Thermo PAL User Guide Version F

Thermo PAL User Guide Version F

Thermo PAL

User Guide for LC Devices

XCALI-97169 Revision F December 2013

© 2013 Thermo Fisher Scientific Inc. All rights reserved.

Exactive, Foundation, LCquan, and MSQ are trademarks, and LCQ, LCQ Fleet, LTQ, LXQ,

Thermo Scientific, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United

States.

The following are registered trademarks in the United States and other countries:

Adobe and Reader are registered trademarks of Adobe Systems Incorporated. Agilent, ChemStation, and

Instant Pilot are registered trademarks of Agilent Technologies Inc. Empower and MassLynx are registered trademarks of Waters Technologies Corporation. Microsoft and Windows are registered trademarks of

Microsoft Corporation.

The following are registered trademarks in the United States and possibly other countries:

Analyst is a registered trademark of AB Sciex Pte. Ltd. Cheminert is a registered trademark of Valco

Instruments Company, Inc. COMBICON is a registered trademark of Phoenix Contact GmbH & Co. Kalrez is a registered trademark of E.I. du Pont de Nemours & Company. PAL is a trademark of CTC Analytics AG.

Ryton is a registered trademark of Chevron Phillips Chemical Company. Simriz is a registered trademark of

Carl Freudenberg KG Corporation.

PEEK is a trademark of Victrex plc.

All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of

Sale shall govern all conflicting information between the two documents.

Release history: Revision A, Dec 2005; Revision B, Feb 2009; Revision C, Apr 2010; Revision D, Mar 2011;

Revision E, Jan 2013; Revision F, Dec 2013

Software version: Thermo Foundation (see page xi); Thermo Xcalibur 2.1 or later; Thermo LC Devices 2.5.0

or later. Firmware version: See page xii.

For Research Use Only. Not for use in diagnostic procedures.

Regulatory Compliance

Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name.

Changes that you make to your system may void compliance with one or more of these EMC and safety standards.

Changes to your system include replacing a part or adding components, options, or peripherals not specifically authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards, replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives.

EMC Directive 2004/108/EC

EMC compliance has been evaluated by CTC Analytics for the HTC PAL™ autosampler.

IEC 61326-1:2005

EN 61326-1:1997, A1:1998

FCC Class A, CFR 47 Part 15:2003

IEC 61326-2-6:2005

CISPR 22:2005, A1:2005, A2:2006

Low Voltage Safety Compliance

Low Voltage Safety Compliance has been evaluated by CTC Analytics for the HTC PAL autosampler.

This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2001,

IEC 61010-1:2001, ANSI/UL 61010 A-1:2004, CAN/CSA 22.2 61010-1:2004.

FCC Compliance Statement

THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO

THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL

INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,

INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.

CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device.

Notice on Lifting and Handling of

Thermo Scientific Instruments

For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one person alone to handle safely.

Notice on the Proper Use of

Thermo Scientific Instruments

In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher

Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement parts from Thermo Fisher Scientific or one of its authorized representatives.

Notice on the Susceptibility to Electromagnetic Transmissions

Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency transmitters, such as mobile phones, in close proximity to the instrument.

For manufacturing location, see the label on the instrument.

WEEE Compliance

This product complies with the European Union’s Waste Electrical & Electronic Equipment (WEEE) Directive

2002/96/EC. It is marked with the following symbol:

Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union

(EU) Member State, and these companies should dispose of or recycle this product. For further information, go to www.thermoscientific.fr/rohs .

WEEE Konformität

Dieses Produkt entspricht der EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC. Es ist mit dem folgenden Symbol gekennzeichnet:

Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Weitere

Informationen finden Sie unter www.thermoscientific.de/rohs .

Conformité DEEE

Ce produit est conforme avec la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et

Electroniques (DEEE). Il est marqué par le symbole suivant:

Thermo Fisher Scientific s'est associé avec une ou plusieurs sociétés de recyclage dans chaque état membre de l’Union

Européenne et ce produit devrait être collecté ou recyclé par celle(s)-ci. Pour davantage d'informations, rendez-vous sur la page www.thermoscientific.fr/rohs .

C

Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi

Supported Firmware Versions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii

Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Chapter 1 Getting Connected. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Ordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Setting Up an LC/MS System with the Autosampler. . . . . . . . . . . . . . . . . . . . . . 2

Connecting the Thermo PAL Autosampler to the Data System Computer . . . . . 4

Connecting the Contact Closure Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Making Contact Closure with Thermo Scientific Devices . . . . . . . . . . . . . . . . 6

Connecting the Start Pump to the Sample Pump in a Dual-Pump

System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Making Contact Closure with the Autosampler, an Agilent Pump, and a Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

Configuring the Thermo PAL Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Using the Autosampler Control Terminal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Selecting the Tray Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Changing the Pulse Time Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Specifying the Instrument Method Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 24

Viewing the Method Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Chapter 3 Creating Custom Templates and Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33

Using the Template Editor to Create Custom Templates . . . . . . . . . . . . . . . . . 33

Testing a Custom Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Viewing the Template Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Standard Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Using the Macro Editor to Create Custom Macros . . . . . . . . . . . . . . . . . . . . . . 41

Defining Variables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Thermo Scientific Thermo PAL User Guide

vii

Contents

Chapter 4 Using the Direct Controls to Operate the Autosampler . . . . . . . . . . . . . . . . . . . . .49

Opening the Direct Control Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Making Single Injections from the Tune Window. . . . . . . . . . . . . . . . . . . . . . . 50

Changing the Tray Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Specifying the Location of the Direct Control Methods . . . . . . . . . . . . . . . . . . 54

Wrapping Direct Control Injections with Additional Macros . . . . . . . . . . . . . . 56

Chapter 5 Using Dynamic Load and Wash (DLW) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Cycle Composer Macros or ICC Cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Priming the Solvent Lines, Wash1 and Wash2 . . . . . . . . . . . . . . . . . . . . . . . 61

Standard DLW Injection Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Fast DLW Injection Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Operating Dynamic Load and Wash (DLW) . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Priming the Solvent Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Location of Solvent and Waste Bottles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

DLW Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

DLW Actuator/Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

DLW Cycle Step-by-Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Cycle for Standard Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Additional Valve Toggle Step to DLW Standard Cycle . . . . . . . . . . . . . . . . . 84

Cycle for Fast Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Appendix A Sample Trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105

Tray Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Tray Position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

Sample Position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111

viii

Thermo PAL User Guide Thermo Scientific

P

Preface

This guide describes how to connect a CTC™ Thermo PAL™ autosampler to other devices in the liquid chromatography/mass spectrometry (LC/MS) system and how to control the autosampler from a Thermo Scientific™ MS data system, such as Thermo Xcalibur™.

ThermoPAL, one of the device drivers provided on the Thermo LC Devices DVD, is the device driver that enables the Xcalibur data system to control the autosampler.

Contents

Related Documentation

System Requirements

Supported Firmware Versions

Cautions and Special Notices

Contacting Us

To suggest changes to the documentation or to the Help

Complete a brief survey about this document by clicking the button below.

Thank you in advance for your help.

Thermo Scientific Thermo PAL User Guide

ix

Preface

Related Documentation

In addition to this guide, the Thermo PAL autosampler software includes Help.

To view product manuals

From the Microsoft™ Windows™ taskbar, do the following:

• For an LC instrument controlled by a Thermo software application, choose Start >

All Programs > Thermo Instruments > Manuals > LC Devices > CTC.

• For the Xcalibur manual set, choose Start > All Programs > Thermo Xcalibur >

Manuals > Xcalibur.

For access to the application Help, follow this procedure.

To view application-specific Help

• From the Thermo Xcalibur Instrument Setup window, choose Help > Thermo Pal

Help.

• If information about setting parameters is available for a specific view, page, or dialog box, click Help or press the F1 key for information about setting parameters.

For more information, visit www.thermoscientific.com

.

x

Thermo PAL User Guide Thermo Scientific

Preface

System Requirements

Ensure that the system meets these minimum requirements.

IMPORTANT Before you install the device driver, ensure that the data system computer has a compatible version of the Thermo Foundation™ platform as noted in the Thermo LC

Devices x.x.x Release Notes.

System

Computer

Software

Minimum requirements

• 2 GHz processor with 1 GB RAM

• DVD drive

• 80 GB available on drive C

• Video card and monitor capable of 1280 × 1024 resolution

• NTFS format

• Adobe™ Reader™ 9.0

• Microsoft Windows operating system:

 Windows 7 Professional (32-bit and 64-bit a

)

 Windows XP Workstation SP3

• Thermo Scientific software:

LC Devices

2.6.0 and later

2.5.0 SP3

2.5.0 SP1 or SP2

Foundation

1.0.2 SP2 and later

1.0.2 SP2

2.0 a

LC Devices 2.8.0 and later are compatible with Windows 7, 32-bit and 64-bit.

(Windows 7 only) If you receive a server failure error when you try to open the Xcalibur

Instrument Setup window, follow the next procedure.

To resolve a server failure for the Xcalibur data system

1. Verify that the installed versions of Foundation platform and LC Devices are compatible

(see

System Requirements

).

2. If the installed LC Devices software is compatible with Foundation, go to

step 3

. If it is not compatible, do the following: a. Use the Windows Control Panel to uninstall all of the modules from LC Devices. b. Install the compatible version of LC Devices. c.

Restart the data system computer.

Thermo Scientific Thermo PAL User Guide

xi

Preface

3. If the installed LC Devices is compatible with Foundation, do the following: a. Open the Windows Control Panel. b. In the top Search box, type Change User Account Control Settings, and then select this link to open the User Account Control Settings dialog box. c.

Move the slider to the Default position ( Figure 1 ).

d. Click OK.

Figure 1.

User Account Control Settings dialog box

Slider set at the

Default position

Supported Firmware Versions

LC Devices supports firmware versions 2.4.0, 2.5.2, 4.1.2, and 4.1.3 for the Thermo PAL autosampler.

xii

Thermo PAL User Guide Thermo Scientific

Preface

Cautions and Special Notices

Make sure you follow the cautions and special notices presented in this guide. Cautions and special notices appear in boxes; those concerning safety or possible system damage also have corresponding caution symbols.

This guide uses the following types of cautions and special notices.

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of data, or invalid test results; or might contain information that is critical for optimal performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Contacting Us

There are several ways to contact Thermo Fisher Scientific for the information you need.

To contact Technical Support

Phone

Fax

E-mail

800-532-4752

561-688-8736 [email protected]

To contact Customer Service for ordering information

Phone

Fax

E-mail

Web site

800-532-4752

561-688-8731 [email protected]

http://www.thermoscientific.com/en/support-landing/support.html

Thermo Scientific Thermo PAL User Guide

xiii

Preface

To copy manuals from the Internet

Go to mssupport.thermo.com

, agree to the Terms and Conditions, and then click

Customer Manuals in the left margin of the window.

To suggest changes to the Help

• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62 .

• Send an e-mail message to the Technical Publications Editor at [email protected]

.

xiv

Thermo PAL User Guide Thermo Scientific

1

Getting Connected

The CTC Thermo PAL is a high-throughput autosampler manufactured by CTC Analytics and supplied by Thermo Fisher Scientific. For high-throughput LC/MS applications, use the

PAL autosampler, a Thermo Scientific or an Agilent™ liquid chromatography (LC) pump, and a Thermo Scientific mass spectrometer (MS).

This chapter describes the contact closure connections between the PAL autosampler, one or two Thermo Scientific LC pumps or an Agilent pump, a Thermo Scientific mass spectrometer, and the Xcalibur data system computer. For information on how to set up the

PAL autosampler, refer to the CTC Analytics PAL System User Manual.

CAUTION Follow all of the recommendations given in the Safety Information section of the CTC Analytics PAL System User Manual. The Safety Information section includes information on the autosampler’s electrical hazards, lithium battery, and safety labels.

Contents

Ordering Information

Setting Up an LC/MS System with the Autosampler

Connecting the Thermo PAL Autosampler to the Data System

Computer

Connecting the Contact Closure Cables

Ordering Information

Thermo Fisher Scientific supplies these cables with the Thermo PAL autosampler:

• Serial communication cable that connects the autosampler to the data system computer

• Contact closure cable that connects the autosampler to the Thermo Scientific LC pump and Thermo Scientific mass spectrometer

Thermo Scientific Thermo PAL User Guide

1

1

Getting Connected

Setting Up an LC/MS System with the Autosampler

To order the HTC PAL or HTS PAL autosampler from Thermo Fisher Scientific, see Table 1

.

