are saved to
the database. The message dialog appears, asking if parameters edited
in the Result Viewer should also be saved to the protocol definition.
4. Click Yes to save the new parameters to the protocol definition.
Note: When GxP Permissions is enabled on the system, parameters
changed in the Result Viewer may not be saved to protocols that have
been signed.
OR
Click No to ignore any changes made and retain the original parameters
configured in the protocol.
Viewing and Reevaluating Results from an
Analysis Application
The Result Viewer appears measurement results, transformed data from the
analysis options configured in the protocol, and the parameters currently
configured for each analysis option.
Multiple “what if?” analyses on transformed data may be performed by editing
the parameters configured for an analysis option and then reevaluating the
data with the new parameters.
This section covers:
• Viewing Results From an Analysis Protocol on page 230
• Reevaluating Results from an Analysis Protocol on page 233
Note: See Viewing Measurement Results in the Result Viewer on page 217 for
information about viewing results reported in the Data screen, recalculating
data reduction, and exporting and saving results.
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Viewing Results From an Analysis Protocol
All analysis options configured in the protocol appear in the navigation pane of
the Result Viewer (Figure 8-12). Transformed data and parameters for the
selected analysis option appear in a series of tabs.
To view analysis results and parameters:
1. In the navigation pane, select the desired analysis option. Only analysis
options configured in the protocol are listed. A series of tabs with
results from the selected analysis option appears (Figure 8-12).
Figure 8-12 Viewing Existing Transformation Parameters in the Results
Viewer
2. Select the tab desired to view. Table 8-4 describes each tab and lists
which analysis options display the tab.
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Table 8-4 Measurement Results Tabs Displayed for Analysis Options
Tab
Description
displays In
Layout View
displays transformed results and
measurement status for the selected
analysis option in a matrix corresponding
to the plate layout.
Transformation
Concentration Cutoff
Note: Results may be rejected as
outliers in any Layout View tab. To
reject a result, right click on the
desired sample and select Reject Well.
Results may be reevaluated with
outliers removed.
List View
displays transformed results and
measurement status for the selected
analysis option in a list.
Transformation
Concentration Cutoff
Standard Curve
displays a graph of the standard curve. See Concentration
Changing the Standard Curve Graph View
on page 231 for information about
customizing the graph display.
Parameters
displays the parameters used to calculate
Variables
the transformed data currently displayed in Transformation
the Layout View and List View tabs.
Concentration Cutoff
Validation
Edit
Edit the parameters configured for the
analysis option using the same
configuration screen that appears in the
Create Protocol wizard. See Reevaluating
Results from an Analysis Protocol on
page 233.
Variables
Transformation
Concentration Cutoff
Validation
Changing the Standard Curve Graph View
The standard curve graph view may be changed by zooming in on a selected
region or changing view options.
To zoom in on a region of the graph:
1. Position the cursor at the desired starting point for the region, then
click and hold the mouse button down. The cursor icon changes to a
magnifying glass.
2. Drag the mouse until the desired region is selected. The selected region
is highlighted in black.
3. Release the mouse button. The selected region is displayed.
To zoom out and view the graph at the original size:
• Right-click on the graph and select Undo Zoom from the menu that
appears.
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To change view options:
• Right-click on the graph and select a view option from the menu that
appears. Table 8-5 describes the view options available.
Table 8-5 Standard Curve Graph View Options
View Option
Description
Viewing Style
Select how the graph is displayed: in Color, Monochrome, or
Monochrome with symbols.
Numeric Precision
Select the numeric precision of graph data displayed on the
screen or exported to text files. Precision up to three decimal
positions may be specified.
Plotting Method
Select how the graph is plotted. Line is the default method.
Data Shadows
Enable shadows that give the graph a 3-D appearance.
Grid Options
Customize the grid display. Grid lines may be displayed,
hidden, or changed to a different style, such as thick, thin, or
dashed.
Include Data Labels
Select to display labels for data points on the curve.
