Thermo PAL User Guide Version E

Thermo PAL User Guide Version E
Thermo PAL
User Guide for LC Devices
XCALI-97169 Revision E
January 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.
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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.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
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
Software version: Thermo Foundation (see page x); Thermo Xcalibur 2.1 or later; Thermo LC Devices 2.5.0 or
later
Firmware version: 2.5.0 for the PAL autosampler
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.
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 is required to comply 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. See www.thermoscientific.com/
rohsweee for further information on Thermo Fisher Scientific’s compliance with these Directives and the recyclers in
your country.
WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen.
Das Produkt ist durch folgendes 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. Mehr Information
über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise,
die nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter
www.thermoscientific.com/rohsweee.
Conformité DEEE
Ce produit doit être conforme à 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 compagnies de recyclage dans chaque état membre de
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les
produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur www.thermoscientific.com/rohsweee.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Supported Firmware Versions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Thermo Scientific
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Selecting the Tray Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Changing the Pulse Time Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Specifying the Instrument Method Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 25
Viewing the Method Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 3
Creating Custom Templates and Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Using the Template Editor to Create Custom Templates . . . . . . . . . . . . . . . . . 35
Testing a Custom Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Viewing the Template Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Standard Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Using the Macro Editor to Create Custom Macros . . . . . . . . . . . . . . . . . . . . . . 43
Defining Variables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Thermo PAL User Guide
vii
Contents
Chapter 4
Using the Direct Controls to Operate the Autosampler . . . . . . . . . . . . . . . . . . . . .51
Opening the Direct Control Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Making Single Injections from the Tune Window. . . . . . . . . . . . . . . . . . . . . . . 52
Changing the Tray Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Specifying the Location of the Direct Control Methods . . . . . . . . . . . . . . . . . . 56
Wrapping Direct Control Injections with Additional Macros . . . . . . . . . . . . . . 58
Chapter 5
Using Dynamic Load and Wash (DLW) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Installing Cycle Composer Macros or ICC Cycles . . . . . . . . . . . . . . . . . . . . . . . 61
General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Priming the Solvent Lines, Wash1 and Wash2 . . . . . . . . . . . . . . . . . . . . . . . 62
Standard DLW Injection Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Fast DLW Injection Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Operating Dynamic Load and Wash (DLW) . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Priming the Solvent Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Location of Solvent and Waste Bottles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
DLW Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
DLW Actuator/Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
DLW Cycle Step-by-Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Cycle for Standard Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Additional Valve Toggle Step to DLW Standard Cycle . . . . . . . . . . . . . . . . . 85
Cycle for Fast Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Appendix A Sample Trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
Tray Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Tray Position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Sample Position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
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Thermo PAL User Guide
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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™ mass spectrometry application, such as the Xcalibur™
data system.
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
• Safety and Special Notices
• Contacting Us
 To suggest changes to documentation or to 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 includes Help.
 To view product manuals
For an LC instrument controlled by a Thermo Scientific software application, choose
Start > All Programs (or Programs) > Thermo Instruments > Manuals > LC Devices >
CTC.
For the Xcalibur manual set, choose Start > All Programs (or Programs) >
Thermo Xcalibur > Manuals > Xcalibur.
 To open Help
• From the Thermo Xcalibur Instrument Setup window, choose Help > Thermo Pal
Help.
• If available for a specific window or dialog box, click Help or press the F1 key for
information about setting parameters.
For more information, visit www.thermoscientific.com.
System Requirements
Table 1 lists the system requirements for the Thermo PAL autosampler drivers provided on
the DVDs for LC Devices 2.5.0 or later.
IMPORTANT Before you install the device drivers provided on the LC Devices DVDs,
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,
where x.x.x is the version you want to install. You can find the Release Notes, which
includes the system requirements, on the LC Devices DVD.
x
Thermo PAL User Guide
Thermo Scientific
Preface
Table 1. System requirements
System
Minimum requirements
Computer
•
•
•
•
•
•
2 GHz processor with 1 GB RAM
DVD drive
80 GB available on drive C
Video card and monitor capable of 1280 × 1024 resolution
Network interface cards, two
NTFS format
Software
• Adobe™ Reader™ 9.0
• Microsoft™ Windows™ operating system:
−
Windows 7 Professional (32-bit and 64-bita)
−
Windows XP Workstation SP3
• Thermo Scientific software:
a LC
LC Devices
Foundation
2.6.0 and later
1.0.2 SP2 and later
2.5.0 SP3
1.0.2 SP2
2.5.0 SP1 or SP2
2.0
2.5.0
1.0.2 SP2
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 Thermo Foundation and LC Devices are compatible
(see Table 1).
