Analyst® 1.6.

2 Software
Installation Guide

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Release Date: June 2013
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Contents

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Important Information to Know Before Installing . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Chapter 2 Software Installation Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Operating System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Network Environment Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Acquisition Workstation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Processing Workstation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Current Shipping Configuration for the Dell Optiplex 9010 for Acquisition
Workstations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Supported Interface Cards and Driver Versions . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Reporter 3.2 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
PDF Reporting Capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
User Account Control Requirements for Windows 7 . . . . . . . . . . . . . . . . . . . . . . .9
Compatibility with Other Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Compatible Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Non-Compatible Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Supported Mass Spectrometers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Key Content of the Analyst 1.6.2 Software DVD . . . . . . . . . . . . . . . . . . . . . . . . .11
Key Contents of the Analyst 1.6.2 Software Web Download Package . . . . . . . . .12
Chapter 3 Installation Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
How to Use These Installation Instructions for Acquisition Workstations
Versus Processing Workstations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Task List for Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Prepare to Install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Assemble the Software DVDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Prepare the Instrument and Workstation for Installation . . . . . . . . . . . . . . . . . .16
Back up the Analyst Data Folder to a Safe Location . . . . . . . . . . . . . . . . . . . . .16
Install the Analyst 1.6.2 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Using the Analyst 1.6.2 Software DVD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Using the Analyst 1.6.2 Software Web Download Package . . . . . . . . . . . . . . .17
Update the Firmware and Configuration Tables . . . . . . . . . . . . . . . . . . . . . . . .18
(Optional) Install Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Run the Analyst Software for the First Time . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Register the Analyst Software Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Chapter 4 Network Installation for Windows XP . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Important Information to Know Before Installing . . . . . . . . . . . . . . . . . . . . . . . . . .21
Create the Network Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Create Images for the Prerequisite Applications . . . . . . . . . . . . . . . . . . . . . . . .21
Create a Distribution Point for the Analyst 1.6.2 Software . . . . . . . . . . . . . . . .22
Installing the Prerequisite Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Install the Analyst 1.6.2 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
Add User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Chapter 5 Troubleshoot Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Appendix A Firmware and Configuration Tables Files . . . . . . . . . . . . . . . . . . . . . .29
Appendix B Peripheral Devices and Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Recommended Firmware Versions for Peripheral Devices . . . . . . . . . . . . . . .31

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Contents

Peripheral Devices Controlled via AAO Software Interface . . . . . . . . . . . . . . . . .37

Appendix C Change the User Account Control Settings in Windows 7 . . . . . . . .39
Appendix D Configure the Intel Dual Port Card . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Configure the Card in Windows XP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Configure the Card in Windows 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Check the DAD Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
Appendix E Upgrade the ADC Card Driver for Windows XP . . . . . . . . . . . . . . . . .47
Upgrade the Driver Software for the ADC Card . . . . . . . . . . . . . . . . . . . . . . . . . .47
Determine Whether the ADC Card is Installed . . . . . . . . . . . . . . . . . . . . . . . . .47
Update the Driver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Appendix F Upgrade the GPIB Card Driver in Windows XP . . . . . . . . . . . . . . . . . .55
Upgrade the Driver Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Appendix G Analyst® Software Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . .57

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Introduction
1
This guide provides information about, and procedures for, installing the Analyst® 1.6.2
software. This guide also includes information on supported peripheral devices and firmware.
Information about troubleshooting installation is also included.
For information about new software features, enhancements, and known issues, refer to the
release notes for the Analyst 1.6.2 software included with the Analyst 1.6.2 software package.

Important Information to Know Before Installing

Read the following points carefully before installing the software:

Note: Back up the Analyst Data folder to a safe location before upgrading. For more
information, see Back up the Analyst Data Folder to a Safe Location on page 16. Do
not rename the existing folder. This folder contains the API Instrument folder, which
contains the basic instrument calibration and parameter settings.

Note: If you upgrade to the Analyst 1.6.2 software from a previous version of the
Analyst software, the previous version will be removed during the upgrade process.

• All versions of the Analyst software require a valid software license. These
licenses are provided with new instrument purchases and can also be
purchased separately from AB SCIEX. If you have any questions regarding
the validity of your current license or to enquire about purchasing additional
licenses, please contact your AB SCIEX sales representative or Technical
Support via support@absciex.com.
• Do not attempt to install the software without following the installation
instructions provided in this guide.
• The Analyst 1.6.2 software data files are not compatible with all previous
versions of the Analyst software. However, you can open data acquired in
the previous versions of the Analyst software in the Analyst 1.6.2 software.
• Results tables created with the Analyst 1.6.2 software cannot be opened in
Analyst 1.5.x software.
• Use the task list provided at the beginning of the installation procedure in
this guide to check off each task as you complete it. The order in which you
perform the installation steps is important.
• All peripheral devices supported in the Analyst 1.4.2 software and later
continue to be supported in the Analyst 1.6.2 software. For more
information, refer to Peripheral Devices and Firmware on page 31.
• The Analyst 1.6.2 software is available as either a software DVD or web
download package for customers upgrading from supported previous
versions of the Analyst software. Refer to Chapter 3: Installation
Instructions for more information.
• Deactivate the hardware profile and close the Analyst software before
installing the Analyst 1.6.2 software.
• For more information about compatibility, refer to Compatibility with Other
Software on page 9.

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Introduction

Support
We are committed to providing the highest level of support. To obtain answers to questions
about any of our products, report issues, or suggest improvements, visit our Web site at
www.absciex.com or write to support@absciex.com.

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Software Installation Requirements
2
This section explains the operating system, hardware, and software requirements that
acquisition and processing workstations must meet for the Analyst® software to operate.

Operating System Requirements

The Analyst 1.6.2 software requires one of these operating systems on a Dell Optiplex 9010
computer:
• Microsoft Windows XP SP3 (32-bit)
• Microsoft Windows 7 SP1 (32-bit)
• Microsoft Windows 7 SP1 (64-bit) (supported only for fresh installation of
the Analyst 1.6.2 software)

The Analyst 1.6.2 software requires one of these operating systems on a Dell Optiplex 990
computer:
• Microsoft Windows XP SP3 (32-bit)
• Microsoft Windows 7 SP1 (32-bit)
• Microsoft Windows 7 SP1 (64-bit) (supported only for fresh installation of
the Analyst 1.6.2 software)

Network Environment Requirements

The Analyst 1.6.2 software supports these network environments:
• Microsoft Windows Server 2003
• Microsoft Windows Server 2008

Acquisition Workstation Requirements

It is highly recommended that you purchase an acquisition workstation, including the
communication interface cards, from AB SCIEX. These configured systems meet all
requirements and undergo extensive testing and verification with the Analyst software. Detailed
specifications for these systems are shipped with the workstation. For more information,
contact your AB SCIEX sales representative.
The Dell Optiplex 9010 computer model is recommended for use with Windows XP and
Windows 7. For acquisition workstations, AB SCIEX recommends the following minimum
computer configuration:
• Intel Core I5-3550s
• 4 Gb DDR3 1600 Mhz SDRAM
• 2 × 2 Tb HDD (RAID1)
• DVD ± RW
• One DP-DVI adapter
• Two single-port Broadcom Ethernet cards
The Analyst 1.6.2 software has been qualified for acquisition on the current PC configuration.
Refer to Current Shipping Configuration for the Dell Optiplex 9010 for Acquisition Workstations.
The Dell Optiplex 990 computer model is supported for use with Windows XP (32-bit),
Windows 7 (32-bit) and Windows 7 (64-bit). The Windows 7 (64-bit) image for Dell Optiplex 990
computer is available from AB SCIEX. Please contact your AB SCIEX sales representative for
details.

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Software Installation Requirements

The Analyst 1.6.2 software has been tested and verified on the Dell Optiplex 990 and 9010
computers.

Note: Newer systems might be available. For more information, contact your
AB SCIEX sales representative.

Processing Workstation Requirements

For processing workstations, AB SCIEX recommends the following minimum computer
configuration:
• Intel Core I5-3550s
• 4 Gb DDR3 1600 Mhz SDRAM
• 2 × 2 Tb HDD (RAID1)
• DVD ± RW
• One DP-DVI adapter
• Two single-port Broadcom Ethernet cards
Some AB SCIEX add-on software requires additional memory, disk space, and processing
speed. For more information, refer to the documentation included with the add-on software.

