Xcalibur Proteome Discoverer - Thermo Fisher...

Xcalibur

Proteome DiscovererVersion 1.3

Installation Guide

XCALI-97359 Revision A May 2011

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© 2011 Thermo Fisher Scientific Inc. All rights reserved.

Xcalibur is a registered trademark of Thermo Fisher Scientific Inc. in the United States. ZCore and Proteome Discoverer are trademarks of Thermo Fisher Scientific Inc. in the United States.

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

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly.

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, May 2011

Software Version: Thermo Proteome Discoverer version 1.3

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

Thermo Scientific manual-name iii

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Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vRelated Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vSystem Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viSpecial Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viContacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Chapter 1 Installing Proteome Discoverer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1Opening the XInstall Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Migrating Personalized Application Data Profiles from Installations Prior

to Proteome Discoverer 1.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Installing the Proteome Discoverer Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Installing the Proteome Discoverer Software Without an Internet

Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Chapter 2 Installing Proteome Discoverer Daemon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19Opening the XInstall Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Installing the Proteome Discoverer Daemon Software . . . . . . . . . . . . . . . . . . . . 20

Chapter 3 Installing Proteome Discoverer Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31Opening the XInstall Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Installing the Proteome Discoverer Viewer Software . . . . . . . . . . . . . . . . . . . . . 32

Chapter 4 Connecting to the Mascot Server. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43Mascot Server Versions Supported. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Checking Your Mascot Server Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Checking the URL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44Checking for Security Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Configuring Mascot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Testing the Connection to the Mascot Server . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Chapter 5 Submitting a Product Change Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51

Contents

Thermo Scientific Proteome Discoverer Installation Guide v

P

Preface

This guide describes how to install the Proteome Discoverer™ 1.3 application for peptide and protein mass spectrometry analyses.

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

Related DocumentationThe Proteome Discoverer application includes Help and these manuals as PDF files:

• Proteome Discoverer User Guide

• Proteome Discoverer Installation Guide

To view product manuals

• Proteome Discoverer User Guide: Go to Start > Programs > Thermo Proteome Discoverer > Proteome Discoverer 1.3 User Guide or Help > User Guide.

• Proteome Discoverer Installation Guide: Go to Start > Programs > Thermo Proteome Discoverer > Proteome Discoverer 1.3 Installation Guide or Help > Installation Guide.

Contents

• Related Documentation

• System Requirements

• Special Notices

• Contacting Us

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Preface

# Proteome Discoverer Installation Guide Thermo Scientific

To open Help

• From the Proteome Discoverer window, choose Help > Help Contents.

• If available for a specific window or view, click Help or press F1 for information about setting parameters.

For more information, visit www.thermo.com.

System RequirementsThe Proteome Discoverer application requires a license. In addition, your system must meet these minimum requirements.

Special NoticesMake sure you follow the precautionary statements presented in this guide. Special notices appear in boxes.

System Requirements

PC • 2 GHz processor with 2 GB RAM• DVD/R-ROM drive• Video card and monitor capable of 1280 × 1024 resolution (XGA)• Screen resolution of 96 dpi• 75 GB available on the C: drive • NTFS format

Software • Microsoft Windows™ XP 32/64 Professional (English version) with latest service pack installed

• Microsoft Windows 7 32/64 Professional (English version)

Note Ensure that port 28199 is not blocked by firewalls.

Note Ensure that the Windows operating system first has the latest Microsoft .NET Framework and Windows updates installed before installing the Proteome Discoverer application.

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.

http://www.thermo.com

PrefaceRunning H/F 2

Thermo Scientific Proteome Discoverer Installation Guide #

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

To contact Technical Support

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

To contact Customer Service for ordering information

To get local contact information for sales or service

Go to www.thermoscientific.com/wps/portal/ts/contactus.

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 documentation or to Help

• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.

• Send an e-mail message to the Technical Publications Editor at [email protected].

Phone 800-532-4752

Fax 561-688-8736

E-mail [email protected]

Knowledge base www.thermokb.com

Phone 800-532-4752

Fax 561-688-8731

E-mail [email protected]

Web site www.thermo.com/ms

mailto:[email protected]

http://www.thermokb.com

http://mssupport.thermo.com


http://www.thermo.com/ms

http://www.thermoscientific.com/wps/portal/ts/contactus

http://mssupport.thermo.com

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Thermo Scientific Proteome Discoverer Installation Guide 1

1

Installing Proteome Discoverer

This guide describes how to install the Proteome Discoverer 1.3 software.

