© 2011 Thermo Fisher Scientific Inc.All rights reserved.

This guide describes how to install the LCquan™ 2.6.1 secure data quantitation package or upgrade LCquan 2.6.0 or earlier to LCquan 2.6.1. If you have LCquan 2.5.6 or earlier software installed, you must remove it before installing the LCquan 2.6.1 upgrade software. However, if you have LCquan 2.6.0 installed, you do not need to remove it before installing the LCquan 2.6.1 upgrade.

Minimum System RequirementsThe minimum computer hardware and software requirements for the LCquan 2.6.1 software are as follows:

Software CompatibilityThe LCquan 2.6.1 software requires the Xcalibur 2.1 SP1 and Foundation 1.0.2 SP2 software. To view the software version information, choose Start > All Programs > Thermo Xcalibur > Version Info.

Thermo LCquan 2.6.1 Installation Guide

Contents

• Minimum System Requirements

• Software Compatibility

• Removing All Configured Devices

• Removing Noncurrent Versions of LCquan, LC Devices, and TSQ Series Software

• Installing Current Versions of .NET, Foundation, Xcalibur, LC Devices, and TSQ Series Software

• Installing the LCquan 2.6.1 Software

• Trademarks

System Requirements

Computer • 2.4 GHz processor dual core with 4 GB RAM

• DVD/CD-ROM drive

• Display resolution 1280×1024 (XGA)

• 250 GB available disc space on the C: drive

• NTFS file format

Software • Microsoft™ Windows™ XP Professional SP3 (U.S. version) or Microsoft Windows 7 Professional 32-bit

• Microsoft Office Pro 2007 or 2010

• Microsoft .NET 3.5 SP1

• Thermo Scientific software:− Thermo Xcalibur™ 2.1 SP1− Thermo Foundation™ 1.0.2 SP2

IMPORTANT If you have LCquan 2.5.6 or earlier installed, you must perform the complete upgrade described below, which includes an upgrade to the Xcalibur 2.1 data system.

Revision A XCALI-97234

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The following instrument control software and layered applications are compatible with Xcalibur 2.1 and Foundation 1.0.2 SP2.

IMPORTANT Xcalibur 2.0.7 compatable software might not work with Xcalibur 2.1.

InstrumentInstrument control software compatible with Xcalibur 2.1 and Foundation 1.0.2 SP2

Aria™ OS Aria OS 1.6.3, 1.6.2f1

Aria X1 vi Aria X1 vi 1.2, 1.1.1

Exactive™ Exactive 1.1 SP2, 1.1 SP1, 1.0

LC Devices LCD 2.4, 2.3, 2.2.1 with SP1, 2.2.1

LCQ Fleet™ LTQ™ 2.6 SP2

LTQ LTQ 2.6 SP2

LTQ FT™ LTQ FT 2.5.5 SP1

LTQ FT Ultra™ LTQ FT 2.5.5 SP1

LTQ Orbitrap™ LTQ Orbi 2.5.5 SP1, FT Programs 2.1

LTQ Orbitrap Velos™ LTQ 2.6

LTQ Velos LTQ 2.6 SP2

LTQ XL™ LTQ 2.6 SP2

LTQ XL with ETD LTQ 2.6 SP2

LXQ™ LTQ 2.6 SP2

MSQ Plus™ MSQ 2.0 SP2

Orbitrap XL and Orbitrap Discovery

LTQ Orbi 2.5.5 SP1, FT Programs 2.1

TSQ Quantum™ XLS and TSQ Quantum GC™

2.3.0 SP1, 2.3.0, 2.0.6, 2.0.5 SP1

TSQ Series (Quantums and Vantage™)

2.3.0 SP1, 2.3.0, 2.2.0, 2.1.1, 2.1.0, 2.0.5 SP1

Layered applicationLayered application software compatible with Xcalibur 2.1 and Foundation 1.0.2 SP2

EnviroLab Forms 3.1, 3.0, 2.5.2

LCquan 2.6

Mass Frontier™ 6.0 SR3, 5.1

MetWorks™ 1.3, 1.2.1

NIST™ Library NIST Library

PathFinder™ 1.0

Pinpoint 1.1, 1.0

PEAKS™ Studio 5.2, 5.1

ProMass™ ProMass 2.8

ProSightPC™ Upcoming SP

Proteome Discoverer™ 1.2, 1.1, 1.0

QuanLab Forms 3.1, 3.0, 2.5.2

QuickQuan™ 2.4

ToxLab Forms 3.1, 3.0, 2.5.2

TraceFinder 1.0.1, 1.0

Watson TSQ Module 1.1, 1.0

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To install or upgrade to the LCquan 2.6.1 software, follow these procedures:1. Removing All Configured Devices2. Removing Noncurrent Versions of LCquan, LC Devices, and

TSQ Series Software3. Installing Current Versions of .NET, Foundation, Xcalibur,

LC Devices, and TSQ Series Software4. Installing the LCquan 2.6.1 Software

Removing All Configured Devices

To remove all configured devices1. Choose Start > All Programs > Thermo Foundation 1.0 >

Instrument Configuration to open the Instrument Configuration window.

2. Select each configured device on the right and click Remove.3. Click Done after removing all devices.

Removing Noncurrent Versions of LCquan, LC Devices, and TSQ Series SoftwareYou must remove the following software before installing the LCquan 2.6.1 software:

• LCquan 2.5.x or earlier• All Thermo LC devices including Thermo Pump• TSQ Series mass spectrometer software

To remove noncurrent versions of the software

1. Close all open applications.2. Choose Start > Settings > Control Panel to open the

Control Panel.3. Double-click Add or Remove Programs to open the Add or

Remove Programs dialog box.4. Remove LCquan 2.5.x or earlier (remove service packs first).