Mark Data Points
Select to mark each data point with a small circular symbol.
Undo Zoom
Select to display a zoomed graph at the original size.
Available only when the graph is zoomed.
Maximize
Select to display a full-screen version of the graph. Close the
maximized view by pressing the Esc key or clicking on the
title bar of the maximized window.
Customization Dialog
Open the Customization dialog box. Customization options
are grouped in a series of tabs:
• General: Enter a title for the graph, change the viewing
style (color or monochrome), set the numeric precision
up to 3 decimal positions, and change the grid
appearance.
• Plot: Change the plotting method, and enable or disable
3-D shadows and data point markers.
• Subsets: This tab contains no configurable options.
• Axis: Change the properties of the X- and Y-axes.
• Font: Change the font used for titles and labels.
• Color: Change the color of any graph attribute except
data points and lines.
• Style: Change the colors and styles of data points and
lines displayed in the graph.
Note: Many of the options available in Customization
are the same as those in the menu that appears when
right-clicking on the graph.
Export Dialog
232
Open the Export dialog box.
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Multi-Mode Analysis Software User Guide
Reevaluating Results from an Analysis Protocol
Multiple “what if?” analyses on transformed data may be performed by editing
the parameters configured for an analysis option and then reevaluating the
data with the new parameters. The parameters used to calculate the
transformed data currently displayed in the Result Viewer are viewed in the
Parameters tab. Parameters are edited in the Edit tab.
To reevaluate measurement results:
1. In the left pane, select an analysis option to edit. Only analysis options
configured in the protocol are listed. The selected analysis option
appears (Figure 8-13).
Note: Select Data to view measurement results and edit data reduction
parameters configured in the protocol. See Viewing Measurement
Results in the Result Viewer on page 217 for more information.
Figure 8-13 Viewing Existing Transformation Parameters in the Results
Viewer
2. Select the Layout View or List View tab to view the current transformed
data. Layout View displays data in a matrix corresponding to the plate
layout; List View displays the same data in a list.
3. Select the Parameters tab to view the parameters used to calculate the
transformed data currently displayed; for example, Figure 8-13 shows
transformation parameters.
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Viewing Measurement Results
4. Select the Edit tab to edit parameters as desired (Figure 8-14).
Parameters in the Edit tab are identical to those in the corresponding
screen in the protocol configuration. Refer to the appropriate section for
more information:
 Configuring Variables on page 170
 Configuring a Transformation Formula on page 177
 Configuring Concentration on page 179
 Configuring Cutoff Values on page 183
 Configuring Validation Rules on page 185
Figure 8-14 Figure8.14Editing Transformation Parameters in the Results
Viewer
5. Edit additional analysis options, if desired.
6. From the tool bar, click Reevaluate current measurement results to
recalculate the results using the edited parameters.
Note: The Reevaluate button appears on the tool bar only when a
parameter in the results, such as the transformation formula, has been
changed.
7. Optionally, save the reevaluated results with a different name to
preserve a record of changes made to the parameters. See Saving
Measurement Results on page 228.
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Viewing Exported Measurement Results
Measurement results may be exported manually from the Results Viewer or
automatically at the end of a protocol run when export options are configured
in Output Settings.
Two file export and save options are available:
• Export to Microsoft Excel: saves results in a format compatible with
Microsoft Excel, and automatically opens Excel. See Viewing
Measurement Results in Microsoft Excel on page 235 for more
information about viewing exported results in Excel.
Note: Multi-Mode Analysis Software automatically determines the
appropriate export method based on the version of Microsoft Office
installed on the host computer. XML (.xml) files are exported when
Office XP is installed. When Office 2000 installed, the measurement
results are copied into a new spreadsheet which must be saved in
Excel. Versions of Excel prior to Office 2000 are not supported by the
Export to Microsoft Excel function, but can open measurement results
stored in tab-delimited data (.dat) files.
•
Create XML and DAT data files: saves results in XML and tab-delimited
data (.dat) files, which may be opened by compatible software
applications.