Opening the XInstall WindowBefore you can access the Proteome Discoverer InstallShield wizard, which installs the software, open the XInstall window.

To open the XInstall window

1. Log on to the computer as an administrator.

If you are installing the software, you must be a software administrator.

2. Verify that you are an administrator by choosing Start > Settings > Control Panel > Administration Tools > Computer Management > Local Users and Groups > Groups > Administrators (this path is different on Windows 7 systems). In the Administrators Properties window, verify that you are a member of the administrators, or have an administrator install the software.

3. Insert the Proteome Discoverer software DVD into the PC.

If the auto-play is set for the DVD drive, the XInstall installation window appears automatically, as shown in Figure 1.

Contents

• Opening the XInstall Window

• Migrating Personalized Application Data Profiles from Installations Prior to Proteome Discoverer 1.2

• Installing the Proteome Discoverer Software

• Installing the Proteome Discoverer Software Without an Internet Connection

1 Installing Proteome DiscovererMigrating Personalized Application Data Profiles from Installations Prior to Proteome Discoverer 1.2

2 Proteome Discoverer Installation Guide Thermo Scientific

Figure 1. XInstall window

If this window does not appear, use Windows Explorer to open the installation file. In the Windows Explorer window, select the appropriate DVD drive and double-click the XInstall_ProteomeDiscoverer.exe file.

Migrating Personalized Application Data Profiles from Installations Prior to Proteome Discoverer 1.2

With versions of the Proteome Discoverer application prior to 1.2, you could install the application for either “All Users” or only the current user. In the latter case, the application data (FASTA files, indexes, workflow templates, and so on) are stored in a personalized application data profile. When upgrading from a previous version, the Proteome Discoverer 1.3 installer is not able to migrate such personalized application data profiles automatically because the 1.3 installer only looks at the “All Users” profile.

If the installer finds such personalized application data profiles, it displays a screen that lists the found profiles with information about how to migrate them (see Figure 2).

1 Installing Proteome DiscovererMigrating Personalized Application Data Profiles from Installations Prior to Proteome Discoverer 1.2


Figure 2. Personalized application data profiles displayed with information on how to migrate them

To retain an existing personalized application data profile

• Copy the application data folder from the specified location to the “All Users” profile folder.

The installation wizard provides the directory information (see Figure 2).

The actual paths of the user profiles depend on the version and language of the Windows operating system. The installation wizard should show you the user profile paths valid for your system.

1 Installing Proteome DiscovererInstalling the Proteome Discoverer Software


Installing the Proteome Discoverer SoftwareUse the Proteome Discoverer InstallShield wizard to install the software.

To install Proteome Discoverer

1. In the XInstall window, click Proteome Discoverer 1.3 software.

The installer automatically recognizes whether the operating system is 32-bit or 64-bit and installs the appropriate version.

The Proteome Discoverer InstallShield wizard appears, as shown in Figure 3.

Figure 3. Welcome page of the Proteome Discoverer InstallShield wizard

Note The following procedure assumes that you have already installed Microsoft .NET Framework 3.5 or Microsoft .NET Framework 4.0 on your computer.

If you do not have Microsoft .NET Framework 3.5 or 4.0 installed on your computer, install it before you install Proteome Discoverer 1.3 (you can install both of them from XInstall). Click Microsoft .NET Framework in the XInstall window shown in Figure 1 and complete the pages of the wizard.

If you do not have Microsoft Visual C++™ 2010 Redistributable installed on your computer, the Microsoft Visual C++ 2010 Redistributable wizard appears at the end of the Proteome Discoverer installation procedure, as shown in Figure 15 on page 14. Complete the pages of the wizard to install Microsoft Visual C++ 2010 Redistributable.



2. Click Next to continue.

The Minimum Product Requirements page appears, as shown in Figure 4.

The installer checks the minimum system requirements, issuing an error message and terminating if one of the requirements is not met. Correct the error before continuing.

If some of the settings are not optimal, the installer issues a warning message but continues.