Current Shipping Configuration for the Dell Optiplex

9010 for Acquisition Workstations
The computer comes installed with the following:
• A embedded Windows XP Professional SP3 (32-bit) OS license.
• A embedded Windows 7 Professional (32-bit or 64-bit) OS license so that
the OS can be upgraded to Windows 7 if required.
This computer is RoHS compliant and can be used as an acquisition workstation or stand-
alone processing computer. Windows XP and Windows 7 come with Internet Explorer 8.0. All
driver software required for the cards is also installed.
The acquisition workstation comes with the following:
• Two Broadcom network card PCIe Ethernet, 1 port
The acquisition workstation supports the following external interfaces and card:
• GPIB (not included)
• Serial (not included)
• NI DAQ ADC PCIe card (not included)

Note: National Instruments USB to GPIB may be required for data acquisition but is
not included.

Note: Edgeport USB may be required for peripheral device control but is not
included.

Caution: Do not change the power management settings in the BIOS. Changing the
power management settings might interfere with batch acquisition by introducing long
delay times between samples.

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Supported Interface Cards and Driver Versions

Table 2-1 shows the driver versions installed on the currently shipping acquisition workstation.
It also lists the supported driver versions.
Table 2-1 Cards and Drivers

Card name Dell Optiplex Dell Optiplex Dell Optiplex with

with Windows with Windows 7 Windows 7 SP1
XP SP3 SP1 (32-bit) (64-bit)
GPIB 2.8 2.8 2.8
ADC 9.2.3 9.2.3 9.2.3
Network card – Intel 9.3.28.0 or later - 9.3.28.0 or later
Pro/1000 PT Dual
port
EdgePort USB 5.3 5.3 5.3
Network Card — 14.6.0.6 or later 14.6.0.6 or later 14.6.0.6 or later
Broadcom

Reporter 3.2 Requirements

To use Reporter 3.2, you must have Microsoft Office 2007, 2010, 2013. Reporter 3.2 is not
compatible with Microsoft Office 2003.

PDF Reporting Capabilities

Select the option to allow reporting in either all formats (Word, Text, Excel, HTML, PDF) or only
the PDF format during the software installation.

User Account Control Requirements for Windows 7

If you are using the Analyst 1.6.2 software with the Windows 7 operating system, we
recommend that you use the Windows default settings for User Account Control. For the
Administrator, the default setting is Default – Notify me only when programs try to make
changes to my computer; for standard users, it is Default – Always notify me.
The acquisition computer comes configured with the default User Account Control settings.

Compatibility with Other Software

The Analyst 1.6.2 software requires the following additional software:
• Microsoft Update for Digital Signature (on Windows XP only)
• .NET 3.5 SP1 (on Windows XP only; it is included in the Windows 7
operating system)
• .NET 4.0
• Microsoft Visual C++ 2008 SP1 Runtime
• Microsoft Visual C++ 2008 SP1 ATL Security Update
• Microsoft Visual C++ 2010 Runtime Libraries
• Visual Studio 2010 Tools for Office Runtime (different for Windows 7 (32-bit)
and Windows 7 (64-bit))

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Software Installation Requirements

• SaveAsPdf
• Microsoft Office 2007 Primary Interop Assemblies (installed if the
workstation has Microsoft Office 2007)
• Microsoft Office 2010 Primary Interop Assemblies (installed if the
workstation has Microsoft Office 2010 or 2013)
• AB SCIEX Reporter Template Suite 3.2 (different for Windows 7 (32-bit)
and Windows 7 (64-bit))

Note: If MS Office 2007 or 2010 was not installed on your system before the Analyst
1.6.1 software installation, then Primary Interop Assemblies will not be installed during
Analyst 1.6.2 software installation. You will need to install them from the
ISSetupPrerequisites folder after installing Microsoft Office, or run setup again.

The additional software is installed automatically when the Analyst 1.6.2 software is installed.
The Analyst 1.6.2 software does not require any additional prerequisites.

Compatible Software
As of this release, these applications are compatible with the Analyst 1.6.2 software on both
the Windows XP and Windows 7 operating systems.
• Cliquid® 3.2.1 software
• ChemoView™ 2.0.2 software (Not compatible on Windows 7 OS)
• MarkerView™ 1.2.1 software
• LightSight® 2.3 software (Not compatible on Windows 7 64-bit OS)
• LipidView™ 1.2 software

Note: Earlier versions of all of these applications are not supported on the Analyst
1.6.2 software.

For information about the compatibility of AAO applications, refer to Peripheral Devices
Controlled via AAO Software Interface on page 37.

Non-Compatible Software
At the time of this release, these applications are not compatible with the Analyst 1.6.2
software:
• MultiQuant™ 2.1.1 software
• ProteinPilot™ 4.5 software
• MPX™ driver software
• DiscoveryQuant™ software
• Smart Monitor 4.3.2.1 software
• BioAnalyst™ software
• Metabolite ID software (for the API series instruments)
• Metabolite ID software (for the QSTAR® series instruments)
• MRMPilot™ software
• Pro ID software
• Pro ICAT software
• Pro QUANT software

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• Pro BLAST software

• oMALDI™ software
• oMALDI Xpert software
• PrepExpress software
• FlashQuant® software
• Automaton software
To inquire about the compatibility of software not included in either of these lists, contact
AB SCIEX support or your sales representative.

Supported Mass Spectrometers

The Analyst 1.6.2 software can control and analyze data from each of the following AB SCIEX
mass spectrometers:
• QTRAP® 4500 LC/MS/MS system
• AB SCIEX Triple Quad™ 4500 LC/MS/MS system
• QTRAP® 5500 LC/MS/MS system
• AB SCIEX Triple Quad™ 5500 LC/MS/MS system
• QTRAP® 6500 LC/MS/MS system
• Triple Quad™ 6500 LC/MS/MS system
• 4000 QTRAP® LC/MS/MS system
• 3200 QTRAP® LC/MS/MS system
• QTRAP® LC/MS/MS system
• API 5000™ LC/MS/MS system
• API 4000™ LC/MS/MS system
• API 3200™ LC/MS/MS system
• API 3000™ LC/MS/MS system
• API 2000™ LC/MS/MS system

Note: Other models of mass spectrometers supported in the Analyst 1.4.2 software
may be compatible with the Analyst 1.6.2 software but have not been specifically
verified.

Key Content of the Analyst 1.6.2 Software DVD

The following software applications, files, folders, and documents are included on the Analyst
1.6.2 software DVD:
• Analyst 1.6.2 software.
• Drivers folder: Contains driver software for all supported cards.
• Extras folder: Contains the following subfolders:
• AAO: Contains the Analyst Access Object release notes and user
guide.
• ACROREAD: Contains the Adobe Acrobat Reader 10.0.1.
• Agilent BOOTP Package: Contains a utility that controls the
Agilent LC devices using Ethernet (in most cases, an additional
Ethernet adapter is required). The folder contains two subfolders,
containing the Windows XP- and Windows 7-compatible versions
of the utility.

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Software Installation Requirements

• Examples: Contains sample methods, data, and results files.

• Instrument Update: Contains the Firmware/Configuration Table
Update Program (ConfigUpdater.exe).
• Peak Finder: Contains a registry file for setting the peak finder
version used on older data files.
• Scripting Cookbook: Contains a guide that provides information
for writing applications to control the Analyst software.
• The Analyst 1.6.2 Software Release Notes.
• The Analyst 1.6.2 Software Installation Guide (this document).
• An Install folder containing safety guides as well as hardware and software
guides and tutorials for all instruments.

Note: For a complete list of documents and their location, see Analyst®
Software Documentation on page 55.

Key Contents of the Analyst 1.6.2 Software Web

Download Package
The following software application and documents are included in the Analyst 1.6.2 software
web download package:
• Analyst 1.6.2 software launcher.
• Bin folder: Contains the files required to run the software.
• Extras folder: Contains the following subfolders:
• Instrument Update: Contains the Firmware/Configuration Table
Update Program (ConfigUpdater.exe).
• Scripting Cookbook: Contains a guide that provides information
for writing applications to control the Analyst software.
• The Analyst 1.6.2 Software Release Notes.
• The Analyst 1.6.2 Software Installation Guide (this document).
• An Install folder containing the hardware, qualified maintenance, safety, site
planning, and software guides as well as tutorials for all instruments. It also
contains all the scripts.