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
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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.
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Thermo PAL User Guide
Thermo Scientific
Preface
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes. Safety and special notices include the following.
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
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
Find software updates and utilities to download at mssupport.thermo.com.
 To contact Customer Service for ordering information
Phone
800-532-4752
Fax
561-688-8731
E-mail
[email protected]
Web site
www.thermo.com/ms
 To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
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 documentation or to 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
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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 2.
Table 2. Thermo PAL ordering information
Description
Part number
HTC PAL
OPTON 13009
HTC PAL with the 98 × 2 mL tray holder
OPTON 13010
HTS PAL
OPTON 13008
Table 3 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 3. Contact closure cables used to connect an Agilent pump
Description
Supplier
Part number
DB15 connector × 15 wire cable
Thermo Fisher Scientific
00012-27716
DB15 connector × 15 wire cable
Agilent
G1103-61611
PAL Interface Cable for APG Remote
DB15 connector × DB9 connector cable
CTC Analytics
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)
Data system
computer
Autosampler
TERMINAL
SER1
LAN
MODBUS
BUZZER L
E
D
WASH
STATION
INTERFACE 1
INTERFACE 2
AUX 1
AUX 2
POWER FUSE
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
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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 4).
Table 4. PAL contact closure port
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Thermo PAL User Guide
PAL model
Port marking
HTC, LC
INTERFACE
HTS
INTERFACE 1
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 5).
Table 5. Contact closure cable connection to Thermo Scientific pump
Pump model
Clear wire
Black wire
Accela Pump
GRAD START (pin 4)
GND
Surveyor LC Pump Plus
PROG. START (pin 4)
GND
Surveyor MS Pump Plus
GRAD START (pin 8)
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
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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
–or–
Surveyor MSQ Plus MS
–or–
Start
In
+ -
+30V Max
Start In
Start In +
Start In -
To mass spectrometer
Autosampler
INTERFACE
AUX
INTERFACE
WASH
STATION
POWER
LED BUZZER
SER3 SER2
SER1
DB15
Cbl Thermo Single Config.
To LC pump
RS232
1 2 3 4 5 6 7 8
Surveyor MS Pump Plus
RS232
UNIT ID
ENET
NC
FW DOWNLOAD
PRESSURE PRESSURE+
NC
NC
+5V @ 150mA
GND
Thermo PAL User Guide
RS232 I/O
PUMP ON
GND
NC
NC
PROG. START
NC
+5V @ 150mA
GND
8
1 2 3 4 5 6 7 8
GRAD START
GND
(-)
INJECT HOLD
(-)
PUMP READY
+5V @ 10mA
GND
PRESSURE
GND
INJECT HOLD
PUMP READY
GRAD. START
PUMP STOP
5V
GND
Accela Pump
USB
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–
Start
In
+ -
+30V Max
Start In
Start In +
Start In -
To mass spectrometer
Autosampler
INTERFACE 1
TERMINAL
SER1
LAN
MODBUS
DB15
WASH
STATION
INTERFACE 1
INTERFACE 2
AUX 1
AUX 2
POWER FUSE
Cbl Thermo Single Config.
To LC pump
RS232
1 2 3 4 5 6 7 8
USB
1 2 3 4 5 6 7 8
RS232 I/O
UNIT ID
ENET
NC
FW DOWNLOAD
PRESSURE PRESSURE+
NC
NC
+5V @ 150mA
GND
Surveyor MS Pump Plus
RS232
PUMP ON
GND
NC
NC
PROG. START
NC
+5V @ 150mA
GND
GRAD START
GND
(-)
INJECT HOLD
(-)
PUMP READY
+5V @ 10mA
GND
PRESSURE
GND
INJECT HOLD
PUMP READY
GRAD. START
PUMP STOP
5V
GND
Accela Pump
Thermo Scientific
BUZZER L
E
D
Surveyor LC Pump Plus
Thermo PAL User Guide
9
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 5 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.
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Thermo PAL User Guide
Thermo Scientific
1 Getting Connected
Connecting the Contact Closure Cables
Figure 9.
Dual-pump setup with two Accela Pumps
INTERFACE 1
To the mass spectrometer
To the autosampler
Cbl Thermo Single Config.
Start pump
355 River Oaks Parkway
San Jose, CA 95134 U.S.A.