Figure 4. Minimum Product Requirements page of the Proteome Discoverer InstallShield wizard

3. Click Next.

The License Agreement page appears, as shown in Figure 5.



Figure 5. License Agreement page of the Proteome Discoverer InstallShield wizard

4. Read the license agreement. If you accept the agreement, select the I Accept the Terms of License Agreement option, and click Next.

5. On the Thermo License Activation page of the wizard, shown in Figure 6, enter your Proteome Discoverer product key. Also enter your complete and correct contact information, which is necessary for registering you correctly on the licensing server.

The product key is in xxxx-xxxx-xxxx-xxxx format. You can find it on the DVD jewel case.



Figure 6. Thermo License Activation page of the Thermo Discoverer InstallShield wizard

6. Click Activate.

The Proteome Discoverer application retrieves your permanent license from the licensing server and licenses your software. The installation continues.

If you are installing an Update Proteome Discoverer license and you have a version of BioWorks installed rather than a previous version of Proteome Discoverer, the dialog box shown in Figure 7 appears.

Figure 7. BioWorks update dialog box

If you have a version of BioWorks installed, click Yes. If not, click No.

If you incorrectly complete one of the fields in the Thermo License Activation dialog box, a red exclamation point appears next to it. Move the cursor over it to see an explanation of the error, as shown in Figure 8. Correct the error before you continue with the installation process.



Figure 8. Error ToolTip

If the product key is accepted and your system finds an older version of the software, the message box shown in Figure 9 opens, prompting you to back up your old database.

Figure 9. Request to back up database

Note In the case of an update, the installer checks for a valid Proteome Discoverer installation before you can continue.

Note Thermo Fisher Scientific recommends that you back up your old database before updating an existing version.



If you are installing an update, the Proteome Discoverer application first checks the system to see if a valid license for the previous version exists. If it does not exist, the application does not install the update.

If you are installing an update on a new computer, contact your support organization, or send an e-mail to [email protected] and include your original product key and your upgrade product key. Thermo Fisher Scientific provides you with a new product key that allows you to install the update directly.

7. Click OK to continue the setup process.

The Choose Destination Location page opens, as shown in Figure 10.

Figure 10. Choose Destination Location page of the Proteome Discoverer InstallShield wizard

8. Click Next.

The Desktop Shortcuts page opens, as shown in Figure 11.

Note If you need help in installing or licensing the software, click Export the License Request in the Thermo License Activation dialog box, save that file, and contact [email protected] with a short description. Attach the file.





Figure 11. Desktop Shortcuts page of the Proteome Discoverer InstallShield wizard

9. If you want to create a Proteome Discoverer software shortcut on your desktop, select the Yes option and then click Next.

The Select Program Folder page opens, as shown in Figure 12.



Figure 12. Select Program Folder page of the Proteome Discoverer InstallShield wizard

10. Enter a different program folder name or select Thermo Proteome Discoverer 1.3 and click Next.

The Start Copying Files page opens, as shown in Figure 13.



Figure 13. Start Copying Files page of the Proteome Discoverer InstallShield wizard

11. Click Back to review all settings or Next to start the installation.

When you click Next, the system begins to install the Proteome Discoverer software.

During the installation, the Setup Status page shown in Figure 14 displays the status of the installation.



Figure 14. Setup Status page of the Proteome Discoverer InstallShield wizard

12. Do one of the following:

• If you need to terminate the installation of the Proteome Discoverer software setup, click Cancel.

• If you do not have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, look for the Welcome page of the Microsoft Visual C++ 2008 Redistributable wizard to appear (see Figure 15), and follow the procedure to install the Microsoft Visual C++ 2008 and 2010 Redistributable.

–or–

• If you do have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, the Installation Qualification message box shown in Figure 18 on page 16 appears. Go to step 17.



Figure 15. Welcome page of the Microsoft Visual C++ Redistributable Setup wizard

The Microsoft Visual C++ Redistributable Setup wizard first installs the 2008 version of the Microsoft Visual C++ Redistributable software, and then it installs the 2010 version.

13. Click Next.

The License Terms page of the wizard opens, as shown in Figure 16.



