Thermo Scientific Agilent 1100 Series User manual

Thermo
Agilent 1100 Series
Getting Connected Guide for LC Devices
XCALI-97190 Revision J December 2013

© 2013 Thermo Fisher Scientific Inc. All rights reserved.
Foundation and MSQ 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.
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of Agilent Technologies Inc. Dell is a registered trademark of Dell Inc. Hewlett Packard and JetDirect are
registered trademarks of Hewlett-Packard Development Company. Microsoft and Windows are registered
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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, Feb 2007; Revision B, July 2007; Revision C, Jan 2009; Revision D, Feb 2011;
Revision E, Dec 2011; Revision F, May 2012; Revision G, July 2012; Revision H, Dec 2012; Revision J,
Dec 2013
Software version: Thermo Foundation (see page vii), Thermo LC Devices 2.2.1 or later
For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific Agilent 1100 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Chapter 1 Checking the Agilent Firmware Versions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Chapter 2 Connecting the Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Ethernet Communication Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Installing a Network Card in an Agilent Module. . . . . . . . . . . . . . . . . . . . . . . . . 4
Connecting the Ethernet Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Installing the External Contact Interface Board . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Connecting the Contact Closure Cable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 3 Specifying the TCP/IP Settings and the BCD Board Location. . . . . . . . . . . . . . . .11
Assigning Contact Closure Control to the Autosampler . . . . . . . . . . . . . . . . . . 11
Specifying the TCP/IP Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Chapter 4 Triggering Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Chapter 5 Turning Off the Solvent Tracking Feature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Chapter 6 Upgrading an HP 1100 Series LC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Contents

Thermo Scientific Agilent 1100 Series Getting Connected Guide for LC Devices v
P
Preface
This guide describes how to connect an Agilent™ 1100 Series liquid chromatograph (LC)
system to the 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™.
This guide also describes how to upgrade a Hewlett Packard™ 1100 Series LC to an
Agilent 1100 Series LC with Ethernet communication.
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 1100 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 (LC Devices 2.2 or later), choose Start > All Programs >
Thermo Instruments > Manuals > LC Devices > Product Family, and then click
the PDF file that you want to view.
• For the Xcalibur manual set, choose Start > All Programs > Thermo Xcalibur >
Manuals > Xcalibur.
• For a Thermo Scientific mass spectrometer, choose Start > All Programs > Thermo
Instruments and so on.
For access to the application Help, follow this procedure.
To view application-specific Help
• From the Xcalibur Instrument Setup window, choose Help > Agilent 1100 Help.
• If information about setting parameters is available for a specific view, page, or dialog
box, click Help or press the F1 key for information about setting parameters.

Preface
Thermo Scientific Agilent 1100 Series Getting Connected Guide for LC Devices vii
System Requirements
Ensure that the system meets these minimum requirements.
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.
Table 1. System requirements
System Minimum requirements
Computer • 2 GHz processor with 1 GB RAM
•DVDdrive
• 80 GB available on drive C
• Video card and monitor capable of 1280 × 1024 resolution
• Network interface cards, two
•NTFSformat
Software • Adobe™ Reader™ 9.0
• 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 1100 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 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.
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 1100 Series Getting Connected Guide for LC Devices ix
Supported Firmware Versions
LC Devices supports the model numbers and firmware versions of the Agilent 1100 Series
modules listed in Table 2. For instructions on how to check the firmware version, see
Chapter 1, “Checking the Agilent Firmware Versions.”
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.
Table 2. Supported firmware versions for the Agilent 1100 Series LC
Module Model number Firmware version
Autosampler G1313A A.06.01 [012]
Thermostatted Autosampler G1329A A.06.01 [012]
Well-plate Autosampler G1367A A.06.01 [012]
Thermostatted Column Compartment G1316A A.06.01 [012]
Diode Array Detector G1315A A.06.01 [012]
Multiple Wavelength Detectora
aOnly works with version B of the Control Module.
G1365B A.06.01 [012]
Variable Wavelength Detector G1314A A.06.01 [012]
Binary Pump G1312A A.06.01 [012]
Quaternary Pump G1311A A.06.01 [012]
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.