Model: Accela Pump
CAUTION
DISCONNECT INPUT
POWER BEFORE
OPENING COVER.
REFER ALL SERVICE
TO QUALIFIED
PERSONNEL ONLY.
Serial No:
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:
60057-60010
Options/Firmware: 12472
Part No:
5,653,876
6,248,157B1
355 River Oaks Parkway
San Jose, CA 95134 U.S.A.
Model: Accela Pump
CAUTION
DISCONNECT INPUT
POWER BEFORE
OPENING COVER.
REFER ALL SERVICE
TO QUALIFIED
PERSONNEL ONLY.
Serial No:
60057-60010
Options/Firmware: 12472
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:
Part No:
61010 - 1
5,653,876
6,248,157B1
Cbl Thermo Dual Config.
Cbl Thermo Dual Config.
61010 - 1
Sample pump
Thermo Scientific
Thermo PAL User Guide
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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)
Cbl 7890
Connect to the
autosampler
REMOTE
INTERFACE 1
170 cm
(5.6 ft)
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
1 Getting Connected
Connecting the Contact Closure Cables
Figure 11. External contact trigger cable (supplied by Thermo Fisher Scientific)
Thermo Scientific
Connect to the
Agilent pump
RELAY CONTACTS
Connect to the MS
Thermo PAL User Guide
13
1
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
–or–
LTQ Series MS
–or–
+30V Max
Start In
Start In +
Start In -
Start
In
+ -
External contact trigger
cable supplied by
Thermo Fisher Scientific
Autosampler
RELAY CONTACTS
AUX 1
AUX 2
INTERFACE 1
INTERFACE 2
POWER
SER3 SER2
Agilent pump
SER1
VIAL- # -OUTPUT RELAY CONTACTS
VALVE IN
REMOTE
RS-232
CAN
CAN
CONFIG
ANALOG
INTERFACE 1
REMOTE
Cable (DB15 connector to
DB9 connector) supplied by
CTC Analytics
Cbl 7890
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Thermo PAL User Guide
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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 -
Start
In
+ -
+30V Max
Start In
External contact trigger
cable supplied by
Thermo Fisher Scientific
Autosampler
RELAY CONTACTS
TERMINAL
SER1
LAN
MODBUS
BUZZER L
E
D
WASH
STATION
INTERFACE 1
INTERFACE 2
AUX 1
AUX 2
POWER FUSE
Agilent pump
VIAL- # -OUTPUT RELAY CONTACTS
REMOTE
RS-232
CAN
CAN
CONFIG
ANALOG
INTERFACE 1
REMOTE
Cable (DB15 connector to
DB9 connector) supplied by
CTC Analytics
Cbl 7890
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 (or Programs) >
Thermo Foundation x.x > Instrument Configuration, where x.x is the installed version
of Thermo Foundation, to open the Thermo Foundation Instrument Configuration
window (Figure 14).
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Getting Started
Configuring the Thermo PAL Autosampler
Figure 14. Thermo Foundation Instrument Configuration window
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.
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2 Getting Started
Configuring the Thermo PAL Autosampler
 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).
Figure 15. Pal Configuration dialog box
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.
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2
Getting Started
Configuring the Thermo PAL Autosampler
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.
• 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 6 lists the parameters for the Pal Configuration dialog box.
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2 Getting Started
Configuring the Thermo PAL Autosampler
Table 6. Pal Configuration dialog box parameters (Sheet 1 of 2)
Parameter
Description
Communications
Com Port
Select the computer port where you plug the autosampler
communication cable.
Auto Select
Instructs the system to automatically determine the computer
port that connects to the autosampler through the
autosampler communication cable.
Check
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
Enable
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.
Thermo Scientific
Import
Import the chosen macro.
Browse
Search through files and folders to find a macro.
Thermo PAL User Guide
21
2
Getting Started
Using the Autosampler Control Terminal
Table 6. Pal Configuration dialog box parameters (Sheet 2 of 2)
Parameter
Description
Active Trays
Tray Name
Hardware configured tray names.
Stack
Stack location of a given tray name.
Allow Use
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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Thermo PAL User Guide
Thermo Scientific
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
Menu
Ins
Job
Del
Job
Pause
F1
F2
F3
F4
Inner knob
(button)
ESC
STOP
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
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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
SW-Out1
4.0 s
Oms...9.9s
Set
Deflt
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Thermo Scientific
2 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 23).
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 24).
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.