Figure 16. License Terms page of the Microsoft Visual C++ Redistributable Setup wizard

14. Make sure to accept the license terms, and then click Install.

The Setup Complete page opens, as shown in Figure 17,

Figure 17. Setup Complete page of the Microsoft Visual C++ Redistributable Setup wizard



15. Click Finish.

The Welcome page of the Microsoft Visual C++ 2010 x86 Redistributable Setup page of the wizard appears.

16. Perform steps step 13 on page 14 through step 15 for the Microsoft Visual C++ 2010 Redistributable Setup.

After finishing the Proteome Discoverer software setup, the system creates the Installation Qualification report.

The Installation Qualification message box is shown in Figure 18.

Figure 18. Installation Qualification message box

17. If you want to view the report, click Yes. If you do not want to view the report, click No to end the installation.

If you click Yes, the Installation Qualification report opens as a PDF file.

If you click No, the system displays the message box shown in Figure 19.

Figure 19. Setup Finished message box

18. Click OK to exit the setup.

The DVD also includes example raw files and the latest revision of the FASTA databases. Click Browse DVD on the Xinstall window (see Figure 1 on page 2) to access those files.


1 Installing Proteome DiscovererInstalling the Proteome Discoverer Software Without an Internet Connection


Installing the Proteome Discoverer Software Without an Internet Connection

If you do not have an Internet connection, use following procedure to install the Proteome Discoverer software.

To install the Proteome Discoverer software without an Internet connection

1. Click Export the License Request on the Thermo License Activation dialog box (see Figure 6 on page 7), save the licensing file, and remove the DVD from the computer. Leave the Thermo License Activation dialog box open.

2. Copy the licensing file and move it to a computer with an Internet connection. Insert the Proteome Discoverer software DVD into that computer.

The Xinstall window appears again (see Figure 1 on page 2).

3. Click Offline Activation.

The Thermo License Activation dialog box, shown in Figure 6 on page 7, appears again with all its boxes empty. The Import License Activation Request dialog box also appears.

4. Browse to the license request file that you moved, and click Open.

5. Enter the appropriate information in all the boxes again.

6. Click Activate.

The Proteome Discoverer application activates the license and stores it in the license request file.

7. Click OK when the following message appears:

Activation was successful.

8. Close the XInstall application window.

9. Copy the license request file, and move the file and the software DVD back to the computer that you want to license.

The Thermo License Activation dialog box remains open.

10. Click Reimport the Activated License Request to Continue Activation.

11. Browse to the activated license request file.

Note Ensure that the license request file is not write-protected.


2

Installing Proteome Discoverer Daemon

This chapter describes how to install the Proteome Discoverer Daemon software.

Opening the XInstall WindowBefore you can access the Proteome Discoverer Daemon InstallShield wizard, which installs the software, you must open the XInstall window. For instructions on this procedure, see “Opening the XInstall Window” on page 1.

If the auto-play is set for the DVD drive after you finish the procedure, the XInstall installation window appears automatically, as shown in Figure 20.

Contents


• Installing the Proteome Discoverer Daemon Software

2 Installing Proteome Discoverer DaemonInstalling the Proteome Discoverer Daemon Software




Installing the Proteome Discoverer Daemon SoftwareUse the Proteome Discoverer Daemon InstallShield wizard to install the software.

To install Proteome Discoverer Daemon

1. In the XInstall window, click Proteome Discoverer Daemon 1.3.


The Proteome Discoverer Daemon InstallShield wizard shown in Figure 21 appears.

Note The following procedure assumes that you have already installed Microsoft .NET Framework 3.5 or Microsoft .NET Framework 4.0 on your computer. If you have not, see “Installing the Proteome Discoverer Software” on page 4 for instructions.

Note The following procedure is only intended for installing the Proteome Discoverer Daemon 1.3 client on a separate machine. By default, Proteome Discoverer Daemon 1.3 is installed during each Proteome Discoverer 1.3 installation.



Figure 21. Welcome page of the Thermo Proteome Discoverer Daemon InstallShield wizard


The Minimum Product Requirements page appears, as shown in Figure 22.





Figure 22. Minimum Product Requirements page of the Proteome Discoverer Daemon InstallShield wizard

3. Click Next.

The License Agreement page of the Proteome Discoverer Daemon InstallShield wizard appears, as shown in Figure 23.