While removing LCquan, you might receive this message. Click Retry to proceed. If necessary, restart the computer.

5. Remove all Thermo LC Devices including Thermo Pump.6. Remove the TSQ Series mass spectrometer software. 7. Restart your computer.

Installing Current Versions of .NET, Foundation, Xcalibur, LC Devices, and TSQ Series SoftwareBefore installing the LCquan 2.6.1 software, install the most current versions of the following software:

• Adobe™ Reader™ 9.0• .NET 3.5 SP1• Foundation 1.0.2 SP2• Xcalibur 2.1 SP1• TSQ Series 2.3 SP2• LC Devices 2.5

Note If you are currently running LCquan 2.6.0, you can install the LCquan 2.6.1 upgrade on top of the existing installation.

Note It is not necessary to remove Xcalibur software.

IMPORTANT Restart your computer if prompted during the software installation.

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To install current versions of the software1. Insert the LCquan 2.6.1 installation CD. The Thermo Scientific

Product Launcher Setup page appears.

2. Click Adobe Reader 9.0 to start the Adobe Reader installation if it is not already installed.

You must have Acrobat Reader to view the Qualification Report.3. Install .NET 3.5 SP1 as follows:

a. Click DotNET 3.5 SP1 to start the .NET 3.5 SP1 installation.

b. If .NET 3.5 SP1 is present, run the Repair option.

If .NET Framework is not present, click Next. c. Accept the terms of the License Agreement and click Install.

d. Click Exit at the end of the installation.

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e. Click Restart Now to restart your computer.

4. Install Foundation 1.0.2 SP2 software as follows:a. Relaunch the LCquan 2.6.1 CD.b. Click Foundation 1.0.2 SP2 to start the Foundation

installation wizard.

c. At the prompt, click Yes to upgrade.

d. At the prompt, click Yes to remove the old application.

e. At the prompt, click Yes if you want to view the Installation Report.

f. On the Welcome page of the InstallShield Wizard, click Next.

g. Accept the terms of the License Agreement and click Next.

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h. Type your user name and company name in the boxes and click Next.

i. Select the Complete option and click Next.

j. Click Install to begin the installation.

k. If prompted, click Yes to overwrite files.

l. At the prompt, click Yes if you want to view the Installation Report.

m.On the last page of the InstallShield Wizard, select the Yes option and then click Finish to restart your computer.

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5. Install Xcalibur 2.1 SP1 software as follows:a. Relaunch the LCquan 2.6.1 CD.b. Click Xcalibur 2.1 SP1 to start the Thermo Xcalibur

installation wizard.

c. On the Welcome page, click Next.

d. Accept the terms of the License Agreement and click Next.

e. Type the user name and company name, and click Next.

f. Select the Complete option and click Next.

g. Click Install to begin the installation.

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h. Click Finish to exit the wizard and restart your computer.

6. Install the TSQ Series software as follows:a. Insert the latest TSQ Series software CD. b. Click TSQ Series 2.3 SP2 to start the installation wizard.

c. On the Welcome page, click Next.

d. Accept the terms of the License Agreement and click Next.

e. For acquisition computers, select the Yes option and click Next.

f. Select the preferred language for manuals and Help and click Next.

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g. Type the serial number for the instrument and click Next.

h. Click Next to start copying the program files.

i. At the prompt, click Yes if you want to view the Installation Report.

j. Click Finish on the last page of the wizard, and if prompted, restart your computer.

7. Install LC Devices 2.5 software as follows:a. Insert the latest LC Devices installation CD. The Thermo

Scientific Product Launcher page appears.b. Click LC Devices 2.5 to start the installation wizard.

c. On the Welcome page, click Next.

d. Accept the terms of the License Agreement and click Next.

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e. Select the check boxes for your LC devices and click Next.

f. Click Next to begin copying the program files.

g. Click Finish to close the wizard.

Installing the LCquan 2.6.1 Software

To install LCquan 2.6.1 software1. Insert the LCquan 2.6.1 CD to start the installation. The

LCquan Setup page appears.

2. Click LCquan 2.6.1 to start the installation wizard. 3. On the Welcome page, click Next.

4. Accept the terms of the License Agreement and click Next.

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5. Ensure that the computer meets the minimum system requirements and click Next.

6. On the Select Features page, select all options and click Next.

7. To install desktop shortcuts, select the Yes option and click Next.

8. Keep the default settings and click Next.

9. Click Next to start copying the program files.

10. At the prompt, click Yes if you want to view the Installation Report.

11. Click Finish to close the wizard.

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12. Configure instruments in the Instrument Configuration window.

Trademarks

LCquan, Foundation, Aria, Exactive, LCQ, Velos, LTQ XL, MSQ Plus, TSQ Quantum GC, PathFinder, Proteome Discoverer, and QuickQuan are trademarks; and Xcalibur, LCQ Fleet, LTQ FT, LTQ FT Ultra, Orbitrap, LXQ, TSQ Quantum, and MetWorks are registered trademarks of Thermo Fisher Scientific Inc. in the United States.

The following are registered trademarks in the United States and other countries:

Microsoft and Windows are registered trademarks of Microsoft Corporation. Adobe Reader is a registered trademark of Adobe Systems Incorporated.

PEAKS is a registered trademark of Bioinformatics Solutions Inc. in the United States and possibly other countries.

Mass Frontier is a trademark of High Chem Ltd. ProMass is a trademark of Novatia LLC. ProSightPC is a trademark of the Board of Trustees of the University of Illinois.

All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.

Note For assistance, contact your local Thermo Fisher Scientific service representative.