Thermo Scientific
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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 (or 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)
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
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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
• Multi Step LC Injection.pme
• LC-Inj DLW Fast_Rev03.pme
• Single Step LC Injection.pme
• LC-Inj DLW Standard_Rev03.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
it will result in 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 35). When you store a custom
template in the same folder as the standard templates, the template appears in the
Template list.
Figure 19 shows the macro sequence and the macro variables for the
Single Step LC Injection template.
Thermo Scientific
Thermo PAL User Guide
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2
Getting Started
Specifying the Instrument Method Parameters
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
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.
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2 Getting Started
Specifying the Instrument Method Parameters
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.
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Getting Started
Specifying the Instrument Method Parameters
Instrument Setup Parameters
Use the Method Setup page (Figure 19 on page 28) to specify instrument method parameters
for the autosampler.
Table 7. Method Setup page parameters (Sheet 1 of 2)
Parameter
Description
Template Selection
Template
Shows the list of default method templates.
After you select a template, the Template list changes to a box
that shows the path to the selected method template file.
Method Folder
Shows the path to the default template folder before you select
a default method template.
After you select a method template (in the Template list), the
Method Folder box disappears.
Browse
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.
New Template
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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Specifying the Instrument Method Parameters
Table 7. 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).
This area also lists the variables associated with the macro
chosen in the Macro Sequence pane.
Variables
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.
Default All
Thermo Scientific
This button changes the variables, used in the selected Macro
Sequence, to their default values.
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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 25).
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).
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Viewing the Method Summary
Figure 20. Method Summary page in the Instrument Setup window
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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 8 on page 37 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 25).
b. Choose Pal Auto Sampler > Template\Macro Editor.
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Using the Template Editor to Create Custom Templates
Figure 21. Template Editor page on the Pal Template\Macro Editor window
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.
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Using the Template Editor to Create Custom Templates
Table 8. Template Editor page parameters (Sheet 1 of 2)
Parameter
Description
Template Description
Enter the method description in this box.
Syringe
Select the syringe volume from this list.
Macro Sequence
Macro Sequence
Shows the macros selected for the method being made in the
Method Template Editor.
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).
Insert Above
Inserts a macro from the Macro list above the macro selected
under Macro Sequence.
Insert Below
Inserts a macro from the Macro list below the macro selected
under Macro Sequence.
Replace
Replaces the macro selected under Macro Sequence with the
macro that is in the Macro list.
Delete
Deletes the macro selected under Macro Sequence.
Run
Automatically executes the macros that constitute the Method
(Macro Sequence).
Step
Executes the Method (Macro Sequence) in a stepwise manner.
Macro
Macro
Select individual PAL macros in this list.
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.
Default All
Thermo Scientific
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 8. Template Editor page parameters (Sheet 2 of 2)
Parameter
Description
Variables
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
Saves the Method Template under the current file name
(overwrites the current file).
Save As
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 9 on page 40 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 35).
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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Creating Custom Templates and Macros
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
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 35).
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
4. Make the appropriate entries and selections.
5. Click Run.
The autosampler executes the macros listed in the template.
Table 9. Run Auto Sampler Method dialog box parameters (Sheet 1 of 2)
Parameter
Description
Vial Index
1
Type the vial index to be used with the method (SL.index).
2
Type the vial index to be used with the method (SL.index2).
Trays
1
Select the tray to be used with the method (SL.tray).
2
Select the second tray to be used with the method (SL.tray2).
Injectors
1
Select the injector to be used with the method (SL.injector).
2
Select the second injector to be used with the method
(SL.injector2).
Volume
1
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Type the injection volume to be used with the method
(SL.volume).
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Creating Custom Templates and Macros
Viewing the Template Summary
Table 9. Run Auto Sampler Method dialog box parameters (Sheet 2 of 2)
Parameter
Description
2
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
Run the selected method.
Cancel
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 35).
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 10 on page 45 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 25).
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
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 48).
b. Define the variable (see “Defining Variables” on page 48).
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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 10. Macro Editor page parameters (Sheet 1 of 3)
Parameter
Description
Macro
This list displays existing autosampler macros. Select the
macro that you want to edit.
Macro Description
Displays a description of the selected macro.
Macro Variables
—
Displays the variables used by the selected macro.
Add
Adds a new variable to the macro variables.
For details, see “Defining Variables” on page 48. 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.
Edit
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.
Delete
Thermo Scientific
Deletes the selected Macro Variable.
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Using the Macro Editor to Create Custom Macros
Table 10. Macro Editor page parameters (Sheet 2 of 3)
Parameter
Description
Command Sequence
—
Lists the sequence of commands that make up the macro
selected in the Macro list.