Figure 23. License Agreement page of the Proteome Discoverer Daemon InstallShield wizard





Figure 24. Choose Destination Location page of the Proteome Discoverer Daemon InstallShield wizard

5. Do the following:

• To copy all needed files to the default location of C:\Program Files\ Thermo\DiscovererDaemon 1.3, click Next.

–or–

• To copy all needed files to a different location, click Browse to browse to that location, and then click Next.




Figure 25. Desktop Shortcuts page of the Proteome Discoverer Daemon InstallShield wizard

6. If you want to create a Proteome Discoverer Daemon shortcut on your desktop, select the Yes option and then click Next.




Figure 26. Select Program Folder page of the Proteome Discoverer Daemon InstallShield wizard

7. Enter a different program folder name or select Thermo Proteome Discoverer 1.3 and click Next.




Figure 27. Start Copying Files page of the Proteome Discoverer Daemon InstallShield wizard


When you click Next, the system begins to install the Proteome Discoverer Daemon 1.3 software.




Figure 28. Setup Status page of the Proteome Discoverer Daemon InstallShield wizard


• If you must terminate the installation of the Proteome Discoverer Daemon 1.3 setup, click Cancel.

• If you do not have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, look for the Welcome page of the Microsoft Visual C++ 2008 Redistributable wizard to appear (see Figure 15 on page 14), and follow the procedure to install the Microsoft Visual C++ 2008 and 2010 Redistributable.

–or–


After finishing the Proteome Discoverer Daemon setup, the system creates the Installation Qualification report. The Installation Qualification message box is shown in Figure 29.





If you click Yes, the Installation Qualification report opens as a PDF file.

If you click No, the system displays the InstallShield Wizard Complete page, shown in Figure 30.

Figure 30. InstallShield Wizard Complete page of the Thermo Discoverer Daemon InstallShield wizard

11. Click Finish to exit the setup.



3

Installing Proteome Discoverer Viewer

If you do a complete installation of the Proteome Discoverer 1.3 application, you automatically install Proteome Discoverer Viewer 1.3 software. This chapter describes how to install the Proteome Discoverer Viewer 1.3 software if you just want to view report results but do not want to install the Proteome Discoverer 1.3 application.

Opening the XInstall WindowBefore you can access the Proteome Discoverer InstallShield wizard, which installs the Proteome Discoverer Viewer software, you must open the XInstall window. For instructions, see “Opening the XInstall Window” on page 1.

If auto-play is set for the DVD drive after you finish the procedure, the XInstall installation window appears automatically, as shown in Figure 31.

Contents


• Installing the Proteome Discoverer Viewer Software

3 Installing Proteome Discoverer ViewerInstalling the Proteome Discoverer Viewer Software




Installing the Proteome Discoverer Viewer SoftwareUse the Proteome Discoverer InstallShield wizard to install the Proteome Discoverer Viewer software.

To install Proteome Discoverer Viewer

1. In the XInstall window, click Proteome Discoverer Viewer 1.3.


The Proteome Discoverer InstallShield wizard shown in Figure 32 appears.

Note The following procedure assumes that you have already installed Microsoft .NET Framework 3.5 or Microsoft .NET Framework 4.0 on your computer. If you have not, install them before proceeding. See “Installing the Proteome Discoverer Software” on page 4 for instructions.

Note You must have access to the Internet to install the Proteome Discoverer Viewer.



Figure 32. Welcome page of the Proteome Discoverer InstallShield wizard




The Minimum Product Requirements page of the Thermo Discoverer InstallShield wizard opens, as shown in Figure 33.



Figure 33. Minimum Product Requirements page of the Thermo Discoverer InstallShield wizard

The License Agreement page of the Thermo Discoverer InstallShield wizard opens, as shown in Figure 34.



Figure 34. License Agreement page of the Thermo Discoverer InstallShield wizard


4. On the Thermo License Activation page of the wizard, shown in Figure 6 on page 7, enter your Proteome Discoverer product key. Also enter your complete and correct contact information, which is necessary for registering you correctly on the licensing server.

The product key is in xxxx-xxxx-xxxx-xxxx format. You can find it on the DVD jewel case.



Figure 35. Thermo License Activation page of the Proteome Discoverer InstallShield wizard

5. Click Activate.

6. Click OK when the following message appears:

Activation was successful.


