Thermo Scientific Agilent 1200 Series User manual

Thermo
Agilent 1200 Series
Getting Connected Guide for LC Devices
XCALI-97250 Revision H April 2014

© 2014 Thermo Fisher Scientific Inc. All rights reserved.
Foundation, MSQ, and TSQ are trademarks, and LCQ, LCQ Fleet, LTQ, LXQ, Surveyor, 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 and Instant Pilot are registered trademarks of
Agilent Technologies Inc. Microsoft and Windows are registered trademarks of Microsoft Corporation.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Rev A, Jan 2009; Rev B, Feb 2011; Rev C, Dec 2011; Rev D, May 2012; Rev E, July 2012;
Rev F, Dec 2012; Rev G, Dec 2013; Rev H, April 2014
Software version: Thermo Foundation (see page vii for versions), Thermo LC Devices 2.2.1 or later
For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices iii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Supported Firmware Versions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Chapter 1 Checking the Agilent Firmware Versions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Checking the Firmware Versions with the Agilent Instant Pilot. . . . . . . . . . . . . . 1
Checking the Firmware Versions from the Xcalibur Data System . . . . . . . . . . . . 2
Chapter 2 Setting Up the LAN Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Determining the LAN Interface Type and Location . . . . . . . . . . . . . . . . . . . . . . 5
Setting the LAN Initialization Mode to “Using Default”. . . . . . . . . . . . . . . . . . . 7
Setting the Stored TCP/IP Address for the LAN Interface. . . . . . . . . . . . . . . . . . 9
Setting the LAN Initialization Mode to “Using Stored”. . . . . . . . . . . . . . . . . . . 16
Chapter 3 Setting Up the Thermo Foundation Instrument Configuration . . . . . . . . . . . . . . .19
Agilent 1200 Series LC System IP Address . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Contact Interface Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Configuring the Agilent LC System’s Modules . . . . . . . . . . . . . . . . . . . . . . . . . 20
Adding the Agilent 1200 Series Modules to the Foundation Instrument
Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Setting the Configuration Options for the LC Modules . . . . . . . . . . . . . . . . 21
Closing Foundation Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . . 27
Chapter 4 Installing the External Contact Interface Board . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Chapter 5 Connecting the Communication Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Ethernet Communication Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Connecting the Ethernet Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Connecting the Contact Closure Cable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Contents

Contents
iv Agilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
Chapter 6 Triggering Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Chapter 7 Vial and Well Locations for the Available Tray Types. . . . . . . . . . . . . . . . . . . . . .39
40-Vial Trays. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
100-Vial Tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
54-Vial Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
96-Well Plates or 96-Deep Well Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
384-Well Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45

Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices v
P
Preface
This guide describes how to connect an Agilent™ 1200 Series liquid chromatograph (LC)
system to a Thermo Scientific™ mass spectrometer (MS) and the data system computer, and
how to establish communication between the LC system and a Thermo Scientific™ MS data
system, such as Thermo Xcalibur™.
To suggest changes to the documentation or to the Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Contents
•Related Documentation
•System Requirements
•Supported Firmware Versions
•Cautions and Special Notices
•Contacting Us

Preface
vi Agilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
Related Documentation
In addition to this guide, you can also access the following documents as PDF files from the
data system computer.
To view the product manuals
From the Microsoft™ Windows™ taskbar, do the following:
• For an LC instrument controlled by a Thermo software application, choose Start >
All Programs > Thermo Instruments > Manuals > LC Devices > Agilent.
• For a Thermo Scientific MS, choose Start > All Programs > Thermo Instruments >
Instrument-name.
• For the Xcalibur application, choose Start > All Programs > Thermo Xcalibur >
Manuals > Xcalibur.
For access to the Xcalibur application Help, follow this procedure.
To view application-specific Help
• From the Xcalibur Instrument Setup window, choose Help > Agilent 1200 Help
and select a topic.
• If information about setting parameters is available for a specific view, page, or dialog
box, click Help or press the F1 key for information about setting parameters.