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).
Insert Above
The command shown in the Command list is inserted above
the command selected (highlighted in blue) under Command
Sequence.
Insert Below
The command shown in the Command list is inserted below
the command selected (highlighted in blue) under Command
Sequence.
Replace
The command selected (highlighted in blue) under
Command Sequence is replaced by the command shown in
the Command list.
Delete
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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Using the Macro Editor to Create Custom Macros
Table 10. Macro Editor page parameters (Sheet 3 of 3)
Parameter
Description
Parameters
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.
Command Description
Shows a description of the selected command in the bottom
pane.
Buttons
Thermo Scientific
Save Macro
Saves the macro (command sequence) under the current file
name (overwrites the current file).
Save As
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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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 11 on page 49 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 43).
2. Click Add to open the Variable Definition dialog box (Figure 28).
Figure 28. Variable Definition dialog box
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.
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Defining Variables
Figure 29. Object variable selections
Table 11. Variable Definition dialog box parameters (Sheet 1 of 2)
Parameter
Description
Variable Type
A Numeric Value
Select this option if the parameter is a numeric value.
If you are editing an existing numerical parameter, this option
is preselected.
An Object
Select this option if the parameter is an object.
If you are editing an existing object parameter, this option is
preselected.
Variable Name
If you are editing an existing variable, this box shows the
name of the variable. If you are adding a variable, type its
name.
OK
Accepts the new Variable Definition or accepts the edits to an
existing Variable Definition.
Cancel
Deletes changes made in the Variable Definition dialog box.
Variable Type–Numeric
Thermo Scientific
Variable Units
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.
Default Value
The nominal or center value of the variable.
Lower Limit
The lowest acceptable value of the variable.
Upper Limit
The highest acceptable value of the variable.
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Defining Variables
Table 11. Variable Definition dialog box parameters (Sheet 2 of 2)
Parameter
Description
Variable Type–Object
Please Check What Objects Select the check boxes for one or more objects that the
This Variable May Be
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 12 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 51).
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 56).
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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 54).
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 12. Methods page parameters (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
Method
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.
Description
Contains a description of the selected method.
Syringe
Lists the size of the configured syringe.
Device Status
Displays the status of the autosampler.
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Changing the Tray Configuration
Table 12. Methods page parameters (Sheet 2 of 2)
Parameter
Description
Vial Index
1
Type the vial index to be used with the method
(SL.index).
2
Type the second vial index to be used with the method
(SL.index2).
Trays
1
Select the tray to be used with the method (SL.tray).
2
Select the second tray to be used with the method
(SL.tray2).
Volume
1
Type the injection volume to be used with the method
(SL.volume).
2
Type the second injection volume to be used with the
method (SL.volume2).
Injectors
1
Select the injector to be used with the method
(SL.injector).
2
Select the second injector to be used with the method
(SL.injector2).
Injections Per Vial
Type the number of replicate injections to be made
from each vial.
Run
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 13 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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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 51).
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)
3. In the Tray list, select the tray that you want to modify.
4. In the Type list, select the tray type.
Table 13. Tray Configuration page parameters (Sheet 1 of 2)
Parameter
Description
Tray
Select the tray location in the three-drawer (deep
drawer) configuration. For information about the
sample trays, see Appendix A, “Sample Trays.”
Range: Tray01–Tray12
Type
Thermo Scientific
Select the tray type.
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Specifying the Location of the Direct Control Methods
Table 13. Tray Configuration page parameters (Sheet 2 of 2)
Parameter
Description
Tray Holder
The allowed values are as follows:
• Stack1, for Tray01–Tra06
• CStack1, for Tray07–Tray12
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.
Vials in X Direction,
Vials in Y Direction
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 14 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 51).
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
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 14. Direct Control Configuration page parameters (Sheet 1 of 2)
Parameter
Description
Wrap Each Direct Control Method Run with the Following Macros
Sequence Entry Exit
Select this check box to wrap methods with the
sequence list entry and exit macros (SLentry and
SLexit).
Method Entry Exit
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
Thermo Scientific
Path
Type the extra path that you want to add for the
method search routine.
Browse
Use this button to search for the path to a file folder.
Add
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 14. Direct Control Configuration page parameters (Sheet 2 of 2)
Parameter
Description
Delete
Use this button to delete a file folder from the method
search routine.
Reset
Use this button to remove all of the user-added file
folders.