Preface
xAgilent 1100 Series Getting Connected Guide for LC Devices Thermo Scientific
The following additional caution-specific symbol appears in the Agilent 1100 Series Getting
Connected Guide for LC Devices.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
To contact Technical Support
To contact Customer Service for ordering information
To copy manuals from the Internet
Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click
Customer Manuals in the left margin of the window.
To suggest changes to the Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
[e-mail].
CAUTION Highlights electric shock-related hazards to human beings. Each electric shock
notice is accompanied by the international High Voltage symbol.
Phone [phone]
Fax [phone]
E-mail [e-mail]
Phone [phone]
Fax [phone]
E-mail [e-mail]
Web site http://www.thermoscientific.com/en/support-landing/support.html

Thermo Scientific Agilent 1100 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 1100 Series LC system
with the device drivers provided on the Thermo Scientific LC Devices software DVD.
To check the firmware version of the LC module
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 handheld
Agilent 1100 Control Module is connected.
For instructions on how to connect the CAN cables, refer to the Agilent 1100 Series LC
reference manuals.
2. On the Control Module, press the ESC key until System appears in the upper left corner
of the LCD display.
3. On the Control Module, press F4 to access the Records LCD display (Figure 2).
Figure 2. Records LCD display
4. Compare the firmware versions to those in Ta ble 2 on page ix.
IMPORTANT When you are done, to prevent data system failure, disconnect the
handheld Control Module cable from the LC stack.
Records
Module Product Serial# Version On-time EMF
Time Ready

Thermo Scientific Agilent 1100 Series Getting Connected Guide for LC Devices 3
2
Connecting the Hardware
This chapter describes how to install the interface boards, connect the Ethernet cables,
and make the contact closure connections required to control an LC/MS
(Agilent LC/Thermo Scientific MS) system from the Xcalibur data system.
Ethernet Communication Kit
To connect the Agilent LC system to a Thermo Scientific mass spectrometer, you must have
the following parts:
• Ethernet Communication Kit (Tabl e 3)
• JetDirect™ 400N LAN card (P/N 00825-01140) or an Agilent LAN card
(Model G1369A)
• Agilent binary-coded decimal (BCD) interface board for contact closure
Contents
•Ethernet Communication Kit
•Installing a Network Card in an Agilent Module
•Connecting the Ethernet Cables
•Installing the External Contact Interface Board
•Connecting the Contact Closure Cable
Table 3. Ethernet Communication Kit (P/N OPTON 30012)
Description Part number
Agilent BCD (contact interface) board 00012-27714
Contact closure cable with 15-pin connector 00012-27716
Ethernet cable, straight shielded Cat5, 3 m (10 ft) 00012-70008
Fast Ethernet switch, 10T/100Base-TX, 5-port 00825-01-00024

2Connecting the Hardware
Installing a Network Card in an Agilent Module
4Agilent 1100 Series Getting Connected Guide for LC Devices Thermo Scientific
Installing a Network Card in an Agilent Module
For the Agilent LC system to communicate with the Xcalibur data system through an
Ethernet connection, one of the modules in the Agilent 1100 Series LC stack must have a
network interface card. If the stack has a detector, the card is usually installed in the detector.
Agilent 1100 Series LC systems with JetDirect network cards must have revision 2 main
boards to function properly with LAN communications. Table 4 lists the required main board
and its starting serial number for each module.
Tip Vendors label network cards with a unique MAC address, which is a 12-digit
hexadecimal number. The first portion of the MAC address identifies the vendor. The
second portion of the MAC address is a unique serial number. For example, a typical mark
on a network card is AD: 0030C1C49982, where 0030C1C49982 is the stack MAC
address. The first portion, 0030C1, identifies the vendor as Hewlett-Packard. The MAC
address of the HP JetDirect 400N network card is located on the back of the card.
Because you need the MAC address when you configure the Agilent stack, record the
network card MAC address before you install the card.
Table 4. Supported main board serial numbers for each module
Module P/N (Main board) Serial numbers for supported version a
aAll serial numbers above the listed number in numeric order are supported.
G1310A
Isocratic pump
G1311-65520 DE64300355 (made in Germany)
US64400233 (made in the U.S.)
G1311A
Quaternary pump
G1311-65520 DE64301137 (made in Germany)
US64401134 (made in the U.S.)
G1312A
Binary pump
G1312-65520 DE64300703 (made in Germany)
US64400425 (made in the U.S.)
G1313A
ALS autosampler
G1313-65520 DE64302092 (made in Germany)
US64400886 (made in the U.S.)
G1314A
Variable wavelength detector
G1314-65520 JP64201926 (made in Japan)
G1315A
Diode array detector
G1315-65520 DE64301532 (made in Germany)
US64400333 (made in the U.S.)