Note Viewer installations do not affect the product key, but Thermo Fisher Scientific strongly recommends that you install the full Proteome Discoverer 1.3 version first to avoid inadvertently installing on the wrong computer when you only intend to install the Proteome Discoverer Viewer.



Figure 36. Choose Destination Location page of the Thermo Discoverer InstallShield wizard

7. Do the following:

• To copy all needed files to the default location of C:\Program Files\Thermo\Discoverer Viewer 1.3, click Next.

–or–

• To copy all needed files to a different location, click Browse to browse to that location, and then click Next.




Figure 37. Desktop Shortcuts page of the Proteome Discoverer InstallShield wizard

8. If you want to create a Proteome Discoverer Viewer 1.3 shortcut on your desktop, select the Yes option and then click Next.




Figure 38. Select Program Folder page of the Proteome Discoverer InstallShield wizard

9. Enter a different program folder name or select Thermo Proteome Discoverer Viewer 1.3 and click Next.




Figure 39. Start Copying Files page of the Thermo Discoverer InstallShield wizard


When you click Next, the system begins to install the Proteome Discoverer Viewer 1.3 software.




Figure 40. Setup Status page of the Proteome Discoverer InstallShield wizard


• If you need to terminate the installation of the Proteome Discoverer Viewer 1.3 setup, click Cancel.

• If you do not have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, look for the Welcome page of the Microsoft Visual C++ 2008 Redistributable wizard to appear (see Figure 15 on page 14), and follow the procedure to install the Microsoft Visual C++ 2008 and 2010 Redistributable.

–or–


After finishing the Proteome Discoverer setup, the system creates the Installation Qualification report. The Installation Qualification message box is shown in Figure 41.





If you clicked Yes, the Installation Qualification report opens as a PDF file.

If you clicked No, the system displays the message box shown in Figure 42.

Figure 42. Setup Finished message box

13. Click OK to exit the setup.



4

Connecting to the Mascot Server

This chapter describes Mascot server versions supported by the Proteome Discoverer software and how to check your Mascot server settings, connect to the Mascot server, and test the connection to the Mascot server.

Mascot Server Versions SupportedThe Mascot server versions that the Proteome Discoverer software supports are as follows:

• Mascot Server 2.1

– Mascot servers running version 2.1 should be usable, but retrieving the result files (protein sequences) from the servers can be a lengthy process, as you can only retrieve the protein sequences one by one.

– Mascot servers running version 2.1 should have all available updates, patches, or both from Matrix Science installed. In particular, you must install a patch that enables MIME format for the result files. Otherwise, the Proteome Discoverer software is not able to receive the search results from the Mascot server.


– Proteome Discoverer 1.3 does not support error tolerant searches.


– Proteome Discoverer 1.3 does not support error tolerant searches and searches against a multiple sequence database.

Contents

• Mascot Server Versions Supported

• Checking Your Mascot Server Settings

• Configuring Mascot

• Testing the Connection to the Mascot Server

4 Connecting to the Mascot ServerChecking Your Mascot Server Settings


Checking Your Mascot Server SettingsBefore you connect to your Mascot server, verify that the URL of the Mascot server is valid, and determine what type of security protects your Mascot server.

Checking the URL

Check the Mascot server URL to be used in the Proteome Discoverer configuration by typing it into a Web browser. If the URL is correct, the Mascot home page appears.

The URL of the Mascot server has the following general form:

http://my.mascotserver.com/mascot/

If your Mascot server is not running on the standard port 80, you must include the actual port number:

http://my.mascotserver.com:xxxx/mascot/

The Mascot server URL to be used in the Proteome Discoverer configuration does not include /cgi or /home.html or similar notation.

The following are examples of invalid URLs:

http://my.mascotserver.com/mascot/cgi

http://my.mascotserver.com/mascot/home.html

The following are examples of valid URLs:

http://my.mascotserver.com/mascot/

http://192.168.2.1/mascot/

http://my.mascotserver.com:8765/mascot/

Checking for Security Options

Check to see if your Mascot server is protected by security options and if so, by what type.

If you are required to log on to the Mascot server or to log on through the Mascot Security page, shown in Figure 43, your Mascot server is protected by Mascot security. For information on accessing the Mascot server protected by this type of security, see “To configure Mascot when your Mascot server is protected by Mascot security” on page 47.