Note: For a complete list of documents and their location, refer to Analyst®
Software Documentation on page 57.

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Installation Instructions
3
This section provides procedures for installing or upgrading to the Analyst® 1.6.2 software. It
can be done using one of the following:
• The Analyst 1.6.2 software DVD: Use the DVD for fresh installation of the
Analyst 1.6.2 software without any previous version of the Analyst software
as a prerequisite. Also, use the DVD to upgrade to the Analyst 1.6.2
software from a supported previous version of this software.
• The Analyst 1.6.2 software web download package: Use the web download
package to upgrade to the Analyst 1.6.2 software from a supported
previous version of this software.

Note: The Analyst 1.6.2 software cannot be installed as a fresh installation

from the Analyst 1.6.2 software web download package.

Using the Analyst 1.6.2 software DVD, you can upgrade to the Analyst 1.6.2 software from the
following previous versions of this software:
• Analyst 1.5.2 Software with Components for SelexION Technology.

Note: If you are upgrading from the Analyst 1.5.2 Software with
Components for SelexION Technology, contact your local sales
representative to get a license for the Analyst 1.6 software.

• Analyst 1.6 Software.

• Analyst 1.6 Software with Components for 6500 Series Instruments.
• Analyst 1.6.1 Software.

Using the Analyst 1.6.2 software web download package, you can upgrade to the Analyst 1.6.2
software from the following previous versions of the Analyst software:
• Analyst 1.6 Software.
• Analyst 1.6 Software with Components for 6500 Series Instruments.
• Analyst 1.6.1 Software.

Note: Upgrading to the Analyst 1.6.2 software from any previous version of the
Analyst software is not supported on the Windows 7 (64-bit) operating system.

Note: If you have the Analyst 1.5.2 software with HotFixes to February
2011 or an earlier version installed, then you can choose between a fresh
installation or upgrade path to install the Analyst 1.6.2 Software. If using the
upgrade path, before installing the Analyst 1.6.2 software, you must first
upgrade to the Analyst 1.6 software.

Note: Your security database will be removed if the Analyst software is

uninstalled. If you have the Analyst 1.5.2 software with HotFixes to February
2011 or an earlier version and would like to maintain your current security
database, then you must follow the upgrade path to the Analyst 1.6 software
before installing the Analyst 1.6.2 software.

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Installation Instructions

Note: The Convert Methods script has been updated for defect fixes and to
allow conversion to and from all supported instruments. The script is not
automatically replaced during the installation of the Analyst 1.6.2 software.
Uninstall the Convert Methods script before upgrading to the Analyst 1.6.2
software. After the upgrade is complete, you can re-install this script. It is
available in the Install > Scripts folder in the Analyst 1.6.2 software DVD or
web download package.

Note: The order of the upgrade procedures is important. Use the Task List
for Installation on page 15 to make sure that you complete each procedure.

Note: You must be logged in as a user with Administrator privileges to

install the Analyst 1.6.2 software.

Note: Removing the Analyst 1.6.2 software from the system will uninstall
the Analyst software completely rather than reverting to the previously
installed configuration. The Analyst Data folder will not be removed, but it is
still recommended that you archive this folder. Instrument settings are
retained but application settings are not.

Note: If you upgrade the acquisition workstation to the Analyst 1.6.2

software, AB SCIEX recommends that you upgrade the processing
workstation as well.

How to Use These Installation Instructions for

Acquisition Workstations Versus Processing
Workstations
The upgrade instructions in this section can be used for both acquisition workstations
(workstations that are connected to an instrument) and processing workstations (workstations
that are not connected to an instrument).
Use the following table to understand which upgrade procedures to complete for each
workstation.
Table 3-1 Procedures for Acquisition and Processing Workstations

Workstation Procedure
Acquisition workstations Complete all procedures in this section (note that some
procedures are optional, or are required only if you have
certain interface cards installed in the workstation).

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Table 3-1 Procedures for Acquisition and Processing Workstations (Continued)

Workstation Procedure
Processing workstations Complete only those procedures marked with the following
icon:
P
You can omit any upgrade procedures related to:
• Cards and driver software
• Upgrading firmware and configuration tables

Task List for Installation

Use the following checklist to make sure that you complete all the required steps.

Tip! Photocopy this checklist so you can check off each step as you proceed
through the installation instructions.

Table 3-2 Checklist

Step Procedure

 P
1. Make sure that the workstation
meets the requirements for
See Software Installation
Requirements on page 7.
installing the Analyst software.

 P
2. Assemble the required and
optional DVDs you need for the
See Assemble the Software DVDs on
page 16.
installation.
Only for installation from web
download package:
Make sure that you have
downloaded the Analyst 1.6.2
software package from the AB
SCIEX Web site.

 P
3. Prepare the instrument and
workstation for the installation.
See Prepare the Instrument and
Workstation for Installation on
page 16.

 P
4. If you are installing on
Windows 7, check your User
See Change the User Account
Control Settings in Windows 7 on
Account Control Settings. page 39.

 P
5. Back up the Analyst Data folder
to a safe location.
See Back up the Analyst Data Folder
to a Safe Location on page 16.

 P
6. Install the Analyst 1.6.2
software.
See Install the Analyst 1.6.2 Software
on page 17.

 7. Update the firmware and See Update the Firmware and

configuration tables, if required. Configuration Tables on page 18.

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Installation Instructions

Table 3-2 Checklist (Continued)

Step Procedure

 P
8. (Optional) Install any scripts. See (Optional) Install Scripts on
page 18.

 P
9. Run the Analyst software for
the first time.
See Run the Analyst Software for the
First Time on page 18.

 P
10. Register the Analyst software
online.
See Register the Analyst Software
Online on page 19.

Prepare to Install

Assemble the Software DVDs

1. Locate the Analyst 1.6.2 software DVD.
2. If required, locate any DVDs containing optional add-on software.

Prepare the Instrument and Workstation for Installation

Note: Do not remove any of the cards from the workstation.

1. Log on to the computer as a user with Administrator privileges.

2. For acquisition workstations, if your workstation has a GPIB connector, make sure the
instrument is powered on and connected to the GPIB connector at the back of the
workstation.
3. If you are upgrading from a previous version of the Analyst software, deactivate any
active hardware profiles before installing the Analyst 1.6.2 software and then exit the
Analyst software.

Back up the Analyst Data Folder to a Safe Location

Do not rename the existing Analyst Data folder. When you upgrade, AB SCIEX
recommends that you use the same Analyst Data folder from your previous installation. This
gives you access to your existing data, such as hardware profiles, methods, and data files. It
also retains your InstrumentData.ins and ParameterSettings.psf files.
• Make a backup copy of the files and subfolders in the Analyst Data folder
(do not rename the folder). The default location is D:\Analyst Data. Create
the backup in a safe location, such as a network drive or a DVD. You are
not required to restore these files as part of a normal upgrade; however, it is
good practice to make sure that a backup exists.
The content of the Analyst Data folder includes the API Instrument folder, which
contains the basic instrument calibration and parameter settings.

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Note: As part of normal installation, the API Instrument folder and the
CompoundLib.db is automatically backed up to the TEMP folder on your system. This
folder is normally stored in <drive>:\Documents and Settings\<name>\Local
Settings\Temp\Analyst_Data_Backup_[Date]. Do not rely on this backup. Always back
up the Analyst Data folder and only use this folder if absolutely necessary.

Install the Analyst 1.6.2 Software

Note: Microsoft Word 2007, 2010, or 2013 is required to generate reports. If you do
not have either MS Word 2007, 2010, or 2013 installed on the system, during the
installation process a warning will be displayed informing you that Word 2007, 2010,
or 2013 is required for the Reporter to function properly. You can either cancel the
installation or continue with it. After the Analyst 1.6.2 software is installed, you can
install Word 2007, 2010, or 2013 if required.