[text box]
Displays the file folders (directories) where the
autosampler searches for methods.
Firmware Version
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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5
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
• Installing 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)
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 72.
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Installing Cycle Composer Macros or ICC Cycles
Installing 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:
• 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 63 and Table 16 on
page 64.
Note The provided macros are written for standard injection valve drives, which are
controlled and activated through the AUX interface.
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
your ThermoPAL driver method folder or the corresponding folder for application within the
integrated system.
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Installing Cycle Composer Macros or ICC Cycles
 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.
Priming the Solvent Lines, Wash1 and Wash2
Use this macro at installation to prime the entire system.
 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 lists the Priming Accela Open AS_Rev01 macro parameters.
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Installing Cycle Composer Macros or ICC Cycles
Table 15. Priming Accela Open AS_Rev01 macro (Sheet 1 of 2)
Macro description
Macro variable
The injection unit moves to the DLW Wash Clean Time solvent 1
Station, position Wash1.
Eject Speed DLW Syringe
The injection unit moves to the DLW Wash Clean Time solvent 1
Station, position Wash2.
Eject Speed DLW Syringe
The DLW system is rinsed with Wash
Solvent 1 in position Waste.
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.
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.
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.
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
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.
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Installing Cycle Composer Macros or ICC Cycles
Table 15. Priming Accela Open AS_Rev01 macro (Sheet 2 of 2)
Macro description
Macro variable
The injection valve is switched back to the
Standby position.
End of macro DLW Priming.
Standard DLW Injection Cycle
Table 16 lists the Stand Injection Accela Open macro parameters.
Table 16. Stand Injection Accela Open macro parameters (Sheet 1 of 3)
Macro description
Macro variable
The PAL system waits first for the Sync
Remark:
Signal Ready before the injection cycle starts. Sync Signal setting Start
The injection valve moves to a defined
Standby position.
Inject to
Standby
The Rear air segment pulls into the Holding Airgap Volume
Loop.
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
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.
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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.
Inject to
Pre Inject Delay
The loop fills with the sample volume as
specified in the Sample list.
(SL.volume)
Injection Speed
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Installing Cycle Composer Macros or ICC Cycles
Table 16. Stand Injection Accela Open macro parameters (Sheet 2 of 3)
Macro description
Macro variable
The injection valve switches to Standby
Post Inject Delay
position, the loop content is injected.
Timer Delay Stator Wash starts and sends a Timer 1
Start signal to the HPLC system.
The plunger of the DLW Syringe moves
(Syr. Eject Speed)
down to dispense the Rear Sample and Air
Segment to Waste. The Holding Loop is still
filled with Wash Solvent 1.
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 Wash2
Station, Wash2 position.
(Syr.Eject Speed)
The needle is rinsed inside and out with
Wash Solvent 2.
Post Clean Time Solvent2
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
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
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.
A Repeat-End loop can be activated with the
Count.
Thermo Scientific
Stator Wash
Stator Wash count: 1 = Cleaning step active
Stator Wash count: 0 = Cleaning step
disabled
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Installing Cycle Composer Macros or ICC Cycles
Table 16. Stand Injection Accela Open macro parameters (Sheet 3 of 3)
Macro description
Macro variable
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
Inject to
deliver Wash Solvent 2 to the Holding Loop Wash2
and into the valve system.
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.
Inject to
Wash1
Stator Wash Time Solvent 1
The injection valve switches back to the
Standby position.
Inject to
(Standby)
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 lists the Fast Injection Accela Open macro parameters.
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Installing Cycle Composer Macros or ICC Cycles
Table 17. Macro Fast Injection Accela Open (Sheet 1 of 2)
Macro description
Macro variable
The PAL system waits first for the Sync
Remark:
Signal Ready before the injection cycle starts. Sync Signal setting Start
The injection valve moves to a defined
position: Standby.
Inject to
Standby
The Rear air segment aspirates 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)
Airgap Volume
Filling Speed
Pullup Delay
The Front air segment aspirates.
The injection unit moves to the specified
injection valve.
The Front- and Airgap-Volume ejects to
Waste.
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
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
Pre Injection Delay
The plunger of the DLW Syringe moves
Injection Speed
down to dispense the Rear Sample and Air
Segment to Waste. The Holding Loop is still
filled with Wash Solvent 1.
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.
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Operating Dynamic Load and Wash (DLW)
Table 17. Macro Fast Injection Accela Open (Sheet 2 of 2)
Macro description
Macro variable
Wash Solvent 1 follows to prepare the valve
for the next injection.
