Thermo Fisher Scientific Accela Open Autosampler LC User guide

Accela Open Autosampler

User Guide for LC Devices

60357-97101 Revision B March 2011

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The contents of this document are subject to change without notice. All technical information in this

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Release history: Revision A, April 2010; Revision B, March 2011.

Software version: Xcalibur 2.1 or later; LC Devices 2.5.0.

Firmware version: 4.1.2 or later.

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

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Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with

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

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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

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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 the Susceptibility

to Electromagnetic Transmissions

Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency

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Thermo Scientific Accela Open Autosampler User Guide vii

C

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

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix

Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

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

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

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

System Synchronization Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Connecting the Accela Open Autosampler Interconnect Cable . . . . . . . . . . . . 5

Connecting the Adapter Cable for an Accela Detector or TSQ Series

MS Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Connecting the Accela Pump Adapter Cable . . . . . . . . . . . . . . . . . . . . . . . . . 11

Connecting the Accela Open Autosampler to the Data System Computer. . . . . 14

Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Adding the Autosampler to the Xcalibur Instrument Configuration . . . . . . . . . 15

Firmware Versions Supported . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Using the Autosampler Control Terminal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Selecting the Tray Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Changing the Pulse Time Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Specifying the Instrument Method Parameters for the Autosampler . . . . . . . . . 24

Viewing the Method Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Chapter 3 Creating Custom Templates and Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35

Using the Template Editor to Create Custom Templates . . . . . . . . . . . . . . . . . 35

Testing a Custom Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Viewing the Template Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Standard Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Using the Macro Editor to Create Custom Macros . . . . . . . . . . . . . . . . . . . . . . 45

Defining Variables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Contents

viii Accela Open Autosampler User Guide Thermo Scientific

Chapter 4 Using the Direct Controls to Operate the Autosampler . . . . . . . . . . . . . . . . . . . . .53

Opening the Direct Control Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Making Single Injections from the Tune Window. . . . . . . . . . . . . . . . . . . . . . . 55

Changing the Tray Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Specifying the Location of the Direct Control Methods . . . . . . . . . . . . . . . . . . 59

Wrapping Direct Control Injections with Additional Macros . . . . . . . . . . . . . . 62

Chapter 5 Using Dynamic Load and Wash (DLW) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63

Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Installing Cycle Composer Macros or ICC Cycles. . . . . . . . . . . . . . . . . . . . . . . 64

General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Priming the Solvent Lines, Wash1 and Wash2 . . . . . . . . . . . . . . . . . . . . . . . 66

Standard DLW Injection Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Fast DLW Injection Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Operating Dynamic Load and Wash (DLW) . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Priming the Solvent Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Location of Solvent and Waste Bottles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

DLW Pumps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

DLW Actuator/Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

DLW Cycle Step-by-Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Cycle for Standard Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Additional Valve Toggle Step to DLW Standard Cycle . . . . . . . . . . . . . . . . . 88

Cycle for Fast Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109

Thermo Scientific Accela Open Autosampler User Guide ix

P

Preface

Accela™ Open Autosampler manufactured by CTC Analytics is supplied by Thermo Fisher

Scientific as part of a solution for high-throughput LC/MS applications. Thermo Pal, one of

the device drivers provided on the LC Devices software CD, is the device driver that enables

the Xcalibur™ data system control of the autosampler.

This user guide provides you with information on how to connect the autosampler to other

devices in the LC/MS system and how to operate it from the Xcalibur data system. This

manual is provided in electronic format only. You can access this manual by choosing the

following from the computer desktop:

Start > All Programs > Thermo Instruments > Manuals > LC Devices > Accela > Accela

OpenAS

To provide us with comments about this document, click the link below. Thank you in

advance for your help.

Related Documentation

The Accela Open Autosampler includes Help and these manuals as PDF files:

• Accela Open Autosampler User Guide

• Accela Open Autosampler Hardware Manual

Preface

xAccela Open Autosampler User Guide Thermo Scientific

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:

Contacting Us

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

To contact Technical Support

Find software updates and utilities to download at mssupport.thermo.com.