Complete the following procedures to upgrade the workstation to the Analyst 1.6.2 software
release.

Using the Analyst 1.6.2 Software DVD

1. If upgrading from a previous version of the Analyst software, make sure that there is
no active hardware profile and close the Analyst software before installing the Analyst
1.6.2 software.
2. Insert the Analyst 1.6.2 software DVD.

Note: If the installation browser does not appear, then browse to the Install
folder on the DVD and then double-click setup.exe.

3. Click Install Analyst 1.6.2 Software.

Note: In Windows 7, several User Account Control warnings appear during

installation. Click Yes to continue.

4. Follow the instructions in the installation wizard to install the software.

Using the Analyst 1.6.2 Software Web Download Package

1. Make sure that there is no active hardware profile and close the Analyst software
before installing the Analyst 1.6.2 software.
2. Extract the files from the compressed Analyst 1.6.2 software web package.
3. Click Launch.exe.

Note: In Windows 7, several User Account Control warnings appear during

installation. Click Yes to continue.

4. Follow the instructions in the installation wizard to install the software.

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Installation Instructions

Update the Firmware and Configuration Tables

Note: For information on the firmware and configuration table versions supported in
the Analyst 1.6.2 software, refer to Firmware and Configuration Tables Files on
page 29.

Use the Firmware and Configuration Table Update program to automatically determine if
firmware or configuration tables must be updated on the system. The utility performs only the
required updates. The utility may also reset the mass spectrometer system controller. This is
normal and is required by the update process.
If the system has a GPIB connection, then, before running this utility, make sure that the mass
spectrometer is turned on and connected to the GPIB card and that the GPIB driver software is
properly installed.
1. If the Analyst 1.6.2 software DVD is not already in the DVD drive, insert it.
2. If the installation browser appears, click Exit.
3. On the DVD drive, navigate to the \Extras\Instrument Update folder and then
double-click ConfigUpdater.exe.
Only for installation from web download package
• In the extracted package, navigate to the \Extras\Instrument Update
folder and then double-click ConfigUpdater.exe.
The Firmware/Configuration Table Update Program page opens, identifying the new
firmware version it will install.
4. Click Next.
5. Follow the on-screen instructions.

Note: If the utility presents you with more than one choice for the
configuration file name, choose the version listed in Firmware and
Configuration Tables Files on page 29.

6. Click Finish.

Note: If you are upgrading the firmware on the 4500, 5500, or 6500
systems, you will be prompted to manually restart the mass spectrometer.

(Optional) Install Scripts

• A number of research-grade scripts are available to extend the functionality
of the Analyst software. For more information on installing scripts, refer to
the Scripts User Guide found in the Start Menu: All Programs > AB SCIEX >
Analyst > Software Guides.

Run the Analyst Software for the First Time

1. Start the Analyst software by double-clicking the icon on the desktop.
2. For acquisition workstations, activate a hardware profile.
3. Make sure that you can acquire or process data.

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Register the Analyst Software Online

Register your installation online at:
www.absciex.com/AnalystReg or contact support@absciex.com.
Ten days from the date of installation, the software prompts you to register the Analyst software
online.
Registration of the software helps AB SCIEX offer better support. AB SCIEX will also notify you
about the availability of upgrades and patches, as well as other software-related information.
You can register from any computer with internet access; it does not have to be the computer
on which the software is installed. Your name and email address, and the name, address, and
telephone number of the company licensing the software are required. Optional information
includes some brief questions on how the Analyst software is used at the site, plus a section for
comments. You can choose whether to be contacted for software updates, product information,
or electronic surveys. Review the privacy statement and contact information on the web site for
details about the information collected and its usage.

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Network Installation for Windows XP
4
This section describes the procedure for installing the Analyst® 1.6.2 software over a network.
For more information, refer to the Analyst software Administrator Console section of the
Laboratory Director’s Guide for the Analyst software, found in the Start menu: All Programs >
AB SCIEX > Analyst > Hardware and Software Guides.

Note: Network installation is not supported with Windows 7.

Note: These procedures should be performed by someone with the prerequisite

knowledge and the support of the IT department.

Important Information to Know Before Installing

For a successful installation, make sure that all workstations are connected to the Active
Directory.

Create the Network Image

Network installation of the Analyst 1.6.2 software requires some prerequisite applications to be
already installed on the system. If they are not already installed or have been removed, install
these applications before installing the Analyst 1.6.2 software.

Create Images for the Prerequisite Applications

1. Create a network image for Microsoft .NET Framework 3.5 SP1. Examples are
provided for two different methods of creating the image:
• Install Microsoft .NET Framework 3.5 SP1 Using the Administrator Mode
Setup on page 22.
• Install Microsoft .NET Framework 3.5 SP1 using Active Directory on
page 22.
2. Create a network image for Microsoft .NET Framework 4.0 SP1. You can use a
similar method to that used for Microsoft .NET Framework 4.0, using the executable
file dotNetFx40_Full_x86_x64.exe.
3. Create network images for these applications by creating a shared folder and then
copying the executable file into it:
• Microsoft Visual C++ 2008 SP1 Runtime Redistributable
• Microsoft Visual C++ 2008 SP1 ATL Security Update
• SaveAsPDF
• Visual Studio 2010 Tools for Office Runtime
• Microsoft Office 2007 Primary Interop Assemblies (required if you will be
using Reporter 3.2 with Microsoft Office 2007)
• Microsoft Office 2010 Primary Interop Assemblies (required if you will be
using Reporter 3.2 with Microsoft Office 2010 or 2013)
• AB SCIEX Reporter Template Suite 3.2
• Document Fix For Converter

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Network Installation for Windows XP

Install Microsoft .NET Framework 3.5 SP1 Using the Administrator Mode
Setup
1. Create a network image by following these steps:
i. Create a shared folder on the server (for example, NetFX35).
ii. Copy the dotnetfx35.exe file into the shared folder from the DVD.
2. Run the Setup by following these steps:
i. Verify that the Microsoft .NET Framework 3.5 SP1 redistributable
package is available on the network server.
ii. Click Start > Run.
iii. Type the following command and then click OK:
\\<server>\<share>\dotnetfx35.exe /q /norestart
where <server> is the server name and <share> is the name of the
shared folder you created. For example,
\\server1\NetFX35\dotnetfx35.exe /q /norestart.

Install Microsoft .NET Framework 3.5 SP1 using Active Directory

1. Create a folder to hold the Microsoft .NET Framework 3.5 SP1 redistributable
package, for example, C:\deploy.
2. Copy the dotnetfx35.exe file into this folder from the DVD.
3. Create the installation points for all the components of the .NET Framework by
following these steps:
i. Create a .bat file that contains the script provided on the
http://msdn.microsoft.com/en-
us/library/cc160717(VS.90).aspx#appendix web page, and save the .bat
file in the folder you created in step 1; for example, C:\deploy. (If you
used a different folder name, change the first line of the script
accordingly.)
ii. Open the Command Prompt window, and execute the .bat file to create
the installation points.
The script creates the installation points for all the components in the AIP
subfolder, and places each installation point in its own subfolder.
iii. Close the Command Prompt window.
4. In Windows Explorer, navigate to the extraction destination folder (AIP) to verify that
the files were extracted.
5. Move the folder and its contents to the network share to be used for deployment.

Create a Distribution Point for the Analyst 1.6.2 Software

1. On a server, create a distribution point for the software.
2. When the installation browser opens, click Exit.
3. To create an administrative image, in a command line, type Msiexec.exe /a
<PathToAnalyst.msi> SHORTFILENAMES=1
TARGETDIR=<PathToDistributionPoint> NAMESOFPROPERTIES=value /qr.
The SHORTFILENAMES parameter is a Windows Installer property that uses short
file names for the names of target files, rather than long file names. If the target
volume does not support long names, this property has to be set to 1.
The NAMESOFPROPERTIES parameter is the list of the following properties of the
Analyst software that can be changed:
• ANALYSTPATH: Destination location of the application (default is
[ProgramFilesFolder]Analyst).