Table 1. Thermo PAL ordering information

Description

HTC PAL

HTC PAL with the 98 × 2 mL tray holder

HTS PAL

Part number

OPTON 13009

OPTON 13010

OPTON 13008

Table 2 lists the contact closure cables used to connect an Agilent pump to a Thermo

Scientific mass spectrometer and the autosampler. You can order the DB15 connector × 15 wire cable from Agilent or Thermo Fisher Scientific.

Table 2. Contact closure cables used to connect an Agilent pump

Description

DB15 connector × 15 wire cable

DB15 connector × 15 wire cable

PAL Interface Cable for APG Remote

DB15 connector × DB9 connector cable

Supplier Part number

Thermo Fisher Scientific 00012-27716

Agilent

CTC Analytics

G1103-61611

CBL 7890

Setting Up an LC/MS System with the Autosampler

Typical stackable setups include placing the autosampler on top of the two pumps, in a dual-pump setup, and to the left of the mass spectrometer. Ensure that the stackable area for the autosampler is level, and that system cables behind the autosampler have adequate space.

CAUTION To prevent damage to the injection unit during operation, place the autosampler on a level surface.

For information on how to assemble the Thermo PAL autosampler and connect the solvent lines, refer to the CTC Analytics PAL System User Manual.

Figure 2

shows the front view of the Thermo PAL autosampler. During installation, the

Thermo Fisher Scientific field service engineer connects the following:

• LC system to the mass spectrometer

• Solvent lines from the injection valve to the LC pump and the Thermo Scientific mass spectrometer

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Thermo PAL User Guide Thermo Scientific

1

Getting Connected

Setting Up an LC/MS System with the Autosampler

Figure 2.

PAL autosampler (supplied by Thermo Fisher Scientific)

Courtesy of CTC Analytics

Injection unit

Control terminal

Syringe

Thermo Scientific Thermo PAL User Guide

3

1

Getting Connected

Connecting the Thermo PAL Autosampler to the Data System Computer

Connecting the Thermo PAL Autosampler to the Data System

Computer

The Thermo PAL autosampler communicates with the data system computer through the supplied RS-232 serial communication cable.

To connect the autosampler to the data system computer

Using the RS-232 serial cable supplied with the autosampler, connect the SER 1 port on the back of the autosampler to the serial port on the back of the data system computer

( Figure 3 and

Figure 4

).

Figure 3.

Data system connection (firmware 2.5.2)

Data system computer

Autosampler

AUX INTERFACE WASH

STATION

POWER LED BUZZER SER3 SER2 SER1

DB9 to DB9 serial cable

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Thermo PAL User Guide Thermo Scientific

1

Getting Connected

Connecting the Contact Closure Cables

Figure 4.

Data system connection (firmware 4.1.2)

Autosampler

TERMINAL SER1 LAN MODBUS

BUZZER

E

D

WASH

STATION

INTERFACE 1 INTERFACE 2 AUX 1 AUX 2 POWER FUSE

Data system computer

DB9 to DB9 serial cable

Connecting the Contact Closure Cables

During an injection cycle, the Thermo PAL autosampler sends and receives electrical signals.

To start an injection cycle, the autosampler must receive a signal from the LC pump. When the autosampler completes an injection cycle, it sends a signal back to the LC pump. For more information about interfacing the autosampler with other devices, refer to the CTC Analytics

PAL System User Manual (Interfacing the PAL to Other Devices section).

This section describes how to hardwire one or two LC pumps and a Thermo Scientific mass spectrometer to the autosampler for contact closure.

To make the contact closure connections, follow the procedure for your LC/MS system:

Making Contact Closure with Thermo Scientific Devices

Connecting the Start Pump to the Sample Pump in a Dual-Pump System

Dual-pump setup with two Accela Pumps

Thermo Scientific Thermo PAL User Guide

5

1

Getting Connected

Connecting the Contact Closure Cables

Making Contact Closure with Thermo Scientific Devices

The accessory kit supplied by Thermo Fisher Scientific contains the contact closure cables that you need to connect the Thermo PAL autosampler to an LC/MS system with one or two

Thermo Scientific LC pumps and a Thermo Scientific mass spectrometer.

Figure 5

shows the Thermo Single Configuration cable assembly that you use to connect one

LC pump and a Thermo Scientific mass spectrometer to the autosampler. The cable assembly consists of a DB15 connector with two 2-pin legs. One leg connects to the LC pump, and the other leg connects to the mass spectrometer. During the installation of the LC/MS system, a

Thermo Fisher Scientific field service engineer uses the appropriate mini COMBICON™ connectors to complete the contact closure cable assembly, and then connects the assembly to the appropriate pins on the LC pump or LC pumps and the mass spectrometer.

Figure 5.

Contact closure cable for LC/MS with one Thermo Scientific LC Pump

300 cm

(10 ft)

Clear

Cbl Thermo Single Config.

To connect the contact closure cable to the LC pump and the MS

1. Connect the DB15 connector of the contact closure cable to the DB15 port on the back of the autosampler.

The port label depends on the autosampler model (see

Table 3 ).

Table 3. PAL contact closure port

PAL model

HTC, LC

HTS

Port marking

INTERFACE

INTERFACE 1

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Thermo PAL User Guide Thermo Scientific

1

Getting Connected

Connecting the Contact Closure Cables

2. Using an 8-pin COMBICON connector, connect one leg of the contact closure cable to

the appropriate pins on the back panel of the Thermo Scientific LC pump (see Table 4

).

Table 4. Contact closure cable connection to Thermo Scientific pump

Pump model

Accela Pump

Surveyor LC Pump Plus

Surveyor MS Pump Plus

Clear wire

GRAD START (pin 4)

PROG. START (pin 4)

GRAD START (pin 8)

Black wire

GND

GND

GND

3. Using a 2-pin COMBICON connector, connect the other leg of the contact closure cable to the Start in pins on the Thermo Scientific MS.

Figure 6

shows the contact closure connection between the autosampler and a Thermo

Scientific LC pump, and Figure 7 on page 9

shows the contact closure connection between the autosampler and a Thermo Scientific mass spectrometer. (

Figure 6

is for firmware 2.5.2 and

Figure 7

is for firmware 4.1.2.)

Thermo Scientific Thermo PAL User Guide

7

1

Getting Connected

Connecting the Contact Closure Cables

Figure 6.

Contact closure connections to a Thermo Scientific LC pump and MS (firmware 2.5.2)

TSQ Series MS LTQ Series MS Surveyor MSQ Plus MS

–or– –or–

+30V Max

Start In

Start

+ -

Start In +

Start In -

To mass spectrometer

INTERFACE

DB15

To LC pump

AUX

Autosampler

INTERFACE

WASH

STATION

POWER

LED BUZZER

SER3 SER2 SER1

RS232 1 2 3 4 5 6 7 8 USB

Accela Pump

8

Thermo PAL User Guide

1 2 3 4 5 6 7 8 RS232 I/O

Surveyor MS Pump Plus

RS232 UNIT ID ENET

Surveyor LC Pump Plus

Thermo Scientific

1

Getting Connected

Connecting the Contact Closure Cables

Figure 7.

Contact closure connections to a Thermo Scientific LC pump and MS (firmware 4.1.2)

TSQ Series MS LTQ Series MS Surveyor MSQ Plus MS

–or– –or–

+30V Max

Start In

Start

+ -

Start In +

Start In -

To mass spectrometer

INTERFACE 1

DB15

To LC pump

Autosampler

TERMINAL SER1 LAN MODBUS

BUZZER L

E

D

WASH

STATION

INTERFACE 1 INTERFACE 2 AUX 1 AUX 2 POWER FUSE

Thermo Scientific

RS232 1 2 3 4 5 6 7 8 USB

Accela Pump

1 2 3 4 5 6 7 8 RS232 I/O

Surveyor MS Pump Plus

RS232 UNIT ID ENET

Surveyor LC Pump Plus

Thermo PAL User Guide

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1

Getting Connected

Connecting the Contact Closure Cables

Connecting the Start Pump to the Sample Pump in a Dual-Pump System

In a dual-pump system, the start pump triggers the sample pump.

To connect the start pump to the sample pump, you can use the contact closure cable that

CTC Analytics supplies, or you can use one insulated electrical wire to connect the ground pins and one insulated electrical wire to connect the GRAD START or PROG. START pins.

Figure 8

shows the contact closure cable that you can order from CTC Analytics.

Figure 8.

Contact closure cable (supplied by CTC Analytics) used to connect two LC pumps

100 cm

(39 inches)

Cbl Thermo Dual Config.

To make contact closure for a dual-pump system

1. Connect the DB15 connector of the Thermo Single Config cable to the INTERFACE 1 or INTERFACE port on the back panel of the autosampler.

2. Connect one of the 2-pin legs of the Thermo Single Config cable to the start pump.

3. Connect the other 2-pin leg of the Thermo Single Config cable to the Thermo

Scientific MS.

4. Connect the start pump to the sample pump:

• Connect the start pump ground pin to the sample pump ground pin.

• Connect the GRAD START or PROG. START pin on the start pump to the GRAD

START or PROG. START connection on the sample pump.

Table 4 on page 7

lists the pin assignments of the Accela Pump, the Surveyor MS

Pump Plus, and the Surveyor LC Pump Plus.

Figure 9

shows two Accela Pumps connected together for contact closure.

10

Thermo PAL User Guide Thermo Scientific

Thermo Scientific

1

Getting Connected

Connecting the Contact Closure Cables

Figure 9.

Dual-pump setup with two Accela Pumps

INTERFACE 1

To the autosampler

To the mass spectrometer

Start pump

355 River Oaks Parkway

San Jose, CA 95134 U.S.A.

Model:

Accela Pump

Serial No:

60057-60010

Part No:

Options/Firmware: 12472

CAUTION

DISCONNECT INPUT

POWER BEFORE

OPENING COVER.

REFER ALL SERVICE

TO QUALIFIED

PERSONNEL ONLY.

61010 - 1

This device complies with FCC Rules, Part 15.

Operation is subject to the following two conditions:

(1) This device may not cause harmful interference, and (2) This device must accept any interference received, including interference that may cause undesired operation.

This product is manufactured under, and covered by, one or more of the following U.S. patents:

5,653,876

6,248,157B1

355 River Oaks Parkway

San Jose, CA 95134 U.S.A.

Model:

Accela Pump

Serial No:

60057-60010

Part No:

Options/Firmware: 12472

CAUTION

DISCONNECT INPUT

POWER BEFORE

OPENING COVER.

REFER ALL SERVICE

TO QUALIFIED

PERSONNEL ONLY.

61010 - 1

This device complies with FCC Rules, Part 15.

Operation is subject to the following two conditions:

(1) This device may not cause harmful interference, and (2) This device must accept any interference received, including interference that may cause undesired operation.

This product is manufactured under, and covered by, one or more of the following U.S. patents:

5,653,876

6,248,157B1

Sample pump

Thermo PAL User Guide

11

1

Getting Connected

Connecting the Contact Closure Cables

Making Contact Closure with the Autosampler, an Agilent Pump, and a Mass

Spectrometer

To make contact closure between the autosampler and an Agilent pump and between an

Agilent pump and a Thermo Scientific mass spectrometer, you must have the following cables:

• PAL interface cable (supplied by CTC or Agilent) for an Agilent pump (

Figure 10

)

• External contact trigger cable supplied by Thermo Fisher Scientific ( Figure 11

)

To make contact closure between the autosampler, an Agilent Pump, and a Thermo

Scientific MS

1. Using the PAL interface cable (

Figure 10 ), connect the Agilent pump to the autosampler

as follows ( Figure 12 on page 14

[firmware 2.5.2] and Figure 13 on page 15

[firmware

4.1.2]):

• Connect the DB15 connector to the INTERFACE (HTC) or INTERFACE 1

(HTS) port on the back panel of the Thermo PAL autosampler.

• Connect the DB9 connector to the REMOTE port on the back panel of the Agilent pump.

Figure 10. PAL interface cable for an Agilent pump (supplied by CTC Analytics)

170 cm

(5.6 ft)

Cbl 7890

Connect to the autosampler

Connect to the Agilent pump

2. Using the external contact trigger cable (

Figure 11

), connect the Agilent pump to the mass spectrometer (

Figure 12 on page 14

[firmware 2.5.2] and Figure 13 on page 15

[firmware 4.1.2]):

• Connect the DB15 connector to the RELAY CONTACTS port on the back of the

Agilent pump.

For information on how to install the external contact board, refer to the Agilent xxxx

Series Getting Connected Guide, where xxxx is your specific Agilent LC system.

• Connect the white wire to the Start In pin and the brown wire to ground on the MS.

Secure the remaining 13 wires to the cable with duct tape.