To contact Customer Service for ordering information

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.

Phone 800-532-4752

Fax 561-688-8736

E-mail us.techsupport.analyze@thermofisher.com

Knowledge base www.thermokb.com

Phone 800-532-4752

Fax 561-688-8731

E-mail us.customer-support.analyze@thermofisher.com

Web site www.thermo.com/ms

Preface

Thermo Scientific Accela Open Autosampler User Guide xi

To copy manuals from the Internet

Go to mssupport.thermo.com and 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

http://www.surveymonkey.com/s.aspx?sm=R7gKOvhLXn3NTkpK2BefHQ_3d_3d.

• Send an e-mail message to the Technical Publications Editor at

techpubs-lcms@thermofisher.com.

Thermo Scientific Accela Open Autosampler User Guide 1

1

Getting Connected

The Accela Open Autosampler is a high-throughput autosampler manufactured by CTC

Analytics and supplied by Thermo Fisher Scientific. For high-throughput LC/MS

applications, use the Accela Open Autosampler, a Thermo Scientific or an Agilent™ liquid

chromatography (LC) pump, and a Thermo Scientific mass spectrometer (MS) detector.

This chapter describes the contact closure connections between the Accela Open

Autosampler, one or two Thermo Scientific LC pumps or an Agilent pump, a Thermo

Scientific MS detector, and the Xcalibur data system computer.

Ordering Information

The Accela Open Autosampler options that Thermo Fisher Scientific supplies include the

serial communication cable that you use to connect the Accela Open Autosampler to the data

system computer and the contact closure cable that you use to connect the Accela Open

Autosampler to a Thermo Scientific LC pump and a Thermo Scientific MS detector.

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 Accela Open Autosampler electrical hazards, lithium battery, and

safety labels.

Contents

•Ordering Information

•System Synchronization Connections

•Connecting the Accela Open Autosampler to the Data System Computer

1 Getting Connected

Setting Up an LC/MS System with the Autosampler

2Accela Open Autosampler User Guide Thermo Scientific

Table 1 lists the Accela Open Autosampler options that you can order from Thermo Fisher

Scientific.

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

Scientific MS detector and an autosampler. You can order the DB15 × 15 wire cable from

Agilent or Thermo Fisher Scientific.

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 MS detector. Ensure that the stackable area for the

autosampler is level, and that system cables behind the autosampler have adequate space.

For information on assembling the Accela Open Autosampler and connecting the solvent

lines, refer to the Accela Open Autosampler Hardware Manual supplied in hard copy format

with the autosampler. During the installation of a Thermo Scientific MS detector, a Thermo

Fisher Scientific field service engineer connects the LC system to the MS detector.

Table 1. Accela Open Autosampler ordering information

Part number Description

OPTON 13008 HTS PAL

OPTON 13009 HTC PAL

OPTON 13010 HTC PAL with the 98 × 2 mL tray holder

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

Part number Supplier Description

CBL 7890 CTC Analytics PAL Interface Cable for APG Remote

DB15 connector × DB9 connector cable

00012-27716 Thermo Fisher Scientific DB15 connector × 15 wire cable

G1103-61611 Agilent DB15 connector × 15 wire cable

CAUTION To prevent damage to the injection unit during operation, place the

autosampler on a level surface.

1 Getting Connected

System Synchronization Connections

Thermo Scientific Accela Open Autosampler User Guide 3

Figure 1 shows a front view of the Accela Open Autosampler. During installation, a Thermo

Fisher Scientific field service engineer connects the solvent lines between the injection valve

and the LC pump and between the injection valve and the Thermo Scientific mass

spectrometer.

Figure 1. Accela Open Autosampler

System Synchronization Connections

The system interconnect cables and adapter cables that synchronize the run signals for an LC

or LC/MS system with an Accela Open Autosampler depend on the Accela pump model, the

mass spectrometer model, and whether the LC system includes an Accela detector.

Table 3 lists the system interconnect and adapter cables that Thermo Fisher Scientific supplies

with the Accela Open Autosampler or by special order.