Note: See Configuring Output Settings on page 187 for more
information about configuring export and file options.
To view saved measurement results:
1. Open the desired software application.
2. Browse to the directory where exported measurement results are
stored, and open the desired file. Exported measurement results are
stored in the data directory selected in Software Settings. See Selecting
a Directory for Saving Exported Measurement Results on page 37.
Viewing Measurement Results in Microsoft Excel
When measurement results for a protocol run are exported to Excel, multiple
workbooks (spreadsheets) are created. A workbook is created for the raw data
read for each detection method configured in the protocol. Reduced and
transformed data are included in a separate workbook.
This section covers:
• Viewing Protocol and Measurement Information on page 236
• Viewing Raw Data on page 237
• Viewing Reduced and Transformed Data on page 237
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Viewing Measurement Results
Viewing Protocol and Measurement Information
Information about the system and parameters configured in the protocol is
saved in the General worksheet. General is included in all worksheets exported
from a set of measurement results (Figure 8-15).
Figure 8-15 Viewing Protocol Information in the General Worksheet (excerpt)
To view the General worksheet:
1. In Excel, access either workbook containing the desired results.
2. Select the General tab in the lower left corner of the window.
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Viewing Raw Data
Measurement results exported to Excel display raw data in matrices
corresponding to the plate layout (Figure 8-16). Data from each measurement
cycle or point is presented in a separate sheet within the workbook.
Note: Results from protocols containing multiple detection methods export
raw data from each detection method to a separate workbook. The title of
workbooks containing raw data always includes the name of the detection
method.
Figure 8-16 Viewing Reduced Data (excerpt)
To view raw data:
1. In Excel, access the workbook containing raw data for the desired
measurement results. Titles of workbooks containing raw data always
contain the name of a specific detection method configured in the
protocol; for example, ABS340 (Figure 8-16).
2. In the worksheet, select the Cycle tab for the desired measurement
cycle.
Viewing Reduced and Transformed Data
Reduced and transformed data are exported to a different Excel workbook
than raw data. Reduced data generally appears in a sheet named
Measurement; transformed data appears in sheets with names corresponding
to the analysis options configured in the protocol.
Note: Transformed data appears in results for protocols with analysis options
configured.
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Viewing Measurement Results
Figure 8-17 Viewing Reduced Data (excerpt)
To view reduced or transformed data:
1. In Excel, access the workbook containing reduced or transformed data
for the desired measurement results. Workbooks containing reduced or
transformed data always contain ResultData in the title.
2. In the worksheet, click the desired tab to view.
Signing Measurement Results
On systems with the GxP Permissions module enabled, measurement results
may be signed to prevent them from being deleted or overwritten. Signed
results from protocols configured with data reduction and/or analysis options
may be reevaluated; however, reevaluated results must be saved using a
different name. Reevaluated results are not signed by default.
Results may be signed at any time by users who are assigned a role containing
the Sign permission. See Configuring Roles for Multi-Mode Analysis Software
User Accounts on page 76 for more information about roles and permissions.
To sign measurement results:
1. In the Results Selection List, select the measurement results to sign.
2. From the tool bar, click Sign the selected result.
OR
From the menu bar select Actions | Sign the selected result.
OR
Right click on the desired results and select Sign the selected result.
3. The Sign the Selected Item dialog appears.
4. In Sign the Selected Item, add an electronic signature by following the
instructions in Adding Electronic Signatures and Comments to Items on
page 84.
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Deleting Measurement Results
Measurement results may be deleted from the Results Selection List. When the
GxP Permissions module is enabled on the system, results that have been
signed may not be deleted. See Signing Measurement Results on page 238.
Note: When GxP Permissions is enabled, only users assigned a role containing
the Delete permission may delete measurement results. See Configuring
Roles for Multi-Mode Analysis Software User Accounts on page 76.