12

Thermo PAL User Guide Thermo Scientific

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Getting Connected

Connecting the Contact Closure Cables

Figure 11. External contact trigger cable (supplied by Thermo Fisher Scientific)

Connect to the MS

Connect to the

Agilent pump

Thermo Scientific Thermo PAL User Guide

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Getting Connected

Connecting the Contact Closure Cables

Figure 12. Contact closure with an Agilent pump, the autosampler, and a Thermo Scientific MS (firmware 2.5.2)

Surveyor MSQ Plus MS TSQ Series MS LTQ Series MS

–or– –or–

Start In +

Start In -

+30V Max

Start In

Start

In

+ -

External contact trigger cable supplied by

Thermo Fisher Scientific

AUX 1 AUX 2

VALVE IN

14

Thermo PAL User Guide

Autosampler

INTERFACE 1 INTERFACE 2 POWER

SER3 SER2 SER1

RELAY CONTACTS

Agilent pump

ANALOG

REMOTE

VIAL- # -OUTPUT RELAY CONTACTS

RS-232 CAN CAN

CONFIG

INTERFACE 1

Cable (DB15 connector to

DB9 connector) supplied by

CTC Analytics

Cbl 7890

REMOTE

Thermo Scientific

1

Getting Connected

Connecting the Contact Closure Cables

Figure 13. Contact closure with an Agilent pump, the autosampler, and a Thermo Scientific MS (firmware 4.1.2)

Surveyor MSQ Plus MS TSQ Series MS LTQ Series MS

–or– –or–

Start In +

Start In -

+30V Max

Start In

Start

+ -

External contact trigger cable supplied by

Thermo Fisher Scientific

Autosampler

TERMINAL SER1 LAN MODBUS

BUZZER L

D

WASH

STATION

INTERFACE 1 INTERFACE 2 AUX 1 AUX 2 POWER FUSE

RELAY CONTACTS

Agilent pump

ANALOG

REMOTE

VIAL- # -OUTPUT RELAY CONTACTS

RS-232

CAN CAN CONFIG

INTERFACE 1

Cable (DB15 connector to

DB9 connector) supplied by

CTC Analytics

Cbl 7890

REMOTE

Thermo Scientific Thermo PAL User Guide

15

2

Getting Started

This chapter describes how to add the autosampler to the Xcalibur instrument configuration, how to specify the available tray types, and how to specify the injection parameters for the autosampler from the Xcalibur data system.

Contents

Configuring the Thermo PAL Autosampler

Using the Autosampler Control Terminal

Specifying the Instrument Method Parameters

Configuring the Thermo PAL Autosampler

The ThermoPAL device driver provides control of the autosampler from the Xcalibur data system. To control the autosampler from the data system, add the autosampler to the Thermo

Foundation Instrument Configuration window and specify its configuration options.

To add the autosampler to the Foundation instrument configuration

1. Turn on the autosampler.

2. From the Microsoft Windows taskbar, choose Start > All Programs > Thermo

Foundation x.x > Instrument Configuration to open the Thermo Foundation

Instrument Configuration window ( Figure 14 ).

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2

Getting Started

Configuring the Thermo PAL Autosampler

Figure 14. Thermo Foundation Instrument Configuration window

18

Thermo PAL User Guide

3. Under Available Devices, double-click the autosampler icon to add it to the Configured

Devices area.

Use the Pal Configuration dialog box to select the PC Com port where the autosampler is connected, specify macros to import, and select sample trays or stacks.

To specify the configuration options for the autosampler

1. Follow the procedure “To add the autosampler to the Foundation instrument configuration” on page 17

.

2. In the Instrument Configuration window, under Configured Devices, double-click the

autosampler icon, and then do the following on the displayed page ( Figure 15 ).

Thermo Scientific

Figure 15. Pal Configuration dialog box

2

Getting Started

Configuring the Thermo PAL Autosampler

Thermo Scientific

3. Under Communications, do the following: a. In the Com Port list, select the communication port on the data system computer that the autosampler connects to. Or, click Auto Select.

Note The auto-select feature works only if the autosampler is connected to the data system computer and is turned on. b. If the autosampler is already connected to the data system computer, click Check to verify the connection.

4. Under Look Ahead Injections, to shorten the time between injections, select the Enable check box.

Tip Do not modify or delete a sequence while the data system is running with the

Look Ahead Injections enabled. Use the stop function to finish the current injection before you modify or delete a sequence.

5. Under Method Template\Macro Editor, to make the Method Template and Macro Editor dialog boxes available in the Instrument Setup window, select the Enable check box.

6. Under Cycle Composer Macro Importer, import the macros that you plan to use to create injection methods as follows: a. In the Import Path box, type the complete path to the location of the macros. Or, click Browse to locate the directory that contains the appropriate macros. b. In the Overwrite Existing Macros list, select one of the following:

Never—The autosampler does not import the specified macro if it has the same file name as an existing macro.

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Getting Started

Configuring the Thermo PAL Autosampler

Ask—The autosampler asks you if you want to overwrite existing macros.

Always—Imported macros overwrite existing macros. c.

Click Import.

7. Under Active Trays, select the trays that you want to use.

You can use trays that have a Yes in the Allow Use column. Clicking the tray name clears the Allow Use cell and removes the tray from the list of available trays in the Xcalibur data system.

IMPORTANT Use the autosampler control terminal to specify the tray information.

You can change the tray information when you control the autosampler from the

Xcalibur data system, but these changes are temporary. When you close and reopen the Xcalibur data system, the tray information resets to the autosampler control terminal settings.

8. Click OK.

9. Configure the other instruments in the LC/MS system, such as the LC pump and the mass spectrometer.

10. In the Thermo Foundation Instrument Configuration window, click Done.

Table 5 lists the parameters for the Pal Configuration dialog box.

Table 5. Pal Configuration dialog box parameters (Sheet 1 of 2)

Parameter

Communications

Com Port

Description

Auto Select

Check

Select the computer port where you plug the autosampler communication cable.

Instructs the system to automatically determine the computer port that connects to the autosampler through the autosampler communication cable.

Instructs the system to verify the computer port that connects to the autosampler through the autosampler communication cable.

Look Ahead Injections

Enable Select this check box to enable Look Ahead Injections.

When enabled, the autosampler sets up for the next injection during the current run. The setup for the next injection involves carrying out the steps up to, but not including, the injection.

Method Template \ Macro Editor

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2

Getting Started

Using the Autosampler Control Terminal

Table 5. Pal Configuration dialog box parameters (Sheet 2 of 2)

Parameter

Enable

Description

Select this check box when you want the Method Template and Macro Editor to be accessed through Instrument Setup.

Ensuring the check box is clear prevents access to the Method

Template and the Macro Editor.

Cycle Composer Macro Importer

Import Path Enter the path to the Cycle Macro to be imported.

Overwrite Existing Macros Select Never, Ask, or Always.

The selection determines if existing macros are to be overwritten when a new macro is imported.

Import the chosen macro.

Search through files and folders to find a macro.

Import

Browse

Active Trays

Tray Name

Stack

Allow Use

Hardware configured tray names.

Stack location of a given tray name.

Click to switch between Yes and blank.

• “Yes” means that the PAL system can access a given tray for obtaining samples (use is allowed).

• A blank means that the PAL system cannot access the tray for obtaining samples (that is, use is not allowed).

Using the Autosampler Control Terminal

For general information about using the autosampler control terminal, refer to the CTC PAL

System User Manual.

To select the sample trays and to change the default pulse time setting to 4.0 seconds, follow these procedures:

Selecting the Tray Type

Changing the Pulse Time Setting

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2

Getting Started

Using the Autosampler Control Terminal

Selecting the Tray Type

To select the tray type

1. On the Job Queue screen, select Menu by pressing the F1 key ( Figure 16

).

Figure 16. Autosampler control terminal with the Job Queue screen displayed

JOB QUEUE

22

Thermo PAL User Guide

Menu

Ins

Job

Del

Job

Pause

F1 F2

F3

F4

ESC STOP

Inner knob

(button)

Outer knob

2. From the Menu screen, open the Tray screen as follows: a. Rotate the outer knob to move the cursor bar (highlight) to Setup, and then press the inner knob (button).

b. Rotate the outer knob to move the cursor bar to Objects, and then press the inner knob (button).

c.

Rotate the outer knob to move the cursor bar to Trays, and then press the inner knob

(button).

The Trays screen lists the available trays.

3. Select a tray as follows: a. Rotate the outer knob to move the cursor bar to the tray that you want, and then press the inner knob (button).

The screen now shows the Tray Type. b. Make the Tray Type active by pressing the inner knob (button) again.

The Tray Type is highlighted.

Thermo Scientific

2

Getting Started

Using the Autosampler Control Terminal c.

Rotate the outer knob to select the tray type. Select NONE if no tray is present

(rotate the outer knob until NONE appears as the Tray Type).

d. Press the inner knob (button) to make the selection.

4. Repeat

step 3

for all the trays to be used.

5. Return to the Job Queue screen by pushing the F4 key (Home) on the control terminal.

Changing the Pulse Time Setting

To control LC systems with a Thermo Scientific LC pump and an autosampler from the

Xcalibur data system, you must change the default pulse time setting for the autosampler from

2 to 4 seconds. The pulse time is the length of time that the autosampler sends an output signal after it makes an injection. The LC pump receives this output signal through the contact closure cable.

IMPORTANT If your LC system contains a Thermo Scientific LC pump and an autosampler, you must change the autosampler’s default pulse time setting. If you leave the default pulse time set to 2 seconds, the status of the LC pump remains at waiting for contact closure after you make an injection.

Change the pulse time setting to 4.0 seconds from the Injected screen (

Figure 17

).

Figure 17. Menu path to Injected screen

Menu

Setup

Objects

Out Signals

Injected

Injected

Destination

Pulse Time

Set

Deflt

SW-Out1

4.0 s

Oms...9.9s

Home

Thermo Scientific Thermo PAL User Guide

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Getting Started

Specifying the Instrument Method Parameters

To change the pulse time setting

1. Open the Injected screen as follows:

a. On the Job Queue screen, press the F1 key to select Menu ( Figure 16 on page 22

).

b. Rotate the outer knob to move the cursor bar (highlight) to Setup, and then press the inner knob (button). c.

Rotate the outer knob to move the cursor bar (highlight) to Objects, and then press the inner knob (button). d. Rotate the outer knob to move the cursor bar (highlight) to Out Signals, and then press the inner knob (button). e.

Rotate the outer knob to move the cursor bar (highlight) to Injected, and then press

the inner knob (button) to display the Injected screen ( Figure 17 on page 23 ).

2. Rotate the outer knob to move the cursor bar (highlight) to Pulse Time, and then press the inner knob (button) to highlight the time cell.

3. Rotate the outer knob to change the pulse time to 4.0 seconds, and then press the inner knob (button) to set this selection as the default.

4. Press the F4 key (Home) to return to the Job Queue screen.

Specifying the Instrument Method Parameters

To inject a sample set automatically, you must create an instrument method that contains the chromatographic conditions and mass spectrometer data acquisition settings, and then create an acquisition sequence that specifies the instrument method and vial location for each run.

This section describes how to specify the basic instrument method parameters for the autosampler. For information on how to create acquisition sequences, refer to the Xcalibur

Sequence Setup view Help topic.

24

Thermo PAL User Guide Thermo Scientific

2

Getting Started

Specifying the Instrument Method Parameters

Creating an Instrument Method

This section provides information about how to create an instrument method.

To specify the instrument method parameters for the autosampler

1. Choose Start > All Programs > Thermo Xcalibur > Xcalibur, and then click the

Instrument Setup icon to open the Instrument Setup window.

Note The Instrument Setup window might take several seconds to open. If you receive a server failure error, follow the instructions on

page xi

.

2. Click the autosampler icon to open its Instrument Setup window.

3. Click the Method Setup tab to open the Method Setup page ( Figure 18 ).

Figure 18. Method Setup page for the autosampler (before you select a template)

Thermo Scientific

4. Under Template Selection, click Browse to open the Browse for Folder dialog box, and then browse to the following folder that contains the autosampler methods (.pme extension):

drive:\Thermo\Instruments\LC Devices\ThermoPAL\PAL\Methods

Thermo PAL User Guide

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2

Getting Started

Specifying the Instrument Method Parameters

5. In the Template list, select a template that represents the task that you want to do.

The autosampler comes with these templates:

• DLW Priming_Rev01.pme

• LC-Inj DLW Fast_Rev03.pme

• LC-Inj DLW Standard_Rev03.pme

• Multi Step LC Injection.pme

• Single Step LC Injection.pme

• Startup-Shutdown.pme

• Thermo PAL.pme autosampler (comprised of three templates):

– Multi Step LC Injection.pme

– Single Step LC Injection.pme

– Startup-Shutdown.pme

If you ordered the DLW option with the autosampler, you can also select the DLW templates.