1 Getting Connected

System Synchronization Connections

4Accela Open Autosampler User Guide Thermo Scientific

To connect the required cables listed in Table 3, follow these procedures as appropriate:

•Connecting the Accela Open Autosampler Interconnect Cable

•Connecting the Adapter Cable for an Accela Detector or TSQ Series MS Detector

•Connecting the Accela Pump Adapter Cable

Table 3. Accela Open Autosampler contact closure and adapter cables

Cable description Part number Use

Accela detector and

MS detector

adapter cable

(supplied with

autosampler)

60157-63026 Required for hardware configurations that

include one or more of the following:

• Accela detector

• TSQ or Exactive mass spectrometer

Accela Open

Autosampler system

interconnect cable

(supplied with

autosampler)

60157-63024 Required for all hardware configurations

Accela Pump

adapter cable

(available by special

order)

60157-63022 Required for the Accela Pump

Note Thermo Fisher Scientific has discontinued the Accela Pump.

1 Getting Connected

System Synchronization Connections

Thermo Scientific Accela Open Autosampler User Guide 5

Connecting the Accela Open Autosampler Interconnect Cable

Figure 2 shows the Accela Open Autosampler interconnect cable (P/N 60157-63024).

Figure 2. Accela Open Autosampler interconnect cable (P/N 60157-63024)

To connect the Accela Open Autosampler interconnect cable to the LC or LC/MS

system modules

1. Plug the DB15 connector (cable end labeled TO A/S) into the Interface 1 receptacle on

the back panel of the Accela Open Autosampler (see Figure 3).

2. Depending on the Accela pump model, do one of the following:

• If your LC system includes an Accela 600 or 1250 Pump, plug the 25-pin connector

(cable end labeled TO PUMP) into the D-Sub25 receptacle on the back panel of the

pump (seeFigure 3).

• If your LC system includes an Accela Pump, go to “Connecting the Accela Pump

Adapter Cable” on page 11.

3. Depending on the LC detector or MS detector setup, do one of the following:

• If your LC or LC/MS system includes an Accela detector or a TSQ Series or Exactive

mass spectrometer, go to “Connecting the Adapter Cable for an Accela Detector or

TSQ Series MS Detector” on page 7.

• Or if your LC/MS system includes an MSQ Plus Mass Detector or an LTQ Series

mass spectrometer, but does not include an Accela detector, go to step 4.

4. Connect the cable labeled TO MSQ/LTQ/LXQ to the mass spectrometer. Do one of the

following:

• For the MSQ Plus Mass Detector, connect the cable to the User I/O Start In pins on

the MS detector’s back panel (see Figure 3).

• For the LTQ Series mass spectrometer, connect the cable to the Peripheral Control

Start In pins on the MS detector’s right panel (see Figure 3).

TO MSQ/LTQ/LXQ

TO PUMP 60157-63024 TO A/S

102 cm (40 in.)

305 cm (120 in.)

1 Getting Connected

System Synchronization Connections

6Accela Open Autosampler User Guide Thermo Scientific

Figure 3. Accela Open Autosampler interconnect cable connections (back panel view of the LC/MS modules)

AUX

AUX 2 POWER FUSEAUX 1INTERFACE 2INTERFACE 1TERMINAL SER1 LAN MODBUS BUZZER WASH

STATION

L

E

D

355 River Oaks Parkway

San Jose, CA, U.S.A

This device complies with FCC Rules, Part 15.

Operation is subject to the following 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:

CAUTION

REFER ALL SERVICE

TO QUALIFIED

PERSONNEL ONLY.

DISCONNECT INPUT

POWER BEFORE

OPENING COVER.

RESERVED

GND

INJECT HOLD

PUMP READY

GRAD. START

5V

USB

D-SUB25

Model: 1250 Pump

Serial No: 925000

DO NOT COVER

RS232

5,653,876 6,248,157 B1

Futher patent pending

DO NOT USE

TOGETHER

WITH

D-SUB25

!

EP 2107241A2

12345678

EN

61010 1

LINE

FUSE

100V 115V 230V 50/60 HZ

T2.0A T1.0A 220VA

!