4 Connecting to the Mascot ServerConfiguring Mascot


Figure 43. Mascot Security page

If you must log in through any other means, your Mascot server is likely protected by the security options of the Web server that Mascot is running on. For information on accessing the Mascot server protected by this type of security, see “To configure Mascot when your Mascot server is protected by Windows or Web-based security” on page 47.

If you do not known which kind of security is enabled for your Mascot server, contact your local system administrator.

Configuring MascotYou can configure Mascot in the Proteome Discoverer application by using any of the following three methods:

• Enter the Mascot server URL into the Configuration view.

• If your Mascot server is protected by Mascot security, use the values in the Mascot Server Authentication area of the Configuration view. The Proteome Discoverer application uses these values to connect to the Mascot server. Make sure that you have the appropriate access rights to the Mascot server. These access rights are directly configured on the Mascot server. If you need help in obtaining these access rights, contact your system administrator.

4 Connecting to the Mascot ServerConfiguring Mascot


• If your Mascot server is protected by Web-based security, use the values in the Web Server Authentication area of the Configuration view. The Proteome Discoverer application uses these values to connect to the Mascot server. Make sure that you have the appropriate access rights to the Mascot server. These access rights are directly configured on the Mascot server. If you need help in obtaining these access rights, contact your system administrator.

The following procedures detail these three methods.

To configure Mascot through URL verification

1. Open the Proteome Discoverer application.

2. Choose Administration > Configuration > Mascot.

3. In the Mascot Server URL box in the Mascot Server area of the Configuration view, enter the URL of the Mascot server, as shown in Figure 44.

Figure 44. Entering the Mascot server URL in the Mascot Server URL box

4. Click in another part of the interface.

4 Connecting to the Mascot ServerTesting the Connection to the Mascot Server


The Proteome Discoverer application checks the URL. If the URL is valid, the Proteome Discoverer application connects with the Mascot server. If the URL is invalid or if the application cannot reach it, the error message shown in Figure 45 appears.

Figure 45. Invalid URL message box

To configure Mascot when your Mascot server is protected by Mascot security



3. In the Mascot Server Authentication area of the Configuration view, enter your user name in the User Name box and your password in the Password box to access the Web server hosting the specified Mascot server.

To configure Mascot when your Mascot server is protected by Windows or Web-based security



3. In the Web Server Authentication area of the Configuration view, enter your user name in the User Name box and your password in the Password box to access the Web server hosting the specified Mascot server.

Testing the Connection to the Mascot ServerThis section explains how to test the connection between the Proteome Discoverer application and the Mascot server.

To test the connection to the Mascot server

1. Start the Mascot Communication Tester by choosing Tools > Mascot Communication Tester.

The Mascot Communication Tester window appears, as shown at the top of Figure . The Proteome Discoverer application automatically populates the fields of the window, including the URL in the Mascot Server Url box.

2. If the URL does not automatically appear or you want to enter it manually, enter the URL of the Mascot server in the Mascot Server Url box.

4 Connecting to the Mascot ServerTesting the Connection to the Mascot Server


This is the same URL that you entered in the Mascot Server URL box in the Configuration view of the Proteome Discoverer application.

If the Web server that hosts the Mascot server enables any user authentication, provide a user name and a password for this authentication in the corresponding boxes in the Mascot Communication Tester.

3. Click Test Communication.

An automated communication test starts, as shown in Figure 46.

Figure 46. Test running in the Mascot Communication Tester window

The upper pane displays the progress of the communication test, and the lower pane provides detailed information. When errors occur, the lower pane displays the particular test that failed, which helps you determine why the connection failed. You can click the blue highlighted links shown in the lower pane to test whether the communication works from within a Web browser.

If this information does not resolve the problem, use the Copy Info button to copy the log information into an e-mail and send it to Thermo Fisher Scientific Customer Service at the e-mail address given in “Contacting Us” on page vii.


5

Submitting a Product Change Request

Before submitting a product change request, read the “Known Issues” section of the release notes and determine if any of the known issues describes your problem. If none of them do, file a product change request that includes all of the following information:

• The severity of the issue

• Whether the issue is already known

• Whether a solution is already available

• As many details as possible, including screen captures of the steps needed to duplicate this problem. If possible, provide some test data, such as .msf files or .raw files.