To delete measurement results:
1. In the Results Selection List, select the results to delete.
2. From the tool bar, click Delete.
OR
From the menu bar select Actions > Delete the selected result.
OR
Right-click on the desired results and select Delete the selected result.
Note: Multiple items may be selected for deletion by holding down the
CTRL or SHIFT key while selecting each item desired.
3. The delete message dialog appears.
4. Click Yes to delete the selected results. The selected results are moved
to the Trash list. To permanently remove the results from the database
see Deleting and Restoring Items on page 48.
Printing Measurement Results
Measurement results may be printed from the Results Selection List or the
Result Viewer. Printed reports include information about the protocol and all
Report Options configured in the protocol.
Depending on how Print Settings are configured, Print and/or Print Preview
may display before the measurement results print. See Configuring Print
Settings on page 38 for information about enabling and disabling Print and
Print Preview.
To print measurement results:
1. To print from the Results Selection List, select the results to print and
click the print button on the tool bar.
OR
To print from the Result Viewer, click the print button on the tool bar.
2. If Print appears, configure printing options as desired and click OK.
OR
If the Print Preview dialog appears, use the tool bar controls to change
the magnification, layout view, or pages displayed, if desired.
3. In the Print Preview dialog, click Print to print out the measurement
results.
4. In the Print Preview dialog, click Close to close the window.
Note: Clicking Close without first clicking Print cancels the printout.
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Viewing Measurement Results
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A
Data Reduction Techniques
Supported Data Reduction Techniques
The tables in this section describe the data reduction techniques supported by
the software:
• Table A-1 describes the techniques available for scan measurements
and measurement sequences configured in protocols.
• Table A-2 describes the techniques available for kinetic measurements.
• Table A-3 describes techniques available for fluorescence polarization
measurements performed on a FilterMax 5 Multi-Mode Microplate
Reader or a SpectraMax Paradigm Multi-Mode Detection Platform.
Table A-1 Scan Measurement Data Reduction Techniques
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Data Reduction
Technique
Description
Parameters
Delta
Difference between the first and last
points measured in a well.
N/A
Mean
Determines the mean value per sample
from the points measured.
N/A
Peak Value
Used to detect the highest measured
value per sample.
Smoothing Points
Standard Deviation
Calculates the standard deviation for each N/A
well.
Coefficient of
Variation
Calculates the coefficient of variation for
each well.
N/A
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Data Reduction Techniques
Table A-2 Kinetic Data Reduction Techniques
Data
Reduction
Technique
Description
Parameters
Average Slope
Determines the average slope of the reaction
curve by calculating the average of all linear
regressions calculated over each group of
Smoothing Points in the kinetic reading
sequence. A decreasing slope shows a decline.
Smoothing Points
Delta
Difference between the first and last kinetic
measurements in a protocol run.
N/A
Delta Max Slope Difference between the first measurement and
the center point of the maximum slope.
Smoothing Points
Note: The center point of the maximum
slope is calculated by determining the
center point between the smoothing points
of the regression line with the maximum
slope.
Delta Time
Absolute
Time elapsed from one preselected
measurement value to another.
Lower Limit Upper
Limit
Delta Time Max
Slope
Time difference in seconds between the first
measurement and the occurrence of the center
point of the maximum slope.
Smoothing Points
Note: The center point of the maximum
slope is calculated by determining the
center point between the smoothing points
of the regression line with the maximum
slope.
Delta Time
Relative
Time elapsed in seconds from the first
measurement to reaching a set
increase/decrease amount from the first
measurement value.
In-/Decrease
Max Declining
Slope
Determines the maximum declining rate of the
reaction curve by calculating a linear regression
over each group of Smoothing Points in the
kinetic reading sequence.
Smoothing Points
Max Inclining
Slope
Determines the maximum inclining rate of the
reaction curve by calculating a linear regression
over each group of Smoothing Points in the
kinetic reading sequence.
Smoothing Points
Max Slope
Smoothing Points
Maximum slope of the curve in measurement
value/min. The line with the highest slope is
calculated, along with maximum reaction speed.