CAUTION Do not use the three DLW templates if you did not order the DLW option with your autosampler. Using these templates for the Thermo PAL autosampler without the DLW option could cause damage to the instrument and cause the injection to not perform any washes at all.

IMPORTANT If you select a DLW template, make sure the Rear Volume +

Injection Volume + Front Volume + 2x Airgap is less than the syringe size. Otherwise, you receive Error 86 (Syringe Volume Out of Range).

In addition to these templates, you can create your own custom templates (see “Using the

Template Editor to Create Custom Templates” on page 33 ). When you store a custom

template in the same folder as the standard templates, the template appears in the

Template list.

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Thermo PAL User Guide Thermo Scientific

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Getting Started

Specifying the Instrument Method Parameters

Figure 19 shows the macro sequence and the macro variables for the

Single Step LC Injection template.

Figure 19. Method Setup page on the Instrument Setup window with the LC-Inj template

Macro sequence for the Single Step

LC Injection template

Variable list

Thermo Scientific

When you select a template, the macros used by the template appear in the Macro

Sequence area. When you click on a macro listed in the Macro Sequence area, the variables used by the Macro appear in the Variables area.

6. Under Variables, keep the parameters set to the defaults, or type the appropriate values for your application.

7. From the Syringe list, select the syringe size that is installed in the autosampler.

The default variable settings for the Single Step LC Injection template and the default setting of 10 μL in the Recommended Injection Volume box are suitable for a 100 μL syringe. Changing the syringe size can change the allowable ranges for the recommended injection volume and the variables specified in the LC-Inj macro.

Thermo PAL User Guide

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Getting Started

Specifying the Instrument Method Parameters

28

Thermo PAL User Guide

IMPORTANT Make sure that the syringe selection matches the size of the installed syringe.

• If the autosampler is set up to recognize the installed syringe size, an error message appears when you download methods that specify a different syringe size.

• If the autosampler is not set up to recognize the installed syringe and the specified syringe size does not match the actual syringe size, the autosampler does not inject the specified injection volume.

8. Under Recommended Injection Volume, in the Volume (μL) box, type the volume of sample that you want the autosampler to inject.

The allowable injection volume range is based on the syringe size.

IMPORTANT For partial loop injections (variable volume), make sure that the recommended injection volume is less than half the sample loop size.

9. Under Look Ahead Injections, if the Delay Time (mins) box is available, type the amount of time that you want the autosampler to wait after it completes the current injection before it starts the next injection.

During a look ahead injection, the autosampler aspirates the sample for the next injection and waits until the end of the current run to inject the sample into the valve. When you add a delay time, the autosampler does not begin the next injection cycle immediately after completing the current injection cycle. If you enter a delay time longer than the method run time, the autosampler begins the next injection at the end of the current run.

This means that adding a long delay time does not add additional run time to the method run time, but it does cancel the effect of using the Look Ahead Injections feature.

Note The Look Ahead Injections feature is available if you selected the Enable check box in the Look Ahead Injections area of the Pal Configuration dialog box.

10. Specify the acquisition parameters for the other devices of the LC or LC/MS instrument.

11. Save the method: a. From the Instrument Setup window, choose File > Save As. b. Select a folder in which to store the method, and then type a name for the method in the File Name box.

c.

Click Save.

The File Summary Information dialog box appears.

d. (Optional) In the Comment box, type additional information about the method.

e.

Click OK.

The Xcalibur data system (or other Thermo Scientific data acquisition applications such as LCquan™) stores the method as a METH file in the specified file location.

Thermo Scientific

2

Getting Started

Specifying the Instrument Method Parameters

Instrument Setup Parameters

Use the Method Setup page ( Figure 19 on page 27 ) to specify instrument method parameters

for the autosampler.

Table 6. Method Setup page parameters (Sheet 1 of 2)

Parameter

Template Selection

Template

Description

Shows the list of default method templates.

Method Folder

After you select a template, the Template list changes to a box that shows the path to the selected method template file.

Shows the path to the default template folder before you select a default method template.

Browse

New Template

After you select a method template (in the Template list), the

Method Folder box disappears.

Opens the Browse for Folder dialog box to locate the directory that contains the method templates.

After you select a method template (in the Template list), the

Browse button changes to the New Template button.

Select this button to bring back the Template list, Method

Folder box, and Browse button.

After you select a method template (in the Template list), this button appears.

Template Description

Template Description Shows a description of the selected template, which appears in the Template box.

Syringe

Syringe Shows a list of the allowed syringe volumes.

Select the appropriate syringe volume.

Macro Sequence

Macro Sequence Shows the sequence of macros that make up the method displayed in the Template box.

Select a macro name to be displayed in the Macro area; its variables also appear in the Variables area.

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Getting Started

Specifying the Instrument Method Parameters

Table 6. Method Setup page parameters (Sheet 2 of 2)

Parameter Description

Recommended Injection Volume

Volume (μL) When you select an instrument method for use to generate a new sequence (on the Xcalibur Home Page), the injection volume is set to what is entered in this box.

For the LCquan application: When “From AS” (From Auto

Sampler) is specified in the LCquan injection volume sequence cell, the autosampler uses the volume in this box when you submit the LCquan sequence for acquisition.

Look Ahead Injections

Delay Time (mins) Enter the Delay Time (in minutes) between injections when using the Look Ahead feature.

You enable the Look Ahead Injections option from the Pal

Configuration dialog box (

Figure 15 on page 19 ). When you

enable this option, the next Look Ahead Injection is delayed the amount of time entered in this box. The delay time countdown begins at the completion of any post-injection steps, which prevents a sample from being held in the injection syringe for the duration of the current run. If the entered Delay Time is too long, or the current run ends prematurely, the entered Delay Time is canceled and the next injection commences in the normal manner.

Macro

— Shows the name of the selected macro, and the sequence number (x) and total number of macros (y) (displayed as

“name”, x of y).

Variables

Default All

This area also lists the variables associated with the macro chosen in the Macro Sequence pane.

Shows the variable parameters used by the selected macro.

• Variables with specific allowed values (discrete variables) appear in lists. You may choose the allowed values of the discrete variables from those presented in the list.

• Continuous variables are displayed in boxes. The allowed values for continuous variables appear when you hold the cursor over the variable’s box. You can type the value for the continuous variable in the box.

This button changes the variables, used in the selected Macro

Sequence, to their default values.

30

Thermo PAL User Guide Thermo Scientific

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Getting Started

Viewing the Method Summary

Viewing the Method Summary

Use the Method Summary page to view the details of the Macro Sequence that makes up an autosampler Method or Template.

The contents of the Method Summary/Template Summary page is read-only.

To view a summary of the autosampler portion of an instrument method

1. Open the Instrument Setup view for the autosampler (see “Specifying the Instrument

Method Parameters” on page 24 ).

2. Choose File > Open, and then select the instrument method.

3. Click the Method Summary tab.

The Method Summary page appears with a summary of the autosampler parameters for the active instrument method (

Figure 20 ).

Thermo Scientific Thermo PAL User Guide

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Getting Started

Viewing the Method Summary

Figure 20. Method Summary page in the Instrument Setup window

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Thermo PAL User Guide Thermo Scientific

3

Creating Custom Templates and Macros

This chapter describes how to create custom templates and macros. It also includes instructions on how to define variables for macro creation. The Thermo PAL autosampler provides three standard templates.

Contents

Using the Template Editor to Create Custom Templates

Testing a Custom Template

Viewing the Template Summary

Standard Macros

Using the Macro Editor to Create Custom Macros

Defining Variables

Using the Template Editor to Create Custom Templates

Use the Template Editor page of the Pal Template\Macro Editor window to make a new template (a sequence of macros). Each macro in the sequence is made up of variables that you may also edit on this page.

Table 7 on page 35 lists the parameters for the Template Editor

page.

To create a custom template

1. Open the Template Editor page as follows ( Figure 21

): a. Open the Instrument Setup window for the autosampler (see

“Specifying the

Instrument Method Parameters” on page 24

). b. Choose Pal Auto Sampler > Template\Macro Editor.

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Creating Custom Templates and Macros

Using the Template Editor to Create Custom Templates

Figure 21. Template Editor page on the Pal Template\Macro Editor window

34

Thermo PAL User Guide

2. (Optional) In the Template Description box, type a description of your custom template.

3. In the Syringe list, select the appropriate syringe size to be specified in the template.

4. Add macros to the template as follows: a. Under Macro, select a macro from the list.

The Insert Above and Insert Below buttons become available.

b. Click Insert Above or Insert Below.

The selected macro appears in the Macro Sequence box.

5. Delete macros from the Macro Sequence box by selecting the macro and clicking Delete.

6. Replace a macro in the Macro Sequence box as follows: a. Under Macro, select a macro from the list.

b. Select the macro that you want to replace in the Macro Sequence box.

c.

Click Replace.

7. Save the template: a. Click Save As.

b. Select a file location, and then type an appropriate name in the File Name box. c.

Click Save.

The autosampler saves the template with the .pma file extension.

Thermo Scientific

Thermo Scientific

3

Creating Custom Templates and Macros

Using the Template Editor to Create Custom Templates

Table 7. Template Editor page parameters (Sheet 1 of 2)

Parameter

Template Description

Syringe

Macro Sequence

Macro Sequence

Description

Enter the method description in this box.

Select the syringe volume from this list.

Shows the macros selected for the method being made in the

Method Template Editor.

Insert Above

Insert Below

Replace

Delete

Run

The macros in this sequence are selected from the Macro list.

Double-clicking a macro under Macro Sequence displays it in the Macro list as described later in this table, along with the variables that make up the macro (in the Variables area).

Inserts a macro from the

Macro

list above the macro selected under Macro Sequence.

Inserts a macro from the

Macro

list below the macro selected under Macro Sequence.

Replaces the macro selected under Macro Sequence with the

macro that is in the Macro

list.

Deletes the macro selected under Macro Sequence.

Automatically executes the macros that constitute the Method

(Macro Sequence).

Executes the Method (Macro Sequence) in a stepwise manner. Step

Macro

Macro Select individual PAL macros in this list.

Default All

When you select a macro, it is highlighted in blue. The sequence number (x) of the selected macro and the total number of macros (y) in the Macro Sequence box (“Macro

x of y”) appear at the top of the Macro list. You can place the

selected macro under Macro Sequence

by using the Insert

Above, Insert Below, or Replace buttons as appropriate.

Changes all of the Method Template Editor variables to their default values.

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Creating Custom Templates and Macros

Testing a Custom Template

Table 7. Template Editor page parameters (Sheet 2 of 2)

Parameter

Variables

Description

Shows the variables that make up the macro in the Macro list.

• Variables with specific allowed values (discrete variables) appear in lists. You may select the allowed values of the discrete variables from those presented in the list.

• Continuous variables are displayed in boxes. The allowed values for continuous variables appear when you hold the cursor over the variable’s box. You can type the value for the continuous variable in the box.

Buttons

Save Template

Save As

Saves the Method Template under the current file name

(overwrites the current file).

Saves the Method Template under a new file name or in a new location that you type in the Save As dialog box.

Testing a Custom Template

This section provides information about testing a custom template. Use the Run Auto

Sampler Method dialog box to enter the Methods information required for the autosampler to

carry out autosampling. Table 8 on page 38 lists the parameters for the Run Auto Sampler

Method dialog box.

To test your new template step-by-step

1. Open the Template Editor dialog box (see

“To create a custom template” on page 33 ).

2. Open the template to review by choosing File > Open Method Template.

The default path to open a template is as follows:

drive:\Thermo\Instruments\LC Devices\ThermoPAL\PAL\Methods

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Testing a Custom Template

3. Under Macro Sequence, click Step to open the Run Auto Sampler Method in Step Mode dialog box (

Figure 22

).

Figure 22. Run Auto Sampler Method In Step Mode dialog box

4. Make the appropriate entries and selections as follows:

• Under Vial Index, type an appropriate vial location for the template you are testing.

• Under Trays, select the appropriate trays.

• In the Injection Per Vial box, type the number of injections that you want to make from each vial.

• Under Volume, type the volume that you want to inject.

5. Click Run.

The autosampler performs the actions specified in the template, step-by-step. At the completion of each step, the autosampler pauses the injection sequence and prompts you with the Pal Method Editor dialog box (

Figure 23

).

Figure 23. Pal Method Editor dialog box

Thermo Scientific

6. Do one of the following:

• To continue stepping through the template, click Step.

• To run the remaining portion of the template, click Run.