To create a product change request, use the Proteome Discoverer Bug Reporter tool, shown in Figure 47, and attach the product change request to the e-mail. Choose Tools > Create Bug Report to access the tool.

Figure 47. Proteome Discoverer Bug Reporter


I

Aapplication data files prior to version 1.2 2

BBioWorks 7bug reports. See product change requests

CChoose Destination Location page of the Proteome Discoverer InstallShield wizard 9, 36

Choose Destination Location page of the Thermo Proteome Discoverer Daemon InstallShield wizard 23

DDesktop Shortcuts page of the Proteome Discoverer InstallShield wizard 9, 37

Desktop Shortcuts page of the Thermo Proteome Discoverer Daemon InstallShield wizard 24

documentation survey vii

EExport the License Request option 9, 17

IInstallation Qualification message box 13, 16, 28, 41Installation Qualification report 16InstallShield Wizard Complete page of the Thermo Proteome Discoverer Daemon InstallShield wizard 29

InstallShield wizard. See Proteome Discoverer Installshield wizard

Llicense agreement 5, 22, 34License Agreement page of the Proteome Discoverer InstallShield wizard 5, 34

License Agreement page of the Thermo Proteome Discoverer Daemon InstallShield wizard 22

License Terms page of the Microsoft Visual C++ Redistributable wizard 14

MMascot

configuring by verifying URL 45–46configuring for Mascot security 45, 47configuring for Web-based security 46–47configuring in Proteome Discoverer application 45

Mascot Communication Tester 47Mascot Security page 44Mascot server

checking for security options 44checking settings 44testing connection to Proteome Discoverer application 47verifying URL 44versions supported 43

Microsoft Visual C++ Redistributable software 4, 13, 28, 41Microsoft Visual C++ Redistributable wizard

2008 132010 4License Terms page 14Setup Complete page 15Welcome page 28, 41

Minimum Product Requirements page of the Proteome Discoverer InstallShield wizard 5, 33

Minimum Product Requirements page of the Thermo Proteome Discoverer Daemon InstallShield wizard 21

Pproduct change requests 49Proteome Discoverer

installing 4installing Proteome Discoverer Daemon 19installing the Proteome Discoverer Viewer 31installing without an Internet connection 17

Index


Index: S

InstallShield wizard 4software required for installation 4

Proteome Discoverer Bug Reporter 49Proteome Discoverer Daemon 19Proteome Discoverer InstallShield wizard

Choose Destination Location page 9, 36Desktop Shortcuts page 9, 37License Agreement page 5, 34Minimum Product Requirements page 5, 33Select Program Folder page 10, 38Setup Status page 12, 40Start Copying Files page 11, 39Thermo License Activation page 6, 35Welcome page 4, 33

Proteome Discoverer Viewer 31

SSelect Program Folder page of the Proteome Discoverer InstallShield wizard 10, 38

Select Program Folder page of the Thermo Proteome Discoverer Daemon InstallShield wizard 25

Setup Complete page of the Microsoft Visual C++ Redistributable wizard 15

Setup Finished message box 16, 42Setup Status page of the Proteome Discoverer InstallShield wizard 12, 40

Setup Status page of the Thermo Proteome Discoverer Daemon InstallShield wizard 27

Start Copying Files page of the Proteome Discoverer InstallShield wizard 11, 39

Start Copying Files page of the Thermo Proteome Discoverer Daemon InstallShield wizard 26

survey link viisystem requirements vi

TThermo License Activation page of the Proteome Discoverer InstallShield wizard 6, 35

Thermo Proteome Discoverer Daemon InstallShield wizardChoose Destination Location page 23Desktop Shortcuts page 24InstallShield Wizard Complete page 29License Agreement page 22Minimum Product Requirements page 21Select Program Folder page 25Setup Status page 27Start Copying Files page 26Welcome page 20–21

WWelcome page of the Proteome Discoverer InstallShield wizard 4, 33

Welcome page of the Thermo Proteome Discoverer Daemon InstallShield wizard 20–21

XXInstall window 1, 19, 31XInstall_ProteomeDiscoverer.exe 2XInstall.exe 20, 32

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