Wash1
Inject to
Needle Gap Valve Clean
Valve Clean Time Solvent 1
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
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
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.
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Operating Dynamic Load and Wash (DLW)
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.
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 102 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™)
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Operating Dynamic Load and Wash (DLW)
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.
Figure 34. DLW manifold and Actuator/Solenoid
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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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DLW Cycle Step-by-Step
Figure 37. Standard: Step 1 – Aspirate rear air segment
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DLW Cycle Step-by-Step
Figure 38. Standard: Step 2 – Get sample and aspirate rear, inject, and front volume
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Using Dynamic Load and Wash (DLW)
DLW Cycle Step-by-Step
Figure 39. Standard: Steps 3 - 4 – Aspirate front air segment
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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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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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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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DLW Cycle Step-by-Step
Figure 43. Standard: Step 11– Switch valve to INJECT position and start chromatographic process
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DLW Cycle Step-by-Step
Figure 44. Standard: Step 12 – Dispense rear sample volume and air segment to waste
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DLW Cycle Step-by-Step
Figure 45. Standard: Steps 13 - 14 – Clean valve with Wash Solvent 2
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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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DLW Cycle Step-by-Step
Figure 48. Standard: Steps 19 - 20 – Wash the syringe needle with Wash Solvent 1
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DLW Cycle Step-by-Step
Figure 49. Standard: End cycle
Additional Valve Toggle Step to DLW Standard Cycle
This section contains information about additional steps that are necessary for a DLW
Standard Cycle.
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DLW Cycle Step-by-Step
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 85.
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
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.
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.
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DLW Cycle Step-by-Step
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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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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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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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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DLW Cycle Step-by-Step
Figure 55. Stator Wash: Step 5 – Wash Solvent 1 cleans second valve
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DLW Cycle Step-by-Step
Figure 56. Stator Wash: Step 6 – Switch valve back to Inject Position (toggle)
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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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DLW Cycle Step-by-Step
Figure 58. Fast: Step 1 – Aspirate rear air segment
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DLW Cycle Step-by-Step
Figure 59. Fast: Step 2 – Get sample and aspirate rear, inject, and front volume
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DLW Cycle Step-by-Step
Figure 60. Fast: Step 3 - 4 – Aspirate front air segment
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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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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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DLW Cycle Step-by-Step
Figure 63. Fast: Step 9 – Switch valve to INJECT position and start chromatographic process
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DLW Cycle Step-by-Step
Figure 64. Fast: Step 10 – Dispense rear sample volume and air segment to waste
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DLW Cycle Step-by-Step
Figure 65. Fast: Steps 11 - 12 – Clean valve with Wash Solvent 2
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DLW Cycle Step-by-Step
Figure 66. Fast: Steps 13 - 14 – Clean valve with Wash Solvent 1
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DLW Cycle Step-by-Step
Figure 67. Fast: Step 15 – Wash the syringe needle with Wash Solvent 1
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DLW Cycle Step-by-Step
Figure 68. Fast: End cycle
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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
Tray Types
Figure 69 through Figure 72 show the tray types for use in the Thermo PAL autosampler.
Figure 69. Tray type VT54
54-position, vial tray (9 × 6)
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Sample Trays
Tray Types
Figure 70. Tray type MT96
96-position, standard shallow micro plate (12 × 8)
Figure 71. Tray type DW96
96-position, deep well micro plate (12 × 8)
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Sample Trays
Tray Types
Figure 72. Tray type MT384
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)
06
Bottom drawer
03
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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A
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
Thermo Scientific
A-B
No.
B-C
No.
C-D
No.
E-F
No.
F-G
No.
G-H
No.