• To stop the run, click Stop Run.

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Creating Custom Templates and Macros

Testing a Custom Template

To run the complete sequence of macros in the template without pausing

1. Open the Template Editor dialog box (see

“To create a custom template” on page 33 ).

2. Open the custom template by choosing File > Template > Open Method Template.

3. Under Macro Sequence, click Run to open the Run Auto Sampler Method dialog box

( Figure 24

).

Figure 24. Run Auto Sampler Method dialog box

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Thermo PAL User Guide

4. Make the appropriate entries and selections (see Table 8

).

5. Click Run.

The autosampler executes the macros listed in the template.

Table 8. Run Auto Sampler Method dialog box parameters (Sheet 1 of 2)

Parameter

Vial Index

1

2

Trays

1

2

1

2

Injectors

Description

Type the vial index to be used with the method (SL.index).

Type the vial index to be used with the method (SL.index2).

Select the tray to be used with the method (SL.tray).

Select the second tray to be used with the method (SL.tray2).

Select the injector to be used with the method (SL.injector).

Select the second injector to be used with the method

(SL.injector2).

Volume

1 Type the injection volume to be used with the method

(SL.volume).

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3

Creating Custom Templates and Macros

Viewing the Template Summary

Table 8. Run Auto Sampler Method dialog box parameters (Sheet 2 of 2)

Parameter

2

Description

Type the second injection volume to be used with the method

(SL.volume2).

Injections Per Vial

— Type the number of replicate injections to be made from each vial.

Buttons

Run

Cancel

Run the selected method.

Cancel any changes and close the dialog box.

Viewing the Template Summary

To view a summary of a template

1. Open the Template Editor dialog box (see

“To create a custom template” on page 33 ).

2. Open the template that you want to review by choosing File > Open Method Template.

The default path to open a template is as follows:

drive:\Thermo\Instruments\LC Devices\ThermoPAL\PAL\Methods

3. Click the Template Summary tab.

The Template Summary page appears with a summary of the active template ( Figure 25 ).

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Creating Custom Templates and Macros

Viewing the Template Summary

Figure 25. Template Summary page

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Standard Macros

Standard Macros

Macros are the building blocks that you use to create templates. Figure 26 shows the macros

that are provided with a standard installation. The default path to the macros is as follows:

drive:\Thermo\Instruments\LC Devices\ThermoPAL\PAL\Macros

Figure 26. Standard macros

Using the Macro Editor to Create Custom Macros

Use the Macro Editor page of the Pal Template\Macro Editor window when you want to

create custom macros. Table 9 on page 43 lists the parameters for the Macro Editor page.

To create a custom macro

1. Open the Macro Editor page as follows (

Figure 27

): a. Open the Instrument Setup window for the autosampler (see

“Specifying the

Instrument Method Parameters” on page 24

). b. Choose Pal Auto Sampler > Template\Macro Editor. c.

Click the Macro Editor tab.

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Creating Custom Templates and Macros

Using the Macro Editor to Create Custom Macros

Figure 27. Macro Editor page of the Template\Macro Editor window

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2. Under Macro, select a macro from the list.

The description of the selected macro appears under Macro Description and a list of macro variables appears under Macro Variables.

3. To add a variable to the macro, do the following: a. Click Add to open the Variable Definition dialog box (

Figure 28 on page 46

). b. Define the variable (see

“Defining Variables” on page 46 ).

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Creating Custom Templates and Macros

Using the Macro Editor to Create Custom Macros

4. Save the macro as follows: a. Click Save As.

b. Select a file location, and then type an appropriate name in the File Name box.

c.

Click Save.

The autosampler saves the macro with the .pma file extension.

Table 9. Macro Editor page parameters (Sheet 1 of 3)

Parameter

Macro

Description

This list displays existing autosampler macros. Select the macro that you want to edit.

Displays a description of the selected macro.

Macro Description

Macro Variables

Add

Displays the variables used by the selected macro.

Adds a new variable to the macro variables.

Edit

Delete

For details, see

“Defining Variables” on page 46

. You define the new variable in the Variable Definition dialog box that opens when you click Add. In this dialog box, you can select the A Numeric Value or An Object option.

• If you select a numeric variable type, you see a pane for entering the new variable name, a list for the variable units, and panes for entering the default value for the variable along with the lower and upper limits for the variable.

• If you select an object variable type, you see a check list of objects that the variable might represent.

Edits an existing macro variable.

You edit a variable in the Edit Parameter dialog box that opens when you click Edit. In this dialog box, you can select the

A Numeric Value or An Object option.

• If you select a numeric variable type, you see a pane for entering a new variable name, a list for the variable units, and panes for entering the default value for the variable along with the lower and upper limits for the variable.

• If you select an object variable type, you see a check list of objects that the variable might represent.

Deletes the selected Macro Variable.

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Using the Macro Editor to Create Custom Macros

Table 9. Macro Editor page parameters (Sheet 2 of 3)

Parameter

Command Sequence

Description

Lists the sequence of commands that make up the macro selected in the Macro list.

Insert Above

Insert Below

Replace

Delete

When you select a command, the command parameters and description appear in the Command area. The command parameters appear in both boxes (continuous variables) and lists (discrete variables).

The command shown in the Command list is inserted above the command selected (highlighted in blue) under Command

Sequence.

The command shown in the Command list is inserted below the command selected (highlighted in blue) under Command

Sequence.

The command selected (highlighted in blue) under

Command Sequence is replaced by the command shown in the Command list.

Deletes the command selected (highlighted in blue) under

Command Sequence.

Command

— Lists the individual autosampler commands. These individual commands make up the command sequence of an autosampler macro. Select the command by moving the cursor over the command (no click is needed), highlighting each command in blue. Clicking the command displays it in this list (highlighted in blue). Simultaneously, the command parameters appear in the Parameters area below the

Command list.

The pane below the Parameters area describes the function of the selected command.

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Creating Custom Templates and Macros

Using the Macro Editor to Create Custom Macros

Table 9. Macro Editor page parameters (Sheet 3 of 3)

Parameter

Parameters

Command Description

Description

Shows the command parameters used by the selected autosampler command.

• Parameters with specific allowed values (discrete parameters) appear in lists. You may choose the allowed values of the discrete parameters from those presented in the list.

• Continuous parameters are displayed in boxes. The allowed values for continuous parameters appear when you hold the cursor over the respective boxes for the parameter. You can type the value for the continuous parameter in its boxes and view other allowed continuous parameter values in a shortcut menu. To activate this menu, right-click the continuous parameter box of interest. The parameter you select from the shortcut menu appears in the box.

Shows a description of the selected command in the bottom pane.

Buttons

Save Macro

Save As

Saves the macro (command sequence) under the current file name (overwrites the current file).

Saves the macro (command sequence) under a new file name, in a new location, or with both a new file name and location that you type in the Save As dialog box.

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Creating Custom Templates and Macros

Defining Variables

Defining Variables

Variables are the building blocks that you use to create macros. Use the Variable Definition dialog box to specify the details of a numerical or object macro variable that you want to add

or edit in the Macro Variables box. Table 10 on page 47 lists the parameters for the Variable

Definition dialog box.

To create custom variables

1. Open the Macro Editor page (

“Using the Macro Editor to Create Custom Macros” on page 41 ).

2. Click Add to open the Variable Definition dialog box (

Figure 28 ).

Figure 28. Variable Definition dialog box

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Thermo PAL User Guide

3. Select a variable type:

• To create a variable that is a numeric value, select the A Numeric Value option, and

then go to step 4

.

• To create an object variable, select the An Object option. A list of objects appears. Go

to step 5 .

4. Complete the definition of a numeric variable as follows: a. In the Variable Name box, type an appropriate name.

b. In the Variable Units list, select a unit of measure.

c.

In the Default Value box, type a default value for the variable.

d. In the Lower Limit box, type a lower limit for the variable.

e.

In the Upper Limit box, type an upper limit for the variable.

f.

Click OK to save the variable and close the Variable Definition dialog box.

5. Complete the definition of an object variable as follows: a. In the Variable Name box, type an appropriate name. b. Select the appropriate objects from the list (

Figure 29

).

c.

Click OK to save the variable and close the Variable Definition dialog box.

Thermo Scientific

Figure 29. Object variable selections

3

Creating Custom Templates and Macros

Defining Variables

Thermo Scientific

Table 10. Variable Definition dialog box parameters (Sheet 1 of 2)

Parameter

Variable Type

A Numeric Value

Description

Select this option if the parameter is a numeric value.

An Object

Variable Name

OK

If you are editing an existing numerical parameter, this option is preselected.

Select this option if the parameter is an object.

If you are editing an existing object parameter, this option is preselected.

If you are editing an existing variable, this box shows the name of the variable. If you are adding a variable, type its name.

Accepts the new Variable Definition or accepts the edits to an existing Variable Definition.

Deletes changes made in the Variable Definition dialog box.

Cancel

Variable Type–Numeric

Variable Units

Default Value

Lower Limit

Upper Limit

If you are editing an existing variable, this list shows the units for the selected variable. If you are adding a variable, you may enter units appropriate for that variable. When you click the list arrow, you can select the appropriate units from the options in the list.

The nominal or center value of the variable.

The lowest acceptable value of the variable.

The highest acceptable value of the variable.

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Defining Variables

Table 10. Variable Definition dialog box parameters (Sheet 2 of 2)

Parameter

Variable Type–Object

Description

Please Check What Objects

This Variable May Be

Select the check boxes for one or more objects that the variable describes.

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4

Using the Direct Controls to Operate the

Autosampler

This chapter describes how to operate the Thermo PAL autosampler from the Direct Control dialog box that you access from the Xcalibur Instrument Setup window or from the Inlet

Direct Control dialog box that you access from the mass spectrometer Tune application. Use the direct controls when you want to control the autosampler before starting a run acquisition.

Contents

Opening the Direct Control Dialog Box

Making Single Injections from the Tune Window

Changing the Tray Configuration

Specifying the Location of the Direct Control Methods

Wrapping Direct Control Injections with Additional Macros

Opening the Direct Control Dialog Box

The direct control pages for the autosampler are available from the Instrument Setup window and the Tune window.

To open the Direct Control dialog box from the Instrument Setup window

1. In the Xcalibur Instrument Setup window, click the autosampler icon.

2. Choose Pal Auto Sampler > Direct Control to open the Direct Control dialog box

( Figure 30

).

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Using the Direct Controls to Operate the Autosampler

Making Single Injections from the Tune Window

Figure 30. Direct Control dialog box

To open the Inlet Direct Control dialog box from the Tune window

1. In the Tune window, choose Setup > Inlet Direct Control.

2. Click the Thermo Pal tab to open the Inlet Direct Control dialog box.

The Inlet Direct Control dialog box has the same functionality as the Direct Control

dialog box shown in Figure 30

.

Making Single Injections from the Tune Window

You can make single injections from the Tune window by using the Methods page of the Inlet

Direct Control dialog box.

Table 11 lists the parameters for the Methods page of the Inlet

Direct Control dialog box.

To make single injections from the Tune window

1. Open the Tune window for your mass spectrometer.

2. Open the Inlet Direct Control dialog box (see

“Opening the Direct Control Dialog Box” on page 49

).

3. Specify the location of the methods that you want to use by using the Direct Control

Configuration page (see “Specifying the Location of the Direct Control Methods” on page 54 ).

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Using the Direct Controls to Operate the Autosampler

Making Single Injections from the Tune Window

4. Specify the tray types that are loaded in the autosampler tray holders (see “Changing the

Tray Configuration” on page 52

).

5. Click the Methods tab.

The Methods page appears. The Syringe area lists the size of the configured syringe. The

Device Status area provides the status of the autosampler.

6. In the Method list, select a method.

A description of the method appears in the Description box. The method list depends on the file locations specified on the Direct Control Configuration page.

Note The visible DLW methods in the Method list are only available if you installed

the DLW option that comes with the autosampler. See Chapter 5, “Using Dynamic

Load and Wash (DLW).”

7. Make the following selections and entries:

• Under Vial Index, type the location of the sample vial.

• Under Trays, select the tray where the sample vial is located.

• Under Volume, type the volume that you want the autosampler to inject.

8. In the Inlet Direct Control dialog box, click the tab for the configured LC pump and start the solvent flow from the LC pump.

Note The Thermo PAL autosampler only downloads the method parameters for the autosampler. It ignores the method parameters for the LC pump and the mass spectrometer.

9. Return to the autosampler Methods page, and then click Run.

Table 11. Methods page parameters (Sheet 1 of 2)

Parameter

Method

Description

Syringe

Device Status

Description

Use this list to select a method file. The visible DLW methods in the Method list are only available if you installed the DLW option that comes with the autosampler.