Note: The accuracy of this calculation
depends on the number of measurement
cycles selected.
242
Mean
Determines the mean value per sample within a
sequence of measurements.
N/A
Time Peak
Used to detect the time elapsed until the peak
value is reached.
Smoothing Points
Peak Value
Used to detect the highest value per sample
within a sequence of measurements.
Smoothing Points
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Multi-Mode Analysis Software User Guide
Table A-3 Fluorescence Polarization Data Reduction Techniques (FilterMax 5 Multi-Mode
Microplate Reader and SpectraMax Paradigm Multi-Mode Detection Platform)
Data Reduction
Description
Technique
Parameters
Polarization
Ratio of the difference between the parallel and the
perpendicular polarization intensitya components divided by
the sum of the two orthogonal fluorescence intensity
components. Polarization is calculated according to the
formula:
G-Factorb Thresholdc
Total Intensity
Provides raw fluorescence intensitya measurements in the
G-Factorb
parallel and the perpendicular polarization planes with respect
to the plane of linearly polarized excitation light. Total intensity
is calculated according to the formula:
Anisotropy
The ratio of the difference between the parallel and
perpendicular polarization intensitya components divided by
the sum of the fluorescence intensity parallel to the excitation
plane plus the fluorescence intensity perpendicular to the
excitation plane multiplied by two. Anisotropy is calculated
according to the formula:
a
b
c
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G-Factorb Thresholdc
In polarization data reduction techniques, intensity defines sample raw data minus the
average of blank replicate raw data.
The G-factor factors out differences in detection efficiency between the polarization
planes. The default G-factor is derived from fluorescein measurements performed on
several instruments. If a more accurate G-factor has been determined for the connected
instrument, it may be entered in the data reduction method configuration.
Threshold defines the minimum number of counts; values measured below the threshold
are noise.
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Data Reduction Techniques
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PathCheck® Pathlength Measurement
Technology
B
Overview
(SpectraMax® Paradigm® Multi-Mode Detection Platform and FilterMax™ F5
Multi-Mode Microplate Reader only)
The Beer–Lambert law states that absorbance is proportional to the distance
that light travels through the sample:
where A is the absorbance,  is the molar absorbtivity of the sample, b is the
pathlength and c is the concentration of the sample. In short, the longer the
pathlength, the higher the absorbance.
Microplate readers use a vertical light path so the distance of the light through
the sample depends on the volume. This variable pathlength makes it difficult
to perform extinction-based assays and also makes it confusing to compare
results between microplate readers and spectrophotometers reading cuvettes.
The standard pathlength of a cuvette is the conventional basis for quantifying
the unique absorbtivity properties of compounds in solution. Quantitative
analyses can be performed on the basis of extinction coefficients, without
standard curves (for example, NADH-based enzyme assays). When using a
cuvette, the pathlength is known and is independent of sample volume, so
absorbance is proportional to concentration.
In a microplate, pathlength is dependent on the liquid volume, so absorbance
is proportional to both the concentration and the pathlength of the sample.
Standard curves are often used to determine analyte concentrations in
vertical-beam photometry of unknowns, yet errors can still arise from pipetting
the samples and standards. The PathCheck® Pathlength Measurement
Technology feature automatically determines the pathlength of aqueous
samples in the microplate and normalizes the absorbance in each well to a
pathlength of 1 cm. This patented approach to correcting the microwell
absorbance values is accurate to within 3% of the values obtained directly in a
1 cm cuvette.
vertical light path
horizontal
light path
cuvette
microplate wells
Figure B-1 Cuvette and Microwell light paths
Reference measurements made using factory-stored values derived from
deionized water can be used to normalize the OD data for microplate wells.
PathCheck Pathlength Measurement Technology is used to normalize the data
acquired from absorbance endpoint microplate readings to a 1 cm pathlength,
correcting the OD for each well to the value expected if the sample were read
in a 1 cm cuvette.