STACK COOLER DW

D-SUB25

INTERFACE 1

Peripheral Control

Start

In Ready

Out Start

Out

TO PUMP

TO A/S

60157-63024

TO MSQ/LTQ/LXQ

Start In +

Ready Out +

Start In -

Ready Out -

PUMP OUT

MAINS IN

MAINS ON/OFF

RESET

USER I/O START IN +

START IN -

USB

READY OUT +

READY OUT -

GAS IN

6 BARS MAX

SOURCE

BACKING

EXHAUST

User I/O

TO PUMP

60157-63024 TO A/S

TO MSQ/LTQ/LXQ

Accela Open

Autosampler

(back panel)

LTQ Series mass spectrometer

(back panel)

MSQ Plus Mass Detector

(back panel)

Accela 600 or

1250 Pump

(back panel)

Accela Open

Autosampler

Accela 600 or

1250 Pump

LTQ Series

mass spectrometer

MSQ Plus

Mass Detector

–or–

Accela Open Autosampler

interconnect cable

1 Getting Connected

System Synchronization Connections

Thermo Scientific Accela Open Autosampler User Guide 7

Connecting the Adapter Cable for an Accela Detector or TSQ Series MS Detector

Use the Accela detector and MS detector adapter cable (see Figure 4) to connect the Accela

Open Autosampler to an Accela detector, a TSQ or Exactive mass spectrometer, or both.

Figure 4. Adapter cable for an Accela detector and a TSQ Series MS detector (P/N 60157-63026)

To connect the LC detector and MS detector adapter cable

1. If you have not already done so, connect the Accela Open Autosampler interconnect cable

to the autosampler and the Accela 600 or 1250 Pump (see “Connecting the Accela Open

Autosampler Interconnect Cable” on page 5).

2. Connect the adapter cable to the interconnect cable by plugging the 2-pin male

connector labeled TO 60157-63024 on the adapter cable

into the 2-pin female connector labeled TO MSQ/LTQ/LXQ on the interconnect cable

(see Figure 5).

Figure 5. Accela Open Autosampler interconnect cable to detector adapter cable connection

TO 60157-63024 60157-63026 TO LCQ FLEET

TO LTQ/LXQ/MSQ

TO TSQ/EXACTIVE

TO PDA

2-pin male

connector 2-pin female

connectors

8-pin female

connector

23 cm (9 in.)

200 cm (79 in.)

TO 60157-63024 60157-63026 TO LCQ FLEET

TO LTQ/LXQ/MSQ

TO TSQ/EXACTIVE

TO PDA

TO MSQ/LTQ/LXQ

TO PUMP

60157-63024 TO A/S

Accela detector and

MS detector

adapter cable

Accela Open

Autosampler

interconnect cable

1 Getting Connected

System Synchronization Connections

8Accela Open Autosampler User Guide Thermo Scientific

3. Using the adapter cable connectors, make the appropriate connections to an Accela

detector, a Thermo Scientific mass spectrometer, or both as follows:

• For an Accela detector (UV/Vis or PDA), connect the 8-pin connector attached to

the cable labeled TO PDA to pins 1 through 8 on the detector’s back panel.

• For an MSQ Plus Mass Detector, connect the 2-pin connector attached to the cable

labeled TO LTQ/LXQ/MSQ to the Start In pins on the mass spectrometer’s back

panel.

• For an LTQ Series mass spectrometer, connect the 2-pin connector attached to the

cables labeled TO LTQ/LXQ/MSQ and TO LCQ FLEET to the Start In pins on the

right side of the mass spectrometer.

• For a TSQ or Exactive mass spectrometer, connect the cable labeled

TSQ/EXACTIVE to the Start In pins on the right side of the mass spectrometer.

Figure 6 and Figure 7 show the contact closure connections for a standalone Accela LC system

and an LC/MS system, respectively.

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Thermo Fisher Scientific Accela Open Autosampler LC User guide

Thermo Fisher Scientific Accela Open Autosampler LC User guide

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