Contains a description of the selected method.

Lists the size of the configured syringe.

Displays the status of the autosampler.

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Changing the Tray Configuration

Table 11. Methods page parameters (Sheet 2 of 2)

Parameter

Vial Index

1

Description

2

Type the vial index to be used with the method

(SL.index).

Type the second vial index to be used with the method

(SL.index2).

Trays

1

2

Select the tray to be used with the method (SL.tray).

Select the second tray to be used with the method

(SL.tray2).

Volume

1

2

Type the injection volume to be used with the method

(SL.volume).

Type the second injection volume to be used with the method (SL.volume2).

Injectors

1

2

Injections Per Vial

Run

Select the injector to be used with the method

(SL.injector).

Select the second injector to be used with the method

(SL.injector2).

Type the number of replicate injections to be made from each vial.

Runs the selected method.

Changing the Tray Configuration

Use the Tray Configuration page of the Direct Control dialog box to specify the tray types to be used for direct control injections. The autosampler uses this tray information instead of the tray information specified in the autosampler Control Terminal.

Table 12

lists the parameters for the Tray Configuration page of the Direct Control dialog

box. For information about the sample trays, see Appendix A, “Sample Trays.”

IMPORTANT The autosampler does not store the tray configuration that you specify on the Tray Configuration page of the Direct Control dialog box. When you close the dialog box, the tray configuration resets to the autosampler Control Terminal settings.

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Using the Direct Controls to Operate the Autosampler

Changing the Tray Configuration

To temporarily change the tray configuration

1. Open the Direct Control dialog box (see “Opening the Direct Control Dialog Box” on page 49 ).

2. Click the Tray Configuration tab to open the Tray Configuration page ( Figure 31 ).

For information about the sample trays, see

Appendix A, “Sample Trays.”

Figure 31. Tray Configuration page (VT54 example)

Thermo Scientific

3. In the Tray list, select the tray that you want to modify.

4. In the Type list, select the tray type.

Table 12. Tray Configuration page parameters (Sheet 1 of 2)

Parameter

Tray

Description

Select the tray location in the three-drawer (deep drawer) configuration. For information about the

sample trays, see Appendix A, “Sample Trays.”

Type

Range: Tray01–Tray12

Select the tray type.

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Using the Direct Controls to Operate the Autosampler

Specifying the Location of the Direct Control Methods

Table 12. Tray Configuration page parameters (Sheet 2 of 2)

Parameter

Tray Holder

Description

The allowed values are as follows:

• Stack1, for Tray01–Tra06

• CStack1, for Tray07–Tray12

Vials in X Direction,

Vials in Y Direction

Tray holders can hold one or more trays. A Stack is a tray holder that is designed to hold micro plates. The autosampler firmware determines the type and number.

Determined by choice of tray type.

Specifying the Location of the Direct Control Methods

Use the Direct Control Configuration page of the Direct Control dialog box to specify the

location of the methods that you can open on the Methods page. Table 13

lists the parameters for the Direct Control Configuration page.

To specify the method folders

1. Open the Direct Control dialog box (see “Opening the Direct Control Dialog Box” on page 49 ).

2. Click the Direct Control Configuration tab to open the Direct Control Configuration

page ( Figure 32 ).

The default path to the methods that appear in the Method list on the Method page is as follows:

drive:\Thermo\Instruments\LC Devices\ThermoPAL\PAL\DirectControlMethods

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Specifying the Location of the Direct Control Methods

Figure 32. Direct Control Configuration page of the Direct Control dialog box

Default folder (directory) for the direct control methods

Thermo Scientific

3. To add additional file locations, type the folder location in the Path box or click Browse to find the appropriate folder, and then click Add.

The new folder location appears in the box below the row of buttons.

4. To delete a file location, select the folder path, and then click Delete.

5. To reset the file location to the default folder, click Reset.

Table 13. Direct Control Configuration page parameters (Sheet 1 of 2)

Parameter Description

Wrap Each Direct Control Method Run with the Following Macros

Sequence Entry Exit

Method Entry Exit

Select this check box to wrap methods with the sequence list entry and exit macros (SLentry and

SLexit).

Select this check box to wrap methods with the method entry and exit macros (Method Entry and

Method Exit).

Note For more information, see

Wrapping Direct Control Injections with Additional

Macros .

Method Search Paths

Path

Browse

Add

Type the extra path that you want to add for the method search routine.

Use this button to search for the path to a file folder.

Use this button to add a file folder for the method search routine.

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Wrapping Direct Control Injections with Additional Macros

Table 13. Direct Control Configuration page parameters (Sheet 2 of 2)

Parameter

Delete

Reset

[text box]

Firmware Version

Description

Use this button to delete a file folder from the method search routine.

Use this button to remove all of the user-added file folders.

Displays the file folders (directories) where the autosampler searches for methods.

Specifies the firmware version downloaded from the autosampler.

Wrapping Direct Control Injections with Additional Macros

Use the Direct Control Configuration page of the Direct Control dialog box to specify whether the autosampler is to run the SL Entry and SL Exit, the Method Entry and Method

Exit, or all of these macros before and after an injection.

To specify the use of the SL Entry and SL Exit macros

Select the Sequence Entry Exit check box.

To specify the use of the Method Entry and Method Exit macros

Select the Method Entry Exit check box.

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Using Dynamic Load and Wash (DLW)

This chapter describes how to use the Dynamic Load and Wash (DLW) option, which includes how to install the Cycle Composer Macros or ICC Cycles, how to operate the DLW, and a step-by-step illustration of the DLW cycles.

Contents

Overview

Cycle Composer Macros or ICC Cycles

Operating Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Overview

This section contains an overview of the Dynamic Load and Wash (DLW) option.

The DLW option (

Figure 33 ) represents a new wash station concept that combines an

injection cycle with wash steps. The linked combination of the two steps, which are usually separate, minimizes cycle time and carryover.

There are two characterizing features for the DLW option:

• The sample solution never contacts the syringe itself; it is held between the holding loop.

• Wash solvents are pumped from back to front into the DLW system to intensely flush all critical parts that are in contact with the sample.

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Using Dynamic Load and Wash (DLW)

Overview

Figure 33. Dynamic Load and Wash (DLW)

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The DLW option consists of two self-priming micro pumps (mounted on a dedicated bracket), and the wetted parts are Ryton™ PPS and Kalrez™ (FFPM). The pump IN ports connect to the wash solvent bottles and the OUT ports connect to the DLW manifold, which is part of the assembly of the dedicated DLW syringe holder. A holding loop separates the syringe from the DLW actuator to prevent sample from contacting these parts.

The syringe and holding loop are preloaded with wash solvent #1 at the start. The sample is picked up and remains separated from wash solvent #1 by an air gap. After loading the loop and injection, wash solvent #1 is pushed into the system, followed directly by wash solvent #2 to flush the critical valve paths.

The DLW syringe assembly moves to the wash station for further cleaning steps and for preparing the syringe and holding loop for the next cycle.

For further details, see “DLW Cycle Step-by-Step” on page 70 .

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Cycle Composer Macros or ICC Cycles

You can only operate the autosampler DLW option with PAL control software, such as the

ThermoPAL driver for the Xcalibur data system or Cycle Editor for ICC interpretation in another data handling system software.

For software control, the autosampler provides three macros or three cycles. The first macro covers the initial and daily priming of the solvent lines and covers a complete injection cycle.

The second macro is used for Standard speed with optimized washing possibilities. The third

is used for a Fast cycle for optimized throughput and less focus on carryover. See Table 14

.

Table 14. The DLW macro definitions

Macro name Macro description

Priming Accela Open For initial and daily routine priming of the solvent lines and DLW manifold. The Clean Time for both wash solvents is a variable for the user to define the intensity of washing.

Standard Injection

Accela Open

Standard injection cycle using all possibilities of the DLW option.

The injection valve inlet port and the needle are washed with both wash solvents (inside and out). You can add an extra Stator Wash for intensive washing of the injection valve (valve toggle).

Fast Injection Accela

Open

Tuned for speed and high-throughput application. It differs from the Standard DLW macro in that some steps are left out to shorten the cycle time.

For detailed descriptions of all macros (or cycles), see Table 15 on page 61 and

Table 16 on page 62 .

Note The provided macros are written for standard injection valve drives, which are controlled and activated through the AUX interface.

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Installing the Cycle Composer Macros or ICC Cycles

The autosampler ships with a DVD containing various cycles for the DLW option. Macros for the Xcalibur data system are installed by the LC Devices installer. Copy these macros to the driver method folder or the corresponding folder for application within the integrated system.

To copy cycles to your Cycle Composer

1. Navigate in Windows Explorer to the ThermoPAL driver folder. The usual folder location is as follows:

drive:\Thermo\Instruments\LC Devices\ThermoPAL\PAL\

2. If you want to add the DLW option macros to an existing method folder, copy the macro

(.pma) and the method (.pme) files from the DLW Option folder on the DVD to the method folder.

If the PAL system is integrated in a data system software that controls the autosampler by using the Cycle Editor for PAL ICC interpretation (for example, Analyst™,

ChemStation™, Empower™, EZChrom, MassLynx™, or Xcalibur), an ICC Cycle is used and not the Cycle Composer Macro. The cycle file extension is .cyx.

Tip You can convert a Cycle Composer macro to a cycle (extension .cyx) by using the

Cycle Editor software. Conversion is available starting with Cycle Editor version

1.4.0.4.

General Considerations

You must establish the duration of the wash steps for each configuration and application.

Consider factors such as the viscosity and surface tension of the individual wash solvent composition and the backpressure of the system.

Be aware that a higher backpressure builds up if the valve bore size (standard valve bore

0.25 mm) or the installed loop internal diameter is lower. Standard loop internal diameter

(ID) for Thermo-defined loops with a volume of 5, 10, and 20 μL is 0.25 mm. The loop with

2 μL content volume has an ID of 0.125 mm.

Keep the tubing internal diameters of the tubing in line with the valve dimensions, loop ID, and flow rate.

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Priming the Solvent Lines, Wash1 and Wash2

Use this macro at installation to prime the entire system. Set the wash time to approximately

120 seconds for each solvent.

After installation, for best results prime the system before activating the first run. For daily preparation of the system, the wash time can be much shorter: approximately 20 seconds. The goal is an entire liquid system free of any air bubbles.

To prime the solvent lines

1. Set the wash time to approximately 120 seconds for each solvent.

2. After installation, for best results prime the system before activating the first run. For daily preparation of the system, the wash time can be much shorter: approximately

20 seconds. The goal is an entire liquid system free of any air bubbles.

Table 15

describes the function of the Priming Accela Open AS_Rev01 macro.

Table 15. Priming Accela Open AS_Rev01 macro (Sheet 1 of 2)

Macro description

The injection unit moves to the DLW Wash

Station, position Wash1.

Clean Time solvent 1

Eject Speed DLW Syringe

The injection unit moves to the DLW Wash

Station, position Wash2.

The DLW system is rinsed with Wash

Solvent 1 in position Waste.

Clean Time solvent 1

Eject Speed DLW Syringe

The injection valve is cleaned first with the content of the DLW syringe (Wash

Solvent 1), followed by Wash Solvent 2 and finally, the last wash to prepare the system for an injection cycle, rinsed with Wash

Solvent 1 again.

Macro variable

Needle Gap is a parameter from Rinse Inj

Atom. The variable in this macro is Needle

Gap Valve Clean.

The function of this parameter is to minimally raise the needle in the injection port to allow rinsing around the needle tip.

Remark: The Atom Rinse Inj is new, available starting with FW 4.1.x. The DLW actuator/solenoid is activated; the Wash

Solvent (pump), the Needle Gap, and the

Rinse Time are selectable.

A Repeat-End loop enables adding an extra rinsing step, valve toggle.

The pressure of the spring-loaded balls in the

DLW Syringe Holder assembly is released by moving approximately 3 mm up (default).

This leaves a gap, between the needle tip and the valve bottom, of approximately 1 mm to enable a flush at this contact point.

Stator Wash:

Counter 0 = disable valve toggle steps

Counter 1 = enable valve toggle steps

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Table 15. Priming Accela Open AS_Rev01 macro (Sheet 2 of 2)

Macro description Macro variable

If the counter is set to 1, follow the described steps below. If the counter is set to 0, the macro finishes at this point.

— The injection moves to the injection valve.

The valve is switched to the Active position.

The valve is rinsed with Wash Solvent 2, followed by Wash Solvent 1.