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• ANALYSTDATAPATH: Destination location of Analyst Data (default is the

NTFS disk with the most free space\Analyst Data).
• SECURITYDATA: Overwrite or not overwrite security database if it is found.
“1“ — overwrite
“0” — not overwrite (default)
• LIBSEARCHDATA: Overwrite or not overwrite Library Search database if it
is found
“1“ — overwrite
“0” — not overwrite (default)
• COMPOUNDDATA: Overwrite or not overwrite Compound database if it is
found.
“1“ — overwrite
“0” — not overwrite (default)
Example: Msiexec /a “d:\install\analyst.msi” SHORTFILENAMES=1
TARGETDIR=”C:\Managed Applications\Analyst16” LIBSEARCHDATA=”1” /qr.
4. After creating the distribution point, copy the Scripts folder, all the documentation
(tutorials and guides) folders, the release notes, and the software installation guide to
this location.

Installing the Prerequisite Applications

1. For Windows XP SP2, install Windows Installer 3.1 by following these steps:.
i. Click Start > Run.
ii. Type the following command and then click OK:
\\<server>\<share>\WindowsInstaller-KB893803-v2-x86.exe /quiet
/norestart
where <server> is the server name and <share> is the name of the
shared folder you created. For example,
\\server1\WinInst31\WindowsInstaller-KB893803-v2-x86.exe /quiet
/norestart
2. Install Microsoft .NET Framework 3.5 SP1 by following these steps:
i. Verify that the Microsoft .NET Framework 3.5 SP1 Runtime package is
available on the network server.
ii. Click Start > Run.
iii. Type the following command and then click OK:
\\<server>\<share>\dotnetfx35.exe /q /norestart
where <server> is the server name and <share> is the name of the
shared folder you created. For example,
\\server1\NetFX35\dotnetfx35.exe /q /norestart.
3. Install Microsoft .NET Framework 4.0 by following the instructions at:
http://msdn.microsoft.com/en-us/library/ee390831.aspx
4. Install the Microsoft Visual C++ 2008 SP1 Runtime Redistributable by typing the
following command in the Command Prompt window:
\\<server>\<share>\Vcredist_x86.exe /q:a
where <server> is the server name and <share> is the name of the shared folder you
created.
5. Install Microsoft Visual C++ 2008 SP1 ATL Security Update by typing the following
command in the Command Prompt window:
\\<server>\<share>\Vcredist_x86.exe /q:a
where <server> is the server name and <share> is the name of the shared folder you
created.

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Network Installation for Windows XP

6. Install Visual Studio 2010 Tools for Office Runtime by typing the following command in
the Command Prompt window:
\\<server>\<share>\vstor40_x86.exe/q:a /c:"install /q /l"
where <server> is the server name and <share> is the name of the shared folder you
created.
7. Install SaveAsPDF by typing the following command in the Command Prompt
window:
\\<server>\<share>\SaveAsPDF.exe /quiet
where <server> is the server name and <share> is the name of the shared folder you
created.
8. Install Microsoft Office 2007 Primary Interop Assemblies by typing the following
command in the Command Prompt window:
\\<server>\<share>\o2007pia.msi /quiet
where <server> is the server name and <share> is the name of the shared folder you
created.

Note: This application will not be installed if Microsoft Office 2007 is not
installed on the workstation.

9. Install Microsoft Office 2010 Primary Interop Assemblies by typing the following
command in the Command Prompt window:
\\<server>\<share>\o2010pia.msi /quiet
where <server> is the server name and <share> is the name of the shared folder you
created.

Note: This application will not be installed if Microsoft Office 2010 or 2013
is not installed on the workstation.

10. Install AB SCIEX Reporter Template Suite 3.2 by typing the following command in the
Command Prompt window:
\\<server>\<share>\ContentControlManager.msi /quiet
where <server> is the server name and <share> is the name of the shared folder you
created.
11. Install DocumentFixForConverter by typing the following command in the Command
Prompt window:
\\<server>\<share>\DocFixForConverter.msi /quiet
where <server> is the server name and <share> is the name of the shared folder you
created.

Install the Analyst 1.6.2 Software

1. Make sure that the Analyst 1.6.2 software DVD is in the DVD drive.
Only for installation from web download package
• Make sure that you have downloaded the Analyst 1.6.2 software web
download package from the AB SCIEX Web site.
• Extract all the files in a folder on your system.

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2. Create an Organizational Unit containing all the workstations where the Analyst 1.6.2
software will be installed.
3. Create a Group Policy for the unit.
4. In the Group Policy dialog, expand the Computer Configuration and Software
Settings nodes.
5. Right-click Software Installation, point to New, and then click Package.
6. Navigate to the .msi package in the distribution point.
7. Restart each workstation.

Add User Accounts

Use this procedure to create user accounts.
If you are upgrading from a previous version of the Analyst software and you choose to keep
your existing user security database when installing the Analyst 1.6.2 software, your user
accounts are preserved and you do not need to perform this procedure.

Note: If you want to upgrade from the Analyst 1.4.x or 1.5.x software and want to
preserve your security database, then first follow the upgrade path to the Analyst 1.6
software or the Analyst 1.6 software before upgrading to the Analyst 1.6.2 software.

1. After installing the Analyst 1.6.2 software over the network, start the Analyst software
and log on as a local user named administrator.
2. In the Security Configuration window, click the People tab.
3. Add new user accounts and then assign roles.
4. Close the Analyst software.
5. Restart the Analyst software and then log on using one of the accounts that you
added in step 3.

Tip! If you are using Integrated Mode, log off from Windows to log in as
another user.

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Troubleshoot Installation
5
This section describes some issues that may be encountered while installing or upgrading to
the Analyst® 1.6.2 software. It suggests possible causes and offers solutions.
AB SCIEX is committed to providing the highest level of support for the Analyst software users.
To obtain answers to questions about any of our products, report problems, or suggest
improvements, visit the Web site at www.absciex.com.
Table 5-1 Troubleshooting

Issue Possible Cause/Solution

After installing, I cannot log on to the Your user name might not have been successfully
Analyst software. added to the security database during the upgrade.
Log on to the computer as the local administrator
and then add your user name to the Analyst
software through the Security Configuration dialog.
I see the error message “Failed to load If you restored any files or folders from a DVD, or
the parameter settings file” when I try to copied over files shipped with your instrument,
start a profile in the Analyst software. these files might be set as read only. To use these
files, remove the read- only setting from the files
through Windows.

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Firmware and Configuration Tables Files
A
The following instrument firmware and configuration table versions must be used with the
Analyst® 1.6.2 software. Instructions for making sure you have the latest versions of these files
are included in the Update the Firmware and Configuration Tables on page 18. These tables
are for reference purposes only.
Table A-1 Firmware Files for the 4500, 5500, and 6500 Series of Instruments

Firmware Version
All systems PIL1400

Table A-2 Firmware Files for Other Mass Spectrometers

Firmware Version
340 Main M401402
332 Main M3L1417
425 Main MIL3002

Table A-3 Configuration Table Files for the Analyst 1.6.2 Software

System Configuration Table File

QTRAP® 4500 LC\MS\MS system FWQTrap4500R01.fw
AB SCIEX Triple Quad™ 4500 LC\MS\MS system FWTripleQuad4500R01.fw
QTRAP® 5500 LC\MS\MS system FWQTrap5500R04.fw
AB SCIEX Triple Quad™ 5500 LC\MS\MS system FWTripleQuad5500R04.fw
QTRAP® 6500 LC\MS\MS system FWQTrap6500R01.fw
AB SCIEX Triple Quad™ 6500 LC\MS\MS system FWTripleQuad6500R01.fw
4000 QTRAP® LC\MS\MS system (U series serial number) B9609010.fw
4000 QTRAP® LC\MS\MS system (AR series serial B9609031.fw
number)
3200 QTRAP® LC\MS\MS system B9631002.fw
QTRAP® LC\MS\MS system B9611003.fw
API 5000™ LC\MS\MS system B9669001.fw
API 4000™ LC\MS\MS system B5366005.fw
API 4000™ LC\MS\MS system (for the NanoDCI source) B5366020.fw
API 3200™ LC\MS\MS system B9633002.fw
API 3000™ LC\MS\MS system A8958000.fw
API 2000™ LC\MS\MS system A7483000.fw

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Peripheral Devices and Firmware
B
The Analyst® software supports the peripheral devices listed in the following table. Firmware
versions that have been fully qualified with the Analyst 1.6.2 software are listed without
parentheses. Versions shown in parentheses have functioned acceptably in more limited
testing.
In most cases, more recent firmware versions from the device manufacturer will work with the
Analyst 1.6.2 software. If you encounter difficulties, change the device firmware to the version
listed in this table. For information on checking and upgrading firmware, refer to the
documentation provided by the peripheral device manufacturer. For information on installation
and configuration of peripheral devices, refer to the Peripheral Devices Setup Guide.