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PathCheck® Pathlength Measurement Technology
The SpectraMax Paradigm Multi-Mode Detection Platform and FilterMax F5
Multi-Mode Microplate Reader offer a water-constant method of pathlength
correction. For the FilterMax F5 Multi-Mode Microplate Reader, the water
constant is stored in the instrument. For the SpectraMax Paradigm Multi-Mode
Detection Platform, the water constant is stored in the Absorbance Detection
Cartridge.
The actual pathlength, d, of a solvent is found from the following equation:
When the water constant is used for pathlength correction, the value of k is
obtained from the instrument or cartridge. This constant is saved in the
instrument or cartridge in the factory and may differ slightly from instrument
to instrument or cartridge to cartridge.
After the pathlength d is found, the following equation is used for the
pathlength correction:
Using the PathCheck Pathlength Measurement Technology
Water Constant
The PathCheck Pathlength Measurement Technology on the SpectraMax
Paradigm Multi-Mode Detection Platform and FilterMax F5 Multi-Mode
Microplate Reader uses a water constant reference. Be aware that if your
sample matrix contains an organic solvent such as ethanol or methanol, the
estimated pathlengths will be lower than the true values, and PathCheck
Pathlength Measurement Technology normalized values will be higher than the
corresponding 1 cm values.
The PathCheck Pathlength Measurement Technology measurement is based on
the absorbance of water in the near infrared region (between 900 nm and
1000 nm). If the sample is completely aqueous, has no turbidity and has a low
salt concentration (less than 0.5 M), the water constant is adequate. The
water constant is determined during manufacture and is stored in the
instrument or cartridge.
To enable PathCheck for Absorbance readings, you must first set up a
detection method with the PathCheck Pathlength Measurement Technology
enabled. See Creating and Editing Detection Methods on page 87.
When you edit a protocol that uses PathCheck Pathlength Measurement
Technology, and you have determined a plate background constant for your
microplate, you can enter the value in the Plate Background field. See Use Plate
Background Constant on page 247 and Creating Protocols on page 146.
After you have read a plate with the PathCheck Pathlength Measurement
Technology enabled, PathCheck Pathlength Measurement Technology program
information is stored permanently in the data file. You have the option of
applying, or not applying, the PathCheck Pathlength Measurement Technology
to the absorbance values as you choose. If you did not have PathCheck turned
on during the plate read, you cannot apply the PathCheck Pathlength
Measurement Technology after the read.
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Multi-Mode Analysis Software User Guide
Background Constant Subtraction and Blanking
Considerations
Raw OD measurements of microplate samples include both pathlengthdependent components (sample and solvent) and a pathlength-independent
component (OD of microplate material). The pathlength-independent
component must be eliminated from the PathCheck Pathlength Measurement
Technology calculation in order to get valid results that have been normalized
by PathCheck Pathlength Measurement Technology. You can accomplish this by
using a plate background constant.
Use Plate Background Constant
To determine Plate Background Constants:
1. Fill a clean microplate with water.
2. Read at the wavelengths you will be reading your samples.
3. The average OD value is the Plate Background Constant. Enter it in the
Plate Background field in the Method Selection step of editing a protocol.
4. If you intend to read your samples at more than one wavelength, there
should be a corresponding number of Background Constants.
It is important that you put water in the wells and not read a dry plate for the
Background Constant. Dry plates have a slightly higher OD value than a waterfilled plate because of differences in refractive indices. Using a dry plate results
in PathCheck Pathlength Measurement Technology normalized values that are
lower than 1 cm cuvette values. Omitting the Background Constant results in
values that have been normalized by the PathCheck Pathlength Measurement
Technology and are higher than 1 cm cuvette values.
PathCheck Pathlength Measurement Technology and
Interfering Substances
Any material that absorbs in the 900 nm to 1000 nm spectral region could
interfere with PathCheck Pathlength Measurement Technology. Fortunately,
there are few materials that do interfere at the concentrations typically used.