Stator Wash Time Solvent 2

Stator Wash Time Solvent 1

Remark: The loop is filled with the last rinse of Wash Solvent 1. Verify the composition of

Wash Solvent 1. The solvent should have a lower elution power than the solvent gradient starting conditions or sample solvent composition. This is important for partial loop filling.

— The injection valve is switched back to the

Standby position.

End of macro DLW Priming.

Standard DLW Injection Cycle

Table 16

describes the function of the Stand Injection Accela Open macro.

Table 16. Stand Injection Accela Open macro parameters (Sheet 1 of 3)

Macro description Macro variable

The PAL system waits first for the Sync

Signal Ready before the injection cycle starts.

The injection valve moves to a defined

Standby position.

Remark:

Sync Signal setting Start

Inject to

Standby

The Rear air segment pulls into the Holding

Loop.

Airgap Volume

Filling Speed

The sum of Rear-, Sample List-, and

Front-Volume aspirates into the Holding

Loop.

Front Volume

Rear Volume

(SL.volume)

The Front air segment aspirates.

Airgap Volume

Filling Speed

Pullup Delay

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Table 16. Stand Injection Accela Open macro parameters (Sheet 2 of 3)

Macro description Macro variable

The injection unit moves to the DLW Wash

Station, Wash1 position.

The needle is inserted (dipped) for 1 second to wash the outer needle surface. No plunger movement at this step.

The injection unit moves to the specified injection valve.

The Front- and Airgap-Volume is ejected.

Inject to

Front Volume

Airgap Volume

Injection Speed

The PAL system waits for the data system.

Wait for DS

The injection valve switches to Active position.

Wait the Pre Inject Delay time.

The loop fills with the sample volume as specified in the Sample list.

Inject to

Pre Inject Delay

(SL.volume)

Injection Speed

Post Inject Delay The injection valve switches to Standby position, the loop content is injected.

Timer Delay Stator Wash starts and sends a

Start signal to the HPLC system.

Timer 1

The plunger of the DLW Syringe moves down to dispense the Rear Sample and Air

Segment to Waste. The Holding Loop is still filled with Wash Solvent 1.

(Syr. Eject Speed)

The DLW Actuator/Solenoid activates to deliver Wash Solvent 2 into the Holding

Loop to clean the injection valve from Port 1 to Port 2.

Wash2

Inject to

Needle Gap Valve Clean

Valve Clean Time Solvent 2

For this step the needle tip is lifted, releasing the sealing pressure to enable rinsing around the tip sealing point.

The injection unit moves to the DLW Wash

Station, Wash2 position.

Wash2

(Syr.Eject Speed)

The needle is rinsed inside and out with

Wash Solvent 2.

Post Clean Time Solvent2

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Table 16. Stand Injection Accela Open macro parameters (Sheet 3 of 3)

Macro description

The injection unit moves back to the DLW

Wash Station, Wash1 position to flush the syringe needle inside and out with Wash

Solvent 1.

Macro variable

The injection unit moves back to the injection valve. The Inlet Port and engraving to waste Port are flushed with Wash Solvent

1 to prepare the valve for the next injection.

Wash1

Inject to

Needle Gap Valve Clean

Valve Clean Time Solvent 1

Wash1

Post Clean Time Solvent 1

This is a preparation step for the next injection, and especially important for biofluid samples.

Cycle end for LC-Inj DLW Standard macro. —

An optional cleaning step is attached to the

DLW Standard injection cycle: Stator Wash or valve toggle.

Stator Wash

Stator Wash count: 1 = Cleaning step active

Stator Wash count: 0 = Cleaning step disabled

A Repeat-End loop can be activated with the

Count.

— If Stator Wash is activated, the following steps are executed.

The injection unit moves to the injection valve. From the last step above, the Holding

Loop is filled with Wash Solvent 1.

Inject to

Delay Stator Wash

(Active)

Timer 1 waits to switch the valve (Toggle) into Active position (fill loop).

The DLW Actuator/Solenoid activates to deliver Wash Solvent 2 to the Holding Loop and into the valve system.

Inject to

Wash2

Stator Wash Time Solvent 2

The first solvent flush arriving at the valve is

Wash Solvent 1 parked in the Holding Loop at the beginning, followed by Wash

Solvent 2.

Wash Solvent changes to Wash Solvent 1.

The injection valve switches back to the

Standby position.

Inject to

Wash1

Stator Wash Time Solvent 1

Inject to

(Standby)

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Using Dynamic Load and Wash (DLW)

Cycle Composer Macros or ICC Cycles

Fast DLW Injection Cycle

The Fast injection cycle differs from the Standard cycle as follows:

• The needle is not dipped in the Wash station Wash1 after sample pickup and before it moves to the injection valve.

• The wash steps after injection are reduced to Valve Clean with Wash Solvent 1 and Wash

Solvent 2. The DLW needle is flushed in the DLW Wash Station with Wash Solvent 1 only.

• Stator Wash (valve toggle) is not available.

Table 17

describes the function of the Fast Injection Accela Open macro.

Table 17. Macro Fast Injection Accela Open (Sheet 1 of 2)

Macro description Macro variable

The PAL system waits first for the Sync

Signal Ready before the injection cycle starts.

Remark:

Sync Signal setting Start

The injection valve moves to a defined position: Standby.

The Rear air segment aspirates into the

Holding Loop.

Inject to

Standby

Airgap Volume

Filling Speed

The sum of Rear-, Sample List-, and

Front-Volume aspirates into the

Holding Loop.

The Front air segment aspirates.

The injection unit moves to the specified injection valve.

The Front- and Airgap-Volume ejects to

Waste.

Front Volume

Rear Volume

(SL.volume)

Airgap Volume

Filling Speed

Pullup Delay

Inject to

Front Volume

Airgap Volume

Injection Speed

The PAL system waits for the data system.

Wait for DS

The injection valve switches to Active position.

Wait the Pre Inject Delay time.

Inject to

Pre Injection Delay

The loop fills with the sample volume as specified in the sample list.

(SL.volume)

The injection valve switches to Standby position, and the loop content is injected.

Injection Speed

Post Inject Delay

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Using Dynamic Load and Wash (DLW)

Operating Dynamic Load and Wash (DLW)

Table 17. Macro Fast Injection Accela Open (Sheet 2 of 2)

Macro description Macro variable

The plunger of the DLW Syringe moves down to dispense the Rear Sample and Air

Segment to Waste. The Holding Loop is still filled with Wash Solvent 1.

Injection Speed

The DLW Actuator/Solenoid activates to deliver Wash Solvent 2 into the Holding

Loop to clean the injection valve from Port 1 to Port 2.

Inject to

Wash2

Needle Gap Valve Clean

Valve Clean Time Solvent 2

For this step the needle tip is lifted, releasing the sealing pressure to enable rinsing around the tip sealing point.

Wash Solvent 1 follows to prepare the valve for the next injection.

The injection unit moves back to the DLW

Wash station, Wash1 position to flush the syringe needle inside and out with Wash

Solvent 1.

Wash1

Inject to

Needle Gap Valve Clean

Valve Clean Time Solvent 1

Wash1

Post Clean Time Solvent 1

This is a preparation step for the next injection, and is especially important for biofluid samples.

Cycle ends for LC-Inj DLW Fast macro.

Operating Dynamic Load and Wash (DLW)

This section describes how to operate the Dynamic Load and Wash (DLW) option.

Priming the Solvent Lines

Location of Solvent and Waste Bottles

DLW Pumps

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Using Dynamic Load and Wash (DLW)

Operating Dynamic Load and Wash (DLW)

Priming the Solvent Lines

Tip For trouble-free DLW operation, make sure the two solvent lines are free of air bubbles at all times. If the solvent lines are being connected for the first time or during a solvent change, you must prime the solvent lines properly until air bubbles are no longer visible. Use solvent degassing for best results.

To make the initial and daily priming efficient and controllable, the Open autosampler comes with a Cycle Composer macro, or ICC cycle.

To prime the solvent lines

1. Load the macros and methods into the folder.

2. Start the corresponding macro for initial or daily priming.

3. Check the solvent lines and prime until air bubbles are no longer visible.

4. Press F4 for Home.

Location of Solvent and Waste Bottles

The DLW option contains self-priming membrane pumps. You can place the solvent bottles either in the fast wash station holder or on the lab bench.

You must place the Waste bottle greater than 30 cm (11.8 in.) below the injection valve. Make sure that the waste liquid can flow into the waste bottle without restriction. Place the waste tubing above the level of the liquid. Ideally, the tube is fixed at the neck of the waste bottle.

Tip Use good laboratory practice to avoid contaminating the wash solvents and the wash bottles. Avoid biological growth in pure water by either replacing it regularly or adding a small percentage of organic solvents, such as methanol or acetonitrile. Certain buffer solutions can decompose at room temperature when exposed to light. Filtering the wash solvents before filling the bottle, especially if using salt buffers, is mandatory to avoid any clogging of the solvent paths.

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Using Dynamic Load and Wash (DLW)

Operating Dynamic Load and Wash (DLW)

DLW Pumps

From the control point of view, the DLW pumps respond in the same manner as the fast wash station. Power-out signals activate the pumps. Because the electric current setting for the

DLW is different, you must load the corresponding PAL Firmware Objects for the DLW wash station type.

The wetted parts in the pump are made from the following materials:

• Membrane: Kalrez (FFPM)

• Body, valves: Ryton PPS

The pumps are self priming with a maximum suction lift of a 3 m column of water.

DLW Actuator/Solenoid

The DLW Actuator/Solenoid has the function of separating and completely shutting off the lines in the direction of the syringe (sample loading) or the wash solvent lines.

After opening the DLW Actuator/Solenoid for the wash solvent lines, you can pump the desired wash solvent into the system by activating the corresponding DLW pump.

Figure 65 on page 100

illustrates this functionality as part of the step-by-step cycle for a standard injection.

The wetted parts in the DLW Actuator Solenoid are made from the following materials:

• Solenoid body: PEEK™

• Seal material: FFKM (Simriz™)

Note PEEK exhibits excellent chemical resistance to most of the chemicals used.

However, the following solvents are not recommended for use with PEEK: DMSO, THF, methylene chloride (dichloromethane), nitric acid, or sulfuric acid. For more details, refer to the compatibility tables provided by the manufacturer of PEEK material or components.

Note Current applied from the actuator control PCB to the actuator/solenoid activates a green LED. This activation does not indicate that the solenoid opens or closes.

Figure 34 shows the DLW manifold and the actuator/solenoid connections. Figure 35 shows

the DLW flow diverter being inserted.

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Thermo PAL User Guide Thermo Scientific

Figure 34. DLW manifold and Actuator/Solenoid

5

Using Dynamic Load and Wash (DLW)

Operating Dynamic Load and Wash (DLW)

Figure 35. Inserting the DLW Flow Diverter

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

DLW Cycle Step-by-Step

This section provides illustrations to demonstrate a step-by-step DLW cycle.

Cycle for Standard Injection

Additional Valve Toggle Step to DLW Standard Cycle

Cycle for Fast Injection

Cycle for Standard Injection

Figure 36 to

Figure 49 illustrate a step-by-step cycle for the standard injection.

Figure 36. Standard: Start the cycle

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Figure 37. Standard: Step 1 – Aspirate rear air segment

5

Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 38. Standard: Step 2 – Get sample and aspirate rear, inject, and front volume

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Figure 39. Standard: Steps 3 - 4 – Aspirate front air segment

5

Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 40. Standard: Steps 5 - 6 – Insert the needle in wash position 1 to clean the outside

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 41. Standard: Steps 7 - 8 – Dispense front air segment and front sample volume to waste

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 42. Standard: Steps 9 - 10 – Switch valve to LOAD position and fill loop with inject volume

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 43. Standard: Step 11– Switch valve to INJECT position and start chromatographic process

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 44. Standard: Step 12 – Dispense rear sample volume and air segment to waste

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 45. Standard: Steps 13 - 14 – Clean valve with Wash Solvent 2

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 46. Standard: Steps 15 - 16 – Wash the syringe needle with Wash Solvent 2

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 47. Standard: Steps 17 - 18 – Clean valve with Wash Solvent 1

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 48. Standard: Steps 19 - 20 – Wash the syringe needle with Wash Solvent 1

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Figure 49. Standard: End cycle

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Additional Valve Toggle Step to DLW Standard Cycle

This section contains information about additional steps that are necessary for a DLW

Standard Cycle.

Considerations for Additional Stator Wash Cleaning Step

The DLW Standard Cycle has the built-in option for the user to switch the injection valve at the end of the chromatographic run before equilibration of the column to the start conditions.

If the method variable “Stator Wash” is set to “1,” the extra cleaning process for the valve, with

“Valve Toggle,” is part of the standard cycle.