2 Connecting the Hardware
Installing a Network Card in an Agilent Module
Thermo Scientific Agilent 1100 Series Getting Connected Guide for LC Devices 5
To install the network interface card in an Agilent module
1. Make sure the module (usually the detector) is turned off and unplugged from line power.
Figure 3 shows the location of the power switches.
When the power switch of a module is in the On position, the LED on the switch is
green. When you turn the power switch of a module to the Off position, the LED
turns off.
If your LC stack contains a detector (for example, a diode-array detector, variable
wavelength detector, or multiple wavelength detector), install the network interface card
in the detector. If your LC stack does not contain a detector, install the network card in
any module with an open slot.
Figure 3. Power switches on the front of the Agilent 1100 Series modules
CAUTION To avoid electric shock, unplug the power cable that connects the Agilent
module to line power. After you turn the power switch to the Off position, the power
supply continues to draw current.
Note You can install an Agilent LAN interface board (Model G1369A) instead of a
JetDirect 400N network card.
Binary pump
Autosampler
Column
compartment
Detector
On
position
Off
position

2Connecting the Hardware
Installing a Network Card in an Agilent Module
6Agilent 1100 Series Getting Connected Guide for LC Devices Thermo Scientific
2. To prevent damage to the interface board, ensure that you are using protection from
electrostatic discharge (ESD). For more information on preventing damage caused by an
electric discharge, refer to the reference manual for the Agilent module.
3. To remove the cover plate from the slot where you plan to install the network interface
card, loosen the two screws that fasten the plate to the chassis of the module.
Figure 4 shows the location of the cover plate on the back panel of an Agilent 1100 Series
detector.
Figure 4. Back panel of an Agilent 1100 Series detector
4. Record the MAC address (12-digit hexadecimal number) located on the back of the
HP JetDirect 400N network card. You use this number to complete the configuration of
the Agilent stack (see Figure 9 on page 12).
5. Insert the HP JetDirect 400N network card into the slot, and then tighten the two screws
that fasten the PCB to the chassis of the module.
CAUTION To prevent damage to an instrument, always use ESD protection when
handling electronic boards and components.
ANALOG ANALOG RS232 RS232 CAN CAN
Cover plate

2 Connecting the Hardware
Connecting the Ethernet Cables
Thermo Scientific Agilent 1100 Series Getting Connected Guide for LC Devices 7
Connecting the Ethernet Cables
To connect the Ethernet communication cable to an Agilent LC stack
1. Connect one Ethernet cable from the JetDirect 400N network card to the Ethernet
switch.
2. Connect the second Ethernet cable from the Ethernet switch to the Ethernet network
card in the data system computer that is dedicated to the LC/MS system (typically
network interface card number 3) (Figure 5).
Figure 5. Ethernet connections
CAUTION Safety and EMC regulations require the use of Category 5 shielded Ethernet
communication cables, maximum 3 m (10 ft) long.
HEWLETT PACKARD
JET DIRECT 400N
BNC
BNC
100 (RJ-45)
100 (RJ-45)
HEWLETT PACKARD
JET DIRECT 400N
USB
ENET
Computer
Dell™ Precision T3500
(subject to change)
JetDirect 400N card
(installed in one of the
Agilent modules)
(Not drawn to scale.)
Ethernet switch
Cat5 shielded
Ethernet cables