Preface
Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices vii
System Requirements
Your system must meet the minimum requirements as stated in the following table.
IMPORTANT Before you install the device drivers, 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 is the version that you want to install.
System Minimum requirements
Computer • 2 GHz processor with 1 GB RAM
•DVDdrive
• 80 GB or greater available on drive C
• Video card and monitor capable of 1280 × 1024 resolution
• Network interface cards, two
•NTFSformat
Software • Adobe™ Reader™ 10
• Microsoft Windows operating system:
Windows 7 Professional (32-bit and 64-bita)
Windows XP Workstation SP3
• Thermo Scientific software:
aLC Devices 2.8.0 and later are compatible with Windows 7, 32-bit and 64-bit
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
2.2.1–2.4 1.0 to 1.0.2 SP1 only

Preface
viii Agilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
(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 page vii).
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.
3. If the installed LC Devices software 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

Preface
Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices ix
Supported Firmware Versions
LC Devices supports the model numbers and firmware versions of the Agilent 1200 Series
modules listed in Table 1. For instructions on how to check the firmware version, see
Chapter 1, “Checking the Agilent Firmware Versions.”
Table 1. Supported firmware versions for the Agilent 1200 Series LC system
Module Model number Firmware version
High Performance Autosampler
(and Thermostat)
G1367B
(G1330B)
A.06.12
High Performance Autosampler SL
(and Thermostat)
G1367C
(G1330B)
A.06.12
Micro Well-plate Autosampler G1377A A.06.03
Thermostatted Column Compartment G1316A A.06.10
Thermostatted Column Compartment SL G1316B A.06.10
Binary Pump G1312A A.06.10
Binary Pump SL G1312B A.06.10
Capillary Pump G1376A A.06.34
Quaternary Pump G1311A A.06.10
Diode Array Detector (DAD) G1315B A.06.10
Diode Array Detector (DAD) G1315C B.01.03
Diode Array Detector (DAD) G1315D B.01.04
Variable Wavelength Detector (VWD) SL G1314C A.06.50

Preface
xAgilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
Cautions and Special Notices
Make sure you follow the cautions and special notices presented in this guide. Cautions and
special notices appear in boxes; those concerning safety or possible system damage also have
corresponding caution symbols.
This guide uses the following types of cautions and special notices.
The following additional caution-specific symbol appears in the Agilent 1200 Series Getting
Connected Guide for LC Devices.
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.
CAUTION Highlights electric shock-related hazards to human beings. Each electric shock
notice is accompanied by the international High Voltage symbol.

Preface
Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices xi
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
For Thermo Scientific™ products Access by phone, fax, email, or website
Technical Support (U.S.) Phone: [phone] Fax: [phone]
Email: [e-mail]
Web—for product support, technical documentation, and knowledge bases:
www.thermoscientific.com/support
Customer Service
(Sales and service)
(U.S.) Phone: [phone] Fax: [phone]
Email: [e-mail]
Web—for product information:
www.thermoscientific.com/lc-ms
Web—for customizing your service request:
1. From any Products & Services web page, click Contact Us.
2. In the Contact Us box, complete the information requested, scroll to the
bottom, and click Send.
User Documentation Web—for downloading documents:
mssupport.thermo.com
1. On the Terms and Conditions web page, click I Agree.
2. In the left pane, click Customer Manuals.
3. To locate the document, click Search and enter your search criteria. For
Document Type, select Manual.
Email—to send feedback directly to Technical Publications:
[e-mail]
Web—to complete a survey about this Thermo Scientific document:
www.surveymonkey.com/s/PQM6P62

Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices 1
1
Checking the Agilent Firmware Versions
This chapter describes how to check the compatibility of the Agilent 1200 Series LC system
with the device drivers provided on the Thermo Scientific LC Devices software DVD.
Checking the Firmware Versions with the Agilent Instant Pilot
You can use the Agilent Instant Pilot™ handheld controller to check the firmware versions of
the Agilent LC modules to ensure their compatibility with the device drivers provided with
LC Devices.
To check the firmware version of the LC modules
1. Make sure that the modules are connected by controller area network (CAN)
communication cables, that all the modules are turned on, and that the Agilent Instant
Pilot is connected.
For instructions on how to connect the CAN cables, refer to the Agilent 1200 Series LC
reference manuals.
2. From the Welcome screen of the Instant Pilot, press the Details button (Figure 2).
The System Info screen appears. The System Info screen contains information about the
firmware versions of the configured system modules.
Contents
•Checking the Firmware Versions with the Agilent Instant Pilot
•Checking the Firmware Versions from the Xcalibur Data System

1Checking the Agilent Firmware Versions
Checking the Firmware Versions from the Xcalibur Data System
2Agilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
Figure 2. Welcome screen on the Agilent Instant Pilot
3. Compare the firmware versions to those in Table 1 on page ix.
Checking the Firmware Versions from the Xcalibur Data System
Before you can check the firmware versions of the Agilent LC modules from the Xcalibur data
system, you must first establish communication between the modules and the Xcalibur data
system.
You can monitor the status of the Agilent modules from the Xcalibur Information view. To
open or close the Information view, choose View > Info View.
To check the firmware versions of the LC modules from the Xcalibur data system
1. Establish communication with the Agilent LC system as follows:
a. Connect the Agilent local area network (LAN) interface to the data system computer.
See “Connecting the Ethernet Cables” on page 34.
b. Configure the Agilent LAN interface to use a stored IP address. See Chapter 2,
“Setting Up the LAN Interface.”
c. Specify the instrument configuration options for the LC modules in the Xcalibur
Instrument Configuration window. See “Configuring the Agilent LC System’s
Modules” on page 20.
IMPORTANT When you are done, to prevent data system failure, disconnect the Instant
Pilot cable from the LC stack.
Esc
Sequence Status Logbook More
10:00
Select a button to continue
Display
Control
Details
Welcome
Quat Pump
Autosampler
Col Comp
Method
Agilent Technologies
789
456
123
0.~
i
Start Stop
Details button

1 Checking the Agilent Firmware Versions
Checking the Firmware Versions from the Xcalibur Data System
Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices 3
2. Choose Start > All Programs > Thermo Xcalibur > Xcalibur to open the Xcalibur
application.
3. From the Xcalibur Roadmap view, choose View > Info View to open the Information
view, and then click the Status tab.
4. On the Status page, click the module name to view its status (Figure 3).
Figure 3. Status page of the Xcalibur Roadmap View (example)
Note To trigger data acquisition from a Thermo Scientific mass spectrometer, you
must install a contact closure board in one of the Agilent modules and connect the
board to the Start In pins on the mass spectrometer power panel. See “Installing the
External Contact Interface Board” on page 29 and “Connecting the Contact Closure
Cable” on page 35.

Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices 5
2
Setting Up the LAN Interface
This chapter describes how to configure the local area network (LAN) interface for the
Agilent 1200 Series LC system. For stable communication with the Xcalibur data system, one
of the modules in the Agilent LC system must contain either an on-board LAN interface or an
Agilent G1369 LAN card.
Determining the LAN Interface Type and Location
Agilent provides two options for the LAN interfaces:
• On-board LAN interface, which might be the standard configuration or you can order as
part of a module
• Agilent G1369 LAN card, which you can order separately
Note For more information, refer to the user manual for the Agilent LAN card.
Contents
•Determining the LAN Interface Type and Location
•Setting the LAN Initialization Mode to “Using Default”
•Setting the Stored TCP/IP Address for the LAN Interface
•Setting the LAN Initialization Mode to “Using Stored”
IMPORTANT Do not install more than one LAN card in the Agilent LC system. If one of
the modules in the LC stack includes an on-board LAN interface, do not install a LAN
card.