Recommended Firmware Versions for Peripheral Devices

It is the responsibility of the user to validate the suitability of the device prior to use. Contact the
manufacturer to determine the supported firmware version.
Table B-1 Eksigent

Peripheral device Tested firmware Communication cable

(and other required
firmware)
ekspert™ ultraLC 100 (1.29 or higher) WC024736 (RS-232 cable)
Autosampler
ekspert ultraLC 100-XL (1.02 or higher) WC024736 (RS-232 cable)
Autosampler
ekspert ultraLC 100 Pump (1.2 or higher) —
ekspert ultraLC 100 Column (2.04 or higher) —
Oven

Table B-2 Agilent 1290 Series

Peripheral device Tested firmware Communication cable

(and other required
firmware)
Binary Pump B.06.30, (B.06.32) WC024736 (RS-232 cable) or
Ethernet
Standard Autosampler A.06.31 (A.06.32, WC024736 or Ethernet
A.06.30)
TCC—Thermostatted Column (A.06.32, A.06.30) WC024736
Compartment
DAD—Diode Array Detector B.02.11, (B.06.32, Ethernet
B.06.30)

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Peripheral Devices and Firmware

Table B-3 Agilent 1260 Series

Peripheral device Tested firmware Communication cable

(and other required
firmware)
Isocratic Pump A.06.33, (A.06.32) WC024736 or Ethernet
Quaternary Pump (A.06.32) WC024736 or Ethernet
Binary Pump (A.06.32) WC024736 or Ethernet
High Performance Autosampler A.06.32 WC024736 or Ethernet
TCC—Thermostatted Column (A.06.32) WC024736
Compartment
DAD—Diode Array Detector (B.06.32) Ethernet

Table B-4 Agilent 1200 Series

Peripheral device Tested firmware Communication cable

(and other required
firmware)
Isocratic Pump (A.06.32, A.06.02) WC024736 (RS-232 cable) or
Ethernet
Quaternary Pump (A.06.32, A.06.02) WC024736 or Ethernet
Binary Pump A.06.32 (A.06.04, WC024736 or Ethernet
A.06.02)
Binary SL Pump (A.06.32, A.06.04, WC024736 or Ethernet
A.06.02)
Capillary Pump (A.06.32, A.06.02) WC024736 or Ethernet
Nanoflow Pump (A.06.32, A.06.02) WC024736 or Ethernet
Standard Autosampler (A.06.32), A.06.10 WC024736 or Ethernet
High Performance Autosampler A.06.32, (A.06.04, WC024736 or Ethernet
A.06.02)
High Performance Autosampler (A.06.32) WC024736 or Ethernet
SL
Micro Well-plate Autosampler (A.06.32, A.06.02) WC024736 or Ethernet
High Performance Autosampler A.06.32 WC024736 or Ethernet
SL Plus
TCC—Thermostatted Column (A.06.32, A.06.02) WC024736 or Ethernet
Compartment
TCC SL—Thermostatted A.06.04, (A.06.32, WC024736 or Ethernet
Column Compartment A.06.02)
DAD—Diode Array Detector (B.06.32, A.06.32, WC024736 or Ethernet
A.06.02)

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 Peripheral Devices and Firmware

Table B-4 Agilent 1200 Series (Continued)

Peripheral device Tested firmware Communication cable

(and other required
firmware)
DAD SL—Diode Array Detector (B.06.32, B.01.02) Ethernet
SL

Table B-5 Agilent 1100 Series

Peripheral device Tested firmware Communication cable

(and other firmware) required
Binary Pump (A.06.10, A.05.11, A.05.06, WC024736* (RS-232 cable),
4.11) WC021365 (GPIB cable), or
Ethernet
Quarternary Pump (A.06.10, 5.04, A.05.11, WC024736, WC021365, or
A.04.11) Ethernet
Isocratic Pump (A.06.10, A.04.11) WC024736, WC021365, or
Ethernet
Capillary Pump (A.06.30, A.04.11) WC024736, WC021365, or
Ethernet
Nano Pump (A.06.30, A.05.06, 5.05, WC024736, WC021365, or
5.04) Ethernet
Standard Autosampler (A.06.10, A.05.11, 5.04, WC024736, WC021365, or
A.04.10) Ethernet
Micro Autosampler (A.06.10, A.05.04, 4.10) WC024736, WC021365, or
Ethernet
Well-plate Autosampler (A.06.31, A.05.07, 4.14, WC024736, WC021365, or
5.02) Ethernet
Micro Well-plate Autosampler (A.06.31, A.05.09, 4.14) WC024736, WC021365, or
Ethernet
TCC—Thermostatted Column (A.06.10, A.05.06, 5.05, WC024736, WC021365, or
Compartment 4.11) Ethernet
DAD—Diode Array Detector (B.06.30, A.06.10, 5.09, WC024736, WC021365, or
A.05.06, 4.11) Ethernet
DAD—Diode Array Detector (B.06.30, B.01.01) WC024736, WC021365, or
SL Ethernet
* WC024736 is a Standard Null Modem cable DB9/DB9 female

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Peripheral Devices and Firmware

Table B-6 CTC

Peripheral device Tested firmware Communication cable

(and other firmware) required
HTS PAL Autosampler (4.2, 4.1.x, 2.4.0) WC024736 (RS-232 cable)
HTC PAL Autosampler 4.1.3, (4.2, 4.1.x, 2.4.0) WC024736
LC PAL Autosampler (4.2, 4.1.x, 2.4.0, 2.3.1) WC024736
DLW (HTC-XT) (4.2.0, 4.1.x and Rev 5 WC024736 or Ethernet
cycle files)

Table B-7 Gilson

Peripheral device Tested firmware Communication cable

(and other firmware) required
215 Autosampler (2.20) WC024735**
215 Autosampler with 819 (1.00) Gilson GSIOC
Valve
233 Autosampler (BV1.11) WC024735
233 Autosampler with 402 (SV2.3, SV1.10) Gilson GSIOC
Syringe
** WC024735 is a standard modem cable DB25 male/DB9 female.

Table B-8 Harvard

Peripheral device Tested firmware Communication cable

(and other firmware) required
Harvard (22 Syringe Pump) 22.90

Table B-9 LC Packings

Peripheral device Tested firmware (and Communication cable

other firmware) required
UltiMate Integrated System (6.00, 5.06) Cables available from LC
Packings
Famos Autosampler (Well- (2.02) Cables available from LC
plate) Packings
Famos Autosampler (Carousel) (1.14) Cables from LC Packings

Table B-10 PE Series 200

Peripheral device Tested firmware Communication cable

(and other firmware) required
Autosampler (1.08) WC024737

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Table B-10 PE Series 200 (Continued)

Peripheral device Tested firmware Communication cable

(and other firmware) required
Column Oven (1134) WC024736
Micro Pump (2.43) WC024736
Quaternary Pumps (2.43) WC024736

Table B-11 Shimadzu

Peripheral device Tested firmware Communication cable

(and other firmware) required
SCL-10Avp System Controller (5.40, 5.33) WC024736 (RS-232 cable)
SIL-10ADvp Autosampler (5.32) All other Shimadzu devices
require 2-pin optical cables
SIL-HTA Autosampler (6.02) to connect to the System
Controller. These are
SIL-HTC Autosampler (6.02, 6.03) available from Shimadzu.
SIL-20ACXR Autosampler 1.20, 1.22
SIL-20AXR Autosampler (1.20 or later)
SIL-30AC Autosampler 2.30, (2.01) —
SIL-30ACMP Autosampler (1.03) —
LC-6AD Pump (1.4) —
LC-8A Pump (1.5) —
LC-10AD Pump (3.1) —
LC-10AS Pump (3.1) —
LC-10AT Pump (3.1) —
LC-10Ai Pump (3.1) —
LC-10ADvp Pump (5.27, 5.25, 5.26) —
LC-10ATvp Pump (5.27) —
LC-20AD Pump (1.21) —
LC-20ADXR Pump 1.21, (1.20) —
LC-30AD Pump 2.3, (2.1) —
CTO-10A[C] Column Oven (3.0) —
CTO-10Avp Column Oven (5.24) —
CTO-10ACvp Column Oven (5.24) —
CTO-10ASvp Column Oven (5.24) —
CTO-30A Column Oven 2.01, (2.1) —