2Connecting the Hardware
Installing the External Contact Interface Board
8Agilent 1100 Series Getting Connected Guide for LC Devices Thermo Scientific
Installing the External Contact Interface Board
If your Agilent 1100 Series autosampler is not already equipped with an external contact
interface board, install one as described below.
To install the external contact interface board
1. If you have not already done so, turn off the autosampler and unplug it from line power.
2. To prevent damage to the interface board, ensure that you are using ESD protection. For
more information on preventing damage caused by an electric discharge, refer to the
reference manual for the Agilent module.
3. To remove the cover plate from the slot where you plan to install the external contact
interface board, loosen the two screws that fasten the plate to the chassis of the
autosampler.
4. Insert the external contact interface board into the slot (see Tabl e 3 for the external
contact interface board part number). Tighten the two screws to fasten the board to the
chassis of the autosampler.
Figure 6 shows an installed external contact interface board.
Figure 6. External contact interface board (BCD board) installed in an Agilent autosampler
CAUTION To prevent personal injury caused by an electric shock, always turn off the
Agilent module and unplug its power supply cord from the electrical outlet before
removing the cover.
CAUTION To prevent damage to an instrument, always use ESD protection when
handling electronic boards and components.
1 8
Screws that secure the cover plate
VIAL- # -OUTPUT RELAY CONTACTS
REMOTE RS232 CAN CAN HP-18 CONFIG

2 Connecting the Hardware
Connecting the Contact Closure Cable
Thermo Scientific Agilent 1100 Series Getting Connected Guide for LC Devices 9
Connecting the Contact Closure Cable
An external contact closure (trigger) cable relays the start signal from the Agilent LC module
to the Thermo Scientific mass spectrometer. One end of the cable has a DB15 connector and
the other end has a set of exposed wires.
Figure 7 shows the contact closure cable set up for a Thermo Scientific TSQ™ Series mass
spectrometer with a 2-pin connector. For ordering information, see “Ethernet
Communication Kit” on page 3.
Figure 7. Contact closure cable set up with a 2-pin connector
To connect the contact closure cable to the mass spectrometer
1. Follow the procedure “To install the external contact interface board” on page 8.
2. Using an appropriate connector for the mass spectrometer, connect the white wire from
the contact closure cable to the Start In+ pin and the brown wire to the Start In– pin on
the mass spectrometer’s input/output (I/O) panel (Figure 8).
3. Connect the cable’s DB15 plug to the RELAY CONTACTS socket located on the LC
module’s installed contact interface board (Figure 8).
Note The instrument control platform for the Thermo Scientific mass spectrometer must
be compatible with the LC Devices instrument control application, and the instrument
control application must be compatible with the Thermo Scientific application installed
on your data system computer. See the LC Devices Release Notes.
2-pin connector supplied
with the mass spectrometer
DB15 connectorDB15 connector

2Connecting the Hardware
Connecting the Contact Closure Cable
10 Agilent 1100 Series Getting Connected Guide for LC Devices Thermo Scientific
Figure 8. Contact closure connections between the Agilent contact interface board and the Thermo Scientific MS
+
-
START IN
START IN
Start In +
Start In
-
START IN
(5V Max)
(5V Max)
+
–
(right-side
panel)
(left-side
panel)
White wire
Brown wire
TSQ Series MS
(back panel)
LCQ Fleet™,
LTQ™ Series, or
LXQ™ MS
(right-side panel)
Surveyor™
MSQ™ MS
(back panel)
LCQ™ Series MS
(back panel)
(Not drawn to scale.)
Contact closure cable
connects to the relay contacts
on the contact interface board.