If the method variable is deactivated (setting “0”), the DLW Standard cycle ends as shown in

Figure 49 on page 83

.

The macro (cycle) is written such that the optional valve toggle steps can be executed before re-equilibration of the column. You must synchronize the time to switch the valve with the chromatographic method by using the method variable Delay Stator Wash. The two wash solvents are timed by the method variables, Stator Wash Time Solvent 1 and Stator Wash

Time Solvent 2. After these wash times have elapsed, the valve switches back to the start position.

Figure 50 illustrates the recommended retention time for Stator Wash or Valve Toggle times.

Figure 50. Timing for Stator Wash Step

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Thermo PAL User Guide

From a chromatographic viewpoint, the optional cleaning step is important to understand.

Assuming that the valve stator between ports 1 and 6 (for example, in the standard

Cheminert™ valve) is contaminated and cannot be cleaned during the injection process, the valve toggle brings the engraving back between the two ports. Flushing the valve with both wash solvents eliminates remaining sample material located between stator ports 1 and 6.

Thermo Scientific

Thermo Scientific

5

Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

What points must you consider when you use the Stator Wash or Valve Toggle option?

Observe the rules if biofluid samples are injected. First, sample contact should always be with an aqueous solution to avoid protein precipitation. After washing with organic solvent (higher elution power), flush the system again with wash solvent 1.

The first toggle near the end of the chromatographic cycle provides the advantage that the sample loop is already flushed out first with the mobile phase with a solvent of high elution power (assuming gradient application).

The second valve toggle time follows immediately after finishing the second solvent flush. You cannot program a second switching time. The waiting time for the second valve toggle should be long enough so that the entire system is flushed out by both wash solvents.

Consider the entire delay volume to determine the second valve switch. The DLW internal volumes are as follows:

Manifold, 90 μL

Holding Loop,108 μL

Syringe Needle Gauge 22, 6.7 μL

Installed Injection Loop

Total delay volume: 205 μL + Loop content volume

Do the second valve toggle (back to starting condition) before the system equilibration time has started. The Loop content is ideally a solvent of a low elution power when switched back.

If you apply isocratic chromatography, the remaining contaminants might be washed into the system and can build up higher background noise for the column, the detector, or both over a longer period of time.

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Additional Cleaning by Using the Stator Wash or Valve Toggle

Figure 51 to

Figure 56 illustrate additional cleaning steps for “Stator Wash.”

Stator Wash: End of Standard Injection Cycle

Figure 51. Start the additional Valve Toggle cleaning step

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Thermo PAL User Guide Thermo Scientific

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 52. Stator Wash: Step 1 - 2 – Switch valve to Load Position (toggle) and clean valve with

Wash Solvent 1

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 53. Stator Wash: Step 3 – Clean valve with Wash Solvent 2

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 54. Stator Wash: Step 4 – Wash Solvent 1 dispenses Wash Solvent 2

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 55. Stator Wash: Step 5 – Wash Solvent 1 cleans second valve

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 56. Stator Wash: Step 6 – Switch valve back to Inject Position (toggle)

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Cycle for Fast Injection

Figure 57 to

Figure 68 illustrate a step-by-step cycle for the Fast Injection.

Figure 57. Fast: Cycle starts

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Figure 58. Fast: Step 1 – Aspirate rear air segment

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 59. Fast: Step 2 – Get sample and aspirate rear, inject, and front volume

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Thermo PAL User Guide Thermo Scientific

Figure 60. Fast: Step 3 - 4 – Aspirate front air segment

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 61. Fast: Steps 5 - 6 – Dispense front air segment and front sample volume to waste

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 62. Fast: Steps 7 - 8 – Switch valve to LOAD position and fill loop with Inject Volume

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 63. Fast: Step 9 – Switch valve to INJECT position and start chromatographic process

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 64. Fast: Step 10 – Dispense rear sample volume and air segment to waste

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 65. Fast: Steps 11 - 12 – Clean valve with Wash Solvent 2

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 66. Fast: Steps 13 - 14 – Clean valve with Wash Solvent 1

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

Figure 67. Fast: Step 15 – Wash the syringe needle with Wash Solvent 1

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Figure 68. Fast: End cycle

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Using Dynamic Load and Wash (DLW)

DLW Cycle Step-by-Step

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A

Sample Trays

This appendix describes the nomenclature for the stack number, tray location number, and sample start location number.

Note You must use the handheld Control Terminal to specify the stack, tray location, and sample start numbers.

For more information about the trays, refer to the Accela Open Autosampler Hardware Manual.

Contents

Tray Types

Tray Position

Sample Position

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Sample Trays

Tray Types

Tray Types

Figure 69

through Figure 72 show the tray types for use in the Thermo PAL autosampler.

Figure 69. Tray type VT54

Figure 70. Tray type MT96

54-position, vial tray (9 × 6)

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Thermo PAL User Guide

96-position, standard shallow micro plate (12 × 8)

Thermo Scientific

A

Sample Trays

Tray Types

Figure 71. Tray type DW96

Thermo Scientific

Figure 72. Tray type MT384

96-position, deep well micro plate (12 × 8)

384-position, high-density shallow micro plate

(24 × 16)

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Sample Trays

Tray Position

Tray Position

The nomenclature for the stack, tray, and sample positions is as follows:

CStk1–TT:SS

Where:

• CStk1 refers to the first stack cooler, which contains multiple tray drawers. (The designation for a second stack cooler is CStk2.)

TT is the tray position within the overall stack.

Figure 73 shows the six tray positions,

numbered 01 through 06, for a three-drawer stack.

Figure 73. Tray positions in a stack cooler with three drawers

Position 02

(back)

Top drawer

04 Middle drawer

Position 01

(front)

03

06 Bottom drawer

05

Front of drawer

SS is the sample position within the designated tray. For examples, see Table 18

and the

formula

that follows the table.

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Sample Trays

Sample Position

Sample Position

For the 54-position tray, use the marked numbers on the tray to specify the sample start

location. For the 96-position well plates, use the position numbers listed in Table 18

. For the

384-position well plate, use the formula

that follows the table to calculate the sample start position number.

Table 18. Position numbers for the 96-position (12 × 8) micro plate

A3

A4

A5

A6

A-B No. B-C No. C-D No. E-F

A1

A2

1

2

B5

B6

17

18

C9

C10

33

34

E1

E2

3

4

5

6

B7

B8

B9

B10

19

20

21

22

C11

C12

D1

D2

35

36

37

38

E3

E4

E5

E6

A7

A8

7

8

A9 9

A10 10

A11 11

A12 12

B1

B2

13

14

B3

B4

15

16

B11

B12

C1

C2

C3

C4

C5

C6

C7

C8

23

24

25

26

27

28

29

30

31

32

D3

D4

D5

D6

D7

D8

D9

D10

D11

D12

39

40

41

42

43

44

45

46

47

48

E7

E8

55

56

E9 57

E10 58

E11 59

E12 60

F1

F2

61

62

F3

F4

63

64

51

52

53

54

No. F-G No. G-H No.

49

50

F5

F6

65

66

G9

G10

81

82

F7

F8

F9

F10

67

68

69

70

G11

G12

H1

H2

83

84

85

86

F11

F12

G1

G2

G3

G4

G5

G6

G7

G8

71

72

73

74

75

76

77

78

79

80

H3 87

H4 88

H5 89

H6 90

H7 91

H8 92

H9 93

H10 94

H11 95

H12 96

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Sample Trays

Sample Position

Use the following formula to calculate the sample position number:

N = ([Row – 1] × W) + Col

Where:

N is the calculated sample position number in the tray.

Row is the sample’s row converted to a number.

A equals 1, B equals 2, C equals 3, and so on.

W is the total number of columns on the tray:

– Equals 12 for the 96-position tray

– Equals 24 for the 384-position tray

Col is the sample’s column number:

– Equals 1 to 12 for the 96-position tray

– Equals 1 to 24 for the 384-position tray

The following example is for the sample position C22 in a 384-position micro plate:

N = ([3 – 1] × 24) + 22 = 48 + 22 = 70

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I

Index

A

autosampler control terminal, using

21

C

cables

DB9 to DB9 serial cable

4

external contact trigger cable

12

PAL interface cable

12

Thermo Dual Configuration cable

10

Thermo Single Configuration cable

6

compliance

FCC

iii

regulatory

iii

compliance, WEEE

v

computer requirements

xi

contact closure connections for a Thermo Scientific LC pump

7

for a Thermo Scientific MS

7

for an Agilent pump

12

for two Thermo Scientific pumps

10

contacting us

xiii

control terminal attached to the autosampler

21

cycle composer macros

59

cycle composer macros or ICC cycles, installing

59

Cycle Editor

59

D

delay time

28

device drivers

xi

Direct Control Configuration page

54

Direct Control dialog box, opening

49

DLW characterizing features

57

cycle

70

cycle for fast injection

92

cycle for standard injection

70

fast injection cycle

65

Thermo Scientific macro definitions

59

operating

66

overview

57

priming solvent lines

61

standard injection cycle

62

DLW Actuator/Solenoid

68

DLW Pumps

68

documentation accessing

x

additional

x

online

xiv

survey

xiv

E

electromagnetic compatibility

iii

EMC compliance

iii

equation, sample position number in tray

110

error message, server failure

xi

external contact board for Agilent pump

12

external contact closure cable connections

7

F

FCC compliance

iii

file types instrument methods (.meth)

28

macro (.pma)

43

templates (.pme)

34

I

ICC cycles

59

Injected screen on hand-held controller

23

Inlet Direct Control, opening

50

Instrument Configuration window

17

Instrument Setup window, opening

25

Thermo PAL User Guide 111

Index: J

J

Job Queue screen

22

L

level surface, importance of

2

lithium battery

1

M

Macro Editor enabling

19

opening

41

page parameters

41

Macro, Instrument Setup

30

macros creating

41

cycle composer

59

importing

19

list of standard

41

mass spectrometry applications

ix

Menu screen

22

method parameters, specifying

25

method templates, list of

26

N

nomenclature for stacks, trays, and samples

105

numeric variables

46

O

object variables

46

ordering information

2

output signal to LC pump

5

P

parameters

Direct Control

Method page

Description

51

Device Status

51

Injections Per Vial

52

Injectors

52

Method

51

Syringe

51

Trays

52

Vial Index

52

Volume

52

Tray Configuration page

Tray

53

Tray Holder

54

Type

53

112

Thermo PAL User Guide

Vials in X Direction

54

Vials in Y Direction

54

Instrument Configuration

20

Auto Select

20

Browse

21

Check

20

Com Port

20

Enable

20

Import

21

Import Path

21

Overwrite Existing Macros

21

Stack

21

Tray Name

21

Instrument Setup

Browse

29

Delay Time

30

Macro Sequence

29

Method Folder

29

New Template

29

Syringe

29

Template

29

Template Description

29

Variables

30

Volume

30

Macro Editor page

Add

43

Command

44

Command Description

45

Command Sequence

44

Delete

43

44

Edit

43

Insert Above

44

Insert Below

44

Macro

43

Macro Description

43

Macro Variables

43

Parameters

45

Replace

44

macros

Fast Injection Accela Open

65

Priming Accela Open AS_Rev01

61

Stand Injection Accela Open

62

Run Auto Sampler Method dialog box

Injectors

38

Trays

38

Vial Index

38

Volume

38

Template Editor page

33

Variable Definition dialog box

A Numeric Value

47

An Object

47

Default Value

47

Lower Limit

47

Upper Limit

47

Thermo Scientific

Variable Name

47

Variable Units

47

part numbers

2

priming solvent lines

61

pulse time of the out signals, setting

24

pumps, self-priming

58

R

Recommended Injection Volume box

28

regulatory compliance

iii

release notes

xi

requirements computer

xi

software

xi

Run Auto Sampler Method dialog box parameters

36

S

safety information

1

safety standards

iii

sample trays

105

self-priming micro pumps

58

server failure error message

xi

software requirements

xi

solvent lines, priming

61 ,

67

stack, cooler

108

survey link

xiv

syringe size, specifying

28

system requirements

xi

T

Template Editor enabling

19

opening

33

Template Editor page parameters

33

templates editing

33

Single Step LC Injection

26

testing

36

Thermo PAL driver for Xcalibur

59

Tray Configuration page

53

tray type, selecting with the PAL Control Terminal

22

Trays

38

trays position in stack

108

sample position

109

type

DW96

107

MT384

107

Thermo Scientific

MT96

106

VT54

106

Trays screen

22

Tune window, making single injections from

50

V

variables, defining

46

W

Waiting for contact closure status for LC pump

23

WEEE compliance

v

Index: R

Thermo PAL User Guide

113

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