Turbidity is the most common interference. If you can detect any turbidity in
your sample, you should not use the PathCheck Pathlength Measurement
Technology. Turbidity elevates the 900 nm measurement more than the
1000 nm measurement and causes an erroneously low estimate of pathlength.
Samples that are highly colored in the upper visible spectrum can have
absorbance extending into the near infrared (NIR) and can interfere with the
PathCheck Pathlength Measurement Technology. Examples include Lowry
assays, molybdate-based assays, and samples containing hemoglobins or
porphyrins. In general, if the sample is distinctly red or purple, you should
check for interference before using the PathCheck Pathlength Measurement
Technology. See Determining Color Interference on page 248.
Organic solvents could interfere with the PathCheck Pathlength Measurement
Technology if they have absorbance in the region of the NIR water peak.
Solvents such as ethanol and methanol do not absorb in the NIR region, so
they do not interfere, except for causing a decrease in the water absorbance to
the extent of their presence in the solution. However, if the solvent absorbs
between 900 nm and 1000 nm, the interference would be similar to the
interference of highly colored samples. If you are considering adding an
organic solvent other than ethanol or methanol with the SpectraMax Paradigm
Multi-Mode Detection Platform, you are advised to run a Spectrum scan
between 900 nm and 1000 nm to determine if the solvent would interfere with
the PathCheck Pathlength Measurement Technology. Spectrum scan is not
available with the FilterMax Multi-Mode Microplate Readers.
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PathCheck® Pathlength Measurement Technology
Determining Color Interference
To determine possible color interference, do the following:
1. Measure the OD at 900 nm and 998 nm (both measured with air
reference).
2. Subtract the 900 nm value from the 998 nm value.
3. Do the same for pure water.
If the delta OD for the sample differs significantly from the delta OD for water,
then it is advisable not to use the PathCheck Pathlength Measurement
Technology feature.
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Mathematical Operators and Functions
C
Supported Mathematical Operators and Functions
The tables in this section describe the mathematical operators and functions
that may be used in formulas:
• Table C-1 describes the mathematical and logical operators supported.
• Table C-2 describes the mathematical functions supported.
Note: In formulas where multiple parameters are configured, separate
parameters with a semicolon; for example, max(S3;S5).
Table C-1 Mathematical and Logical Operators Table
5008530 A
Operator
Description
+
Sums two numbers.
=
Compares two expressions to determine if they are equal.
/
Divides two numbers and returns a numeric result.
<>
Compares two expressions to determine if they are not equal.
>
Compares two expressions to determine if one is greater than the
other.
³
Compares two expressions to determine if one is greater than or
equal to the other.
<
Compares two expressions to determine if one is less than another.
£
Compares two expressions to determine if one is less than or equal
to another.
*
Multiplies two numbers.
-
Performs subtraction of two expressions.
-
Unary negation operator indicating the negative value of a numeric
expression
AND
Logical AND operator. Performs a logical conjunction on two
expressions.
NOT
Logical NOT operator. Performs logical negation on an expression.
OR
Logical OR operator. Performs logical disjunction on two
expressions.
249
Mathematical Operators and Functions
Table C-2 Mathematical Functions
250
Function
Description
abs(number)
Returns the absolute value of a number.
acos(number)
Returns the arccosine of a number.
asin(number)
Returns the arcsine of a number.
atan(number)
Returns the arctangent of a number.
cos(number)
Returns the cosine of a number.
exp(number)
Returns e (the base of natural logarithms) raised to a
power.
log(number)
Returns the natural logarithm of a number.
max(num1;num2)
Returns the greater of two supplied numeric
expressions.
min(num1;num2)
Returns the lesser of two supplied numeric
expressions.
pow(base, exponent)
Returns the value of a base expression taken to a
specified power.
sin(number)
Returns the sine of a number.
sqrt(number)
Returns the square root of a number.
tan(number)
Returns the tangent of a number.
5008530 A
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