A1
1
B5
17
C9
33
E1
49
F5
65
G9
81
A2
2
B6
18
C10
34
E2
50
F6
66
G10
82
A3
3
B7
19
C11
35
E3
51
F7
67
G11
83
A4
4
B8
20
C12
36
E4
52
F8
68
G12
84
A5
5
B9
21
D1
37
E5
53
F9
69
H1
85
A6
6
B10
22
D2
38
E6
54
F10
70
H2
86
A7
7
B11
23
D3
39
E7
55
F11
71
H3
87
A8
8
B12
24
D4
40
E8
56
F12
72
H4
88
A9
9
C1
25
D5
41
E9
57
G1
73
H5
89
A10
10
C2
26
D6
42
E10
58
G2
74
H6
90
A11
11
C3
27
D7
43
E11
59
G3
75
H7
91
A12
12
C4
28
D8
44
E12
60
G4
76
H8
92
B1
13
C5
29
D9
45
F1
61
G5
77
H9
93
B2
14
C6
30
D10
46
F2
62
G6
78
H10
94
B3
15
C7
31
D11
47
F3
63
G7
79
H11
95
B4
16
C8
32
D12
48
F4
64
G8
80
H12
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Thermo PAL User Guide
111
A
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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Thermo PAL User Guide
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I
Index
A
autosampler control terminal, using 22
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
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 22
cycle composer macros 61
cycle composer macros or ICC cycles, installing 61
Cycle Editor 61
D
delay time 29
device drivers xi
Direct Control Configuration page 56
Direct Control dialog box, opening 51
DLW
characterizing features 59
cycle 72
cycle for fast injection 94
cycle for standard injection 72
fast injection cycle 66
operating 68
Thermo Scientific
overview 59
priming solvent lines 62
standard injection cycle 64
DLW Actuator/Solenoid 69
DLW Pumps 69
documentation survey xiv
E
electromagnetic compatibility iii
equation, sample position number in tray 112
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) 29
macro (.pma) 45
templates (.pme) 36
I
ICC cycles 61
Injected screen on hand-held controller 24
Inlet Direct Control, opening 52
Instrument Configuration window 17
Instrument Setup window, opening 26
J
Job Queue screen 23
L
level surface, importance of 2
lithium battery 1
Thermo PAL User Guide
113
Index: M
M
Macro Editor
enabling 19
opening 43
page parameters 43
Macro, Instrument Setup 31
macros
creating 43
cycle composer 61
importing 20
list of standard 43
mass spectrometry applications ix
Menu screen 23
method parameters, specifying 26
method templates, list of 27
N
nomenclature for stacks, trays, and samples 107
numeric variables 48
O
object variables 48
ordering information 2
output signal to LC pump 5
P
parameters
Direct Control
Method page
Description 53
Device Status 53
Injections Per Vial 54
Injectors 54
Method 53
Syringe 53
Trays 54
Vial Index 54
Volume 54
Tray Configuration page
Tray 55
Tray Holder 56
Type 55
Vials in X Direction 56
Vials in Y Direction 56
Instrument Configuration 20
Auto Select 21
Browse 21
Check 21
Com Port 21
Enable 21
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Thermo PAL User Guide
Import 21
Import Path 21
Overwrite Existing Macros 21
Stack 22
Tray Name 22
Instrument Setup
Browse 30
Delay Time 31
Macro Sequence 30
Method Folder 30
New Template 30
Syringe 30
Template 30
Template Description 30
Variables 31
Volume 31
Macro Editor page
Add 45
Command 46
Command Description 47
Command Sequence 46
Delete 45–46
Edit 45
Insert Above 46
Insert Below 46
Macro 45
Macro Description 45
Macro Variables 45
Parameters 47
Replace 46
macros
Fast Injection Accela Open 66
Priming Accela Open AS_Rev01 62
Stand Injection Accela Open 64
Run Auto Sampler Method dialog box
Injectors 40
Trays 40
Vial Index 40
Volume 40
Template Editor page 35
Variable Definition dialog box
A Numeric Value 49
An Object 49
Default Value 49
Lower Limit 49
Upper Limit 49
Variable Name 49
Variable Units 49
part numbers 2
priming solvent lines 62
pulse time of the out signals, setting 25
pumps, self-priming 60
Thermo Scientific
Index: R
R
W
Recommended Injection Volume box 29
regulatory compliance iii
release notes x
requirements
computer xi
software xi
Run Auto Sampler Method dialog box parameters 38
Waiting for contact closure status for LC pump 24
WEEE compliance v
S
safety information 1
safety standards iii
sample trays 107
self-priming micro pumps 60
server failure error message xi
software requirements xi
solvent lines, priming 62, 68
stack, cooler 110
survey link xiv
syringe size, specifying 29
system requirements x
T
Template Editor
enabling 19
opening 35
Template Editor page parameters 35
templates
editing 35
Single Step LC Injection 27
testing 38
Thermo PAL driver for Xcalibur 61
Tray Configuration page 55
tray type, selecting with the PAL Control Terminal 23
Trays 40
trays
position in stack 110
sample position 111
type
DW96 108
MT384 109
MT96 108
VT54 107
Trays screen 23
Tune window, making single injections from 52
V
variables, defining 48
Thermo Scientific
Thermo PAL User Guide
115
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