2Setting Up the LAN Interface
Determining the LAN Interface Type and Location
6Agilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
To determine which module contains the LAN interface
Check the back panels of the modules for either an on-board LAN interface (Figure 4) or
a LAN card (Figure 5).
Figure 4. Location of the on-board LAN interface port (example)
Figure 5. Location of the LAN card (pump module, example)
Note If the LC stack does not have a built-in LAN interface, Agilent recommends
that you install the Agilent G1369 LAN card in the detector, if part of the system. If
an Agilent detector is not part of the system, install the LAN card in the pump or
autosampler module. For instructions, refer to the manuals that came with the
Agilent 1200 Series LC system.
LANUSB
REMOTE
RS-232
CANCAN
CONFIG
REMOTE FLASH
PCMCIA
ANALOG
1
ANALOG
2
Configuration switches
for an on-board LAN interface
On-board LAN interface port
REMOTE RS-232
CONFIG
ANALOG CANCAN
Agilent Technologies
Activity
Speed
G1369 LAN Interface
Agilent G1369 LAN card

2 Setting Up the LAN Interface
Setting the LAN Initialization Mode to “Using Default”
Thermo Scientific Agilent 1200 Series Getting Connected Guide for LC Devices 7
Setting the LAN Initialization Mode to “Using Default”
Before you configure the LAN interface parameters, set the LAN initialization mode to use
the default IP address. The initialization mode is set with three of the eight configuration
switches located on the LAN board.
• On-board LAN interface—Use switches 6, 7, and 8 located on the back of the module
that has the LAN connector.
• Agilent G1369 LAN card—Use switches 4, 5, and 6 located on the LAN card.
Follow one of these procedures:
•To set the on-board LAN interface’s initialization mode to use the default IP address
•To set the LAN card’s initialization mode to use the default IP address
To set the on-board LAN interface’s initialization mode to use the default IP address
Set the initialization switches on the back panel (Figure 6) as follows:
Figure 6. Back panel on-board LAN configuration switches set to the default IP address
To set the LAN card’s initialization mode to use the default IP address
1. For the module that contains the LAN card, turn off the power switch and unplug its
power supply cord.
2. If an Ethernet cable connects to the Ethernet port (LAN), disconnect the cable.
3. Ensure that you wear electrostatic discharge (ESD) protection.
Refer to the LC modules’ manuals for additional safety information and for information
about preventing ESD damage caused by an electrical discharge.
Switch # 678
Position Off On On
CONFIG
On
position
Off
position
Switches 7 and 8 are
in the On (up) position.
CAUTION To prevent personal injury caused by an electric shock, always turn off the
module and unplug the power supply cord from the electrical outlet before removing
the cover.

2Setting Up the LAN Interface
Setting the LAN Initialization Mode to “Using Default”
8Agilent 1200 Series Getting Connected Guide for LC Devices Thermo Scientific
4. Remove the LAN card from the module.
For instructions, refer to the manual for the Agilent G1369 LAN card. This LAN card
has a configuration switch that you can configure for the initialization modes. The card
ships with all eight switches set to the Off (down) position, which is the “Bootp”
initialization mode.
5. Set the initialization switches on the LAN card (Figure 7) as follows:
The On position for the toggle switch is up and the Off position is down. With these
switch settings, the LAN card uses the factory default settings to enable a Transmission
Control/Internet Protocol (TCP/IP) connection to the LAN interface with a Telnet
session.
Figure 7. Configuration switches on the Agilent G1369 LAN card
6. Reinstall the LAN card.
7. Using the Category 5 Ethernet cable, connect the LAN card directly to the dedicated
Ethernet port in the data system computer.
8. Plug in the disconnected power supply cord, and then turn on the LC modules.
CAUTION To prevent damage to an instrument, always use ESD protection when
handling electronic boards and components.
Switch # 456
Position Off On On
Note The Agilent default settings are IP address 192.168.254.11 and subnet mask
255.255.0.0.
12345678