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Peripheral Devices and Firmware

Table B-11 Shimadzu (Continued)

Peripheral device Tested firmware Communication cable

(and other firmware) required
CTO-30AS Column Oven (0.07) —
SPD-10A Detector (3.0) —
SPD-10Ai Detector (3.0) —
SPD-10AV Detector (3.0) —
SPD-10AVi Detector (3.0) —
SPD-10Avp Detector (5.22) —
SPD-10AVvp Detector (5.23, 5.22) —
OptionBox-L Subcontroller (3.2) —
SubcontrollerVP (5.20) —
FCV-12AH Valve N/A —
FCV-13AL Valve N/A —
FCV-14AH Valve N/A —
CBM-20A with Ethernet Switch 2.30 —
(system controller with 8 fiber (1.06,
optic ports)
1.05 or later,
2.1 or higher for use with 30-
Series devices)
CBM-20A Lite with Ethernet — —
Switch (system controller with 4
fiber optic ports; installs onto
pump or autosampler)
LC-20AD Solvent Delivery Unit (1.07, 1.04 or later) —
LC-20AB Binary Solvent — —
Delivery Unit
LC-20AT Solvent Delivery Unit — —
SIL-20A Autosampler — —
SIL-20AC Autosampler 1.20, (1.04 or later) —
Rack Changer — —
Rack Changer C — —
CTO-20A Column Oven — —
CTO-20AC Column Oven (1.07, 1.04) —
SPD-20A UV-VIS Detector — —
SPD-20AV UV-VIS Detector (1.03) —

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Table B-12 Spark-Holland

Peripheral device Tested firmware Communication cable

(and other firmware) required
Endurance Autosampler (2.05) Requires the Analyst®
Software Driver Kit p/n
0920-768 from Spark
(sales@spark.nl)

Table B-13 Valco

Peripheral device Tested firmware Communication

(and other firmware) cable required
2 Position Valve (C.9) —

Peripheral Devices Controlled via AAO Software

Interface
The Analyst Access Object (AAO) is an interface to the Analyst software that allows peripheral
device vendors to develop device control software that can be plugged into the Analyst
software to enable integrated LC/MS control.
Vendors that have released AAO software are listed below. For additional information, contact
vendors directly.
• Alcott Chromatography
• Cohesive Technologies
• Dionex Corp.
• Eksigent Technologies
• ESA Inc.
• Flux Instruments AG
• Jasco Inc.
• Leap Technologies
• Maylab Analytical Instruments
• PerkinElmer Inc.
• Shimadzu Corporation
• Shiseido Co. Ltd.
• Spark Holland
• Waters Corp.
AAO applications that are compatible with the Analyst 1.6 and Analyst 1.5.x software versions
will be compatible with the Analyst 1.6.2 software on the Windows XP and Windows 7(32-bit)
operating systems (OS).
AAO applications that are compatible with the Analyst 1.6 and Analyst 1.5.x software versions
will be compatible with the Analyst 1.6.2 software on the Windows 7 (64-bit) OS only if they run
as 32-bit applications in the WOW64 mode.
Contact the AAO vendor to confirm application compatibility for the Windows 7 (32-bit and 64-
bit) OS.

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Change the User Account Control Settings in
Windows 7 C
If you are using the Analyst® 1.6.2 software with the Windows 7 operating system, AB SCIEX
recommends that you use the Windows default settings for User Account Control. For the
Administrator, the default setting is Default (Notify me only when programs try to make
changes to my computer); for standard users, it is Always notify me.
1. Open Windows Control Panel.
2. Click System and Security > Change User Account Control settings.
3. On the User Account Control Settings dialog, move the slider bar to the desired
level.
• For the Administrator, select Default – Notify me only when
programs try to make changes to my computer, and then click
OK.
Figure C-1 User Account Control setting for the Administrator

• For standard users, select Default – Always notify me when,

and then click OK.

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Change the User Account Control Settings in Windows 7

Figure C-2 User Account Control setting for standard users

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Configure the Intel Dual Port Card
D
If your computer is equipped with the Intel Pro 1000/PT Dual Port Ethernet card, you can
configure it using the procedures covered in this appendix.

Configure the Card in Windows XP

Note: This procedure assumes that you are using a T3400 or Optiplex 960
workstation. For other computer systems, screens and steps might vary slightly.

1. Open Windows Control Panel.

2. Open the Network Connections control panel.

Tip! If the View is by Category, select Network and Internet Connections >
Network Connections.

3. Right-click Local Area Connection 2 or 3 and then click Properties.

Figure D-1 Local Area Connection 2 Properties dialog

4. Click Internet Protocol.

5. Click Properties.
Figure D-2 Internet Protocol (TCP/IP) Properties dialog

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Configure the Intel Dual Port Card

6. Select Use the following IP address.

7. In the IP address field, type the default IP address.
8. Press Tab.
The Subnet mask field is automatically filled.
9. Click OK and then close the Local Area Connection 2 (or 3) Properties dialog.

Configure the Card in Windows 7

1. Open Windows Control Panel.
2. Open the Network and Sharing Center.

Tip! If the View is by Category, select Network and Internet Connections >
Network Sharing Center.

3. Click Change Adapter Settings (in the top left corner).

4. Click Network Connections.
The Network Connections window opens.
5. Right-click Local Area Connection 2 or 3 and then click Properties.
Figure D-3 Local Area Connection Properties dialog

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 Configure the Intel Dual Port Card

6. Click Internet Protocol Version 4 (TCP/IPv4).

Note: The Analyst 1.6.1 software has not been tested with Internet
Protocol Version 6 (TCP/IPv6).

7. Click Properties.
Figure D-4 Internet Protocol (TCP/IP) Properties dialog

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Configure the Intel Dual Port Card

8. Select Use the following IP address.

9. In the IP address field, type the default IP address.
10. Press Tab.
The Subnet mask field is automatically filled.
11. Click OK and then close the Local Area Connection 2 (or 3) Properties dialog.

Check the DAD Settings

1. Make sure that the DAD unit is connected to the Ethernet Port A (if using Local Area
Connection 2) or Port B (if using Local Area Connection 3).
2. On the back of the DAD unit, check the Initializing Mode switches. The switches
should be set as listed in Table D-1.
Table D-1 Initializing Mode switches and their settings

Switch name Setting

SW 6 OFF
SW 7 ON
SW 8 ON

For more information, refer to the Agilent 1200 Series Diode Array and Multiple
Wavelength Detector SL User Manual.
3. Make sure that the DAD is using the default LAN settings (IP address
192.168.254.11).

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4. In Windows XP, to confirm the connection between the workstation and the DAD,
from Windows, follow these steps:
i. Click Start > Run.
ii. In the Open box, type ping 192.168.254.11-t and then click OK.
5. In Windows 7, to confirm the connection between the workstation and the DAD, from
Windows, follow these steps:
i. Click Start.
ii. In the Search box type ping 192.168.254.11-t and then click OK.
6. When the message “Reply from 192.168.254.11” appears, indicating that the
communication is successful, continue to step 7.

Note: If the message “Request Timed Out” appears, then the

communication has failed. Check your connections, IP settings, and cables,
and then repeat step 1 to step 5.

7. Using the Analyst software, add the DAD to a hardware profile. For more information,
refer to the operator’s guide that comes with the instrument.

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Configure the Intel Dual Port Card

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Upgrade the ADC Card Driver for Windows XP
E
This section provides procedures for upgrading the driver software for the optional National
Instruments ADC card.

Note: This procedure is not required for Windows 7. The Windows 7 workstation
comes with the correct driver version installed.

Upgrade the Driver Software for the ADC Card

If the workstation is not running a supported version of the ADC driver software, you can
upgrade to version 9.2.3. NI-DAQmx 9.2.3 is available on the Analyst® 1.6.2 software DVD.

Determine Whether the ADC Card is Installed

1. Open Windows Control Panel.
2. Open the Administrative Tools control panel.

Tip! If the View is by Category, select Performance and Maintenance >

Administrative Tools.

Figure E-1 Administrative Tools window

3. Click Computer Management.

4. Expand System Tools.
5. Click Device Manager.
6. If present, expand Data Acquisition Devices.

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Upgrade the ADC Card Driver for Windows XP

7. In the list of installed software, look for PCI-6032, PCI-6259, or PCIe-6259 and then
do one of the following:
• If the entries are present, complete the steps in the following
procedure.
• If the entries are not present, you do not have the ADC card
installed and do not need to update the driver.

Update the Driver

1. Right-click PCI-6032, PCI-6259, or PCIe-6259 and then click Uninstall.
A confirmation message is shown.
2. Click OK.
3. Close the Computer Management window to return to Control Panel.
4. Open the Add or Remove Programs control panel.

Tip! If the View is by Category, select Add or Remove Programs > Add
or Remove Programs.

5. Click National Instruments Software.

6. Click Change/Remove.
7. On the National Instruments Software panel, click NI-DAQ old version.
8. Click Remove.
A confirmation message appears.
9. Click Yes.
A message is shown prompting you to restart the computer.
10. Click No.
11. Navigate to the folder where the new NI-DAQmx 9.2.3 software has been extracted.
12. Double-click Setup.exe.
The Product Information window opens.
13. Click Next.

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Figure E-2 Destination Directory dialog

14. Click Next.

Figure E-3 Select Installation Option dialog

15. Click Custom.

16. Click Next.

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Upgrade the ADC Card Driver for Windows XP

Figure E-4 Features Dialog

17. Click Next.

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 Upgrade the ADC Card Driver for Windows XP

Figure E-5 License Agreement dialog

18. Click I accept the license agreement.

19. Click Next.

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Upgrade the ADC Card Driver for Windows XP

Figure E-6 Supplemental License Terms Dialog

20. Click I accept the license agreement.

21. Click Next.

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 Upgrade the ADC Card Driver for Windows XP

Figure E-7 Start Installation Dialog

22. Click Next.

When the installation is complete, the Completion window opens.
23. Click Next.
You are prompted to restart your computer.
24. Click Restart.
When the computer restarts, an NI Product Registration window appears.
Registration is optional and is not required to continue.
The Found New Hardware Wizard appears prompting you to connect to Windows
Update to search for a new driver.
25. Select No, not this time.
26. When prompted for the location of the new software, select Install the software
automatically (Recommended).
27. Click Next.
After the installation is complete, the Completion window appears.
28. Click Finish.
The ADC card driver is now installed.

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Upgrade the ADC Card Driver for Windows XP

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Upgrade the GPIB Card Driver in Windows XP
F
This section provides procedures for upgrading the driver software for the optional National
Instruments GPIB card.

Note: This procedure is not required for Windows 7. The Windows 7 workstation
comes with the correct driver version installed.

Upgrade the Driver Software

1. Make sure the hardware profile is deactivated.
2. Open Windows Control Panel.
3. Open the Add/Remove Programs control panel.

Tip! If the View is by Category, select Add or Remove Programs > Add
or Remove Programs.

4. Double-click Add/Remove Programs.

5. From the list of installed software, click National Instruments Software.
6. Click Change/Remove.
Figure F-1 National Instruments Software dialog

7. Select all the items in the NI Products list, and then click Remove.
8. Follow the instructions to remove the software.
9. Click Finish.
10. When prompted, click Yes to restart the computer.
11. Make sure the Analyst® 1.6.2 software DVD is in the DVD drive.
12. Browse to the Drivers folder.
13. In the GPIB 2.8 folder, click Setup.exe.
14. Follow the instructions in the installation wizard.
15. Register the software.

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Upgrade the GPIB Card Driver in Windows XP

16. Click Finish.

17. When prompted, click Yes to restart the computer.

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Analyst® Software Documentation
G
Several guides and tutorials are installed with the Analyst 1.6.2 software. The following table
provides a list and the location of available documents.
Start Menu: All Programs > AB SCIEX > Analyst
• Hardware and Software Guides (See Table G-1 for a list of software
documentation)
• Tutorials
• Safety Guides
• Qualified Maintenance Guides
Application Folder: <drive>:\Program Files\Analyst\Help\
• Hardware and Software Guides
• Tutorials
• Safety Guides
• Qualified Maintenance Guides
Table G-1 Software Documentation

Document Description
Getting Started Guide Provides procedures for setting up and using the
Analyst software to create methods, acquire
samples, and analyze data.
Advanced User Guide Describes the features and functionality of the
Analyst software.
3200 Series of Instruments System Covers the following information for the 3200 series
User Guide of instruments: safety and system information,
hardware profiles, projects, instrument tuning and
calibrating, basic acquisition methods, batches,
analyzing and processing data, information about
Turbo V ion source, generic parameters, calibration
ions and solutions, and cleaning and maintaining
the 3200 instruments.
4500 Series of Instruments System Covers the following information for the 4500 series
User Guide of instruments: safety and system information,
hardware profiles, projects, instrument tuning and
calibrating, basic acquisition methods, batches,
analyzing and processing data, information about
Turbo V ion source, generic parameters, calibration
ions and solutions, and cleaning and maintaining
the 4500 instruments.
5500 Series of Instruments System Covers the following information for the 5500 series
User Guide of instruments: safety and system information,
hardware profiles, projects, instrument tuning and
calibrating, basic acquisition methods, batches,
analyzing and processing data, information about
Turbo V ion source, generic parameters, calibration
ions and solutions, and cleaning and maintaining
the 5500 instruments.

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Analyst® Software Documentation

Table G-1 Software Documentation (Continued)

Document Description
6500 Series of Instruments System Covers the following information for the 6500 series
User Guide of instruments: safety and system information,
hardware profiles, projects, instrument tuning and
calibrating, basic acquisition methods, batches,
analyzing and processing data, information about
IonDrive™ Turbo V ion source, generic parameters,
calibration ions and solutions, and cleaning and
maintaining the 6500 instruments.
Laboratory Director’s Guide Describes the security functionality of the Analyst
software.
Scripts User Guide Provides procedures for installing and using the
Analyst software scripts.
Manual Tuning Tutorial Provides procedures for manually tuning your
instrument.
Manual Compound Optimization Provides procedures for manually optimizing the
Tutorial instrument for a particular analyte.
Automatic Optimization Tutorial Provides procedures for using Compound
Optimization to optimize the instrument for a
particular analyte.
IDA Tutorial Provides procedures for using the IDA Method
Wizard to create an IDA experiment.
Scheduled MRM™ Algorithm Tutorial Provides procedures for using the Scheduled
MRM™ algorithm feature.
Analyst® Software Show Me Provides an introduction and describes basic
functionality of the Analyst software.
Peripheral Devices Setup Guide Provides procedures for connecting peripheral
devices to the computer and instrument.
Standard Quantitation Tutorial Provides procedures for creating a method that can
be used to obtain a quantitation curve using
prepared standards.
Peptide and Protein Quantitation Provides procedures for creating methods that you
Tutorial can use for peptide and protein quantitation.
SelexION Technology User Guide Provides information about the SelexION™
technology supported in the Analyst software for
separation of compounds.
Help Provides procedures for setting up and using the
Analyst software to create methods, acquire
samples, and analyze data.

Table G-2 Instrument Documentation

Document Description
System Hardware Guides Provide information about the instruments.

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Table G-2 Instrument Documentation (Continued)

Document Description
Safety Practices Provides information about instrument safety as
well as safety requirements for the laboratory.
Qualified Maintenance Procedures Provides procedures for cleaning and maintaining
the instrument.
Note: Only trained operators should perform any
cleaning or maintenance procedure.
Ion Optics Tutorial Provides information about the instrument ion
optics.

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