TPP Tandem search

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==Introduction== ==Introduction==
-This tutorial will cover the application of the [[software:TPP | Trans Proteomic Pipeline (TPP)]] to do a database search of acquired MS/MS spectra using [http://www.thegpm.org/TANDEM/ X!Tandem]. The data used in this tutorial comes from this [[TPP_Tutorial | TPP Tutorial]].+This tutorial will cover the application of the [[software:TPP | Trans Proteomic Pipeline (TPP)]] to do a database search of acquired MS/MS spectra using [http://www.thegpm.org/TANDEM/ X!Tandem]. The data used in this tutorial comes from this [[TPP_Tutorial | TPP Tutorial]]. The [[TPP_Tutorial | TPP Tutorial]] begins with passing the results from a SEQUEST search through TPP in order to statistically evaluate and quantify the proteins identified. This tutorial on the other hand will cover omitted steps: using TPP to perform a database search. The search engine X!Tandem will be used in this tutorial as it has two advantages: 1) no commercial license is needed to use the software 2) distributed with the TPP installation.
 + 
 +==Systems Requirements==
 + 
 +This tutorial requires that TPP be installed. TPP is distributed for both Linux and Windows platform, however this tutorial will focus on the Window platform. Since the graphical interface of TPP ([[TPP:Using_Petunia | Petunia]]) is through a web browser, either Internet Explorer or Firefox is required. Although the search engine X!Tandem is required, no separate installation is needed as it will be installed as part of the TPP installation.
 +The TPP installer can be found at [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 sourceforge].
 +The current version (at the time this was written) is 4.0.2. Download the installer: ''TPP_Setup_v4_0_JETSTREAM_rev_2.exe''.
 + 
 +The mass spectrometer data is provided in mzXML format and can be downloaded via
 +[http://www.insilicos.com/spctools/data/tutorial_wiki.exe www.insilicos.com/spctools/data/tutorial_wiki.exe].
 + 
 +[[Formats:mzXML | mzXML]] is a instrument independent data format and the rationale is to provide a standard format that can used by various data analysis software like TPP. Various raw, proprietary file format from vendors of mass spectrometer can be converted to mzXML

Revision as of 17:54, 20 October 2008

Performing XTandem search using the Trans Proteomic Pipeline (TPP) Tutorial

TPP V4.0.2, 2008. Note: Screenshots may vary from the TPP build you are using because the application is in development.

This document was originally assembled by Lik Wee Lee of ISB. (work in progress)

Contents


Introduction

This tutorial will cover the application of the Trans Proteomic Pipeline (TPP) to do a database search of acquired MS/MS spectra using X!Tandem. The data used in this tutorial comes from this TPP Tutorial. The TPP Tutorial begins with passing the results from a SEQUEST search through TPP in order to statistically evaluate and quantify the proteins identified. This tutorial on the other hand will cover omitted steps: using TPP to perform a database search. The search engine X!Tandem will be used in this tutorial as it has two advantages: 1) no commercial license is needed to use the software 2) distributed with the TPP installation.

Systems Requirements

This tutorial requires that TPP be installed. TPP is distributed for both Linux and Windows platform, however this tutorial will focus on the Window platform. Since the graphical interface of TPP ( Petunia) is through a web browser, either Internet Explorer or Firefox is required. Although the search engine X!Tandem is required, no separate installation is needed as it will be installed as part of the TPP installation. The TPP installer can be found at sourceforge. The current version (at the time this was written) is 4.0.2. Download the installer: TPP_Setup_v4_0_JETSTREAM_rev_2.exe.

The mass spectrometer data is provided in mzXML format and can be downloaded via www.insilicos.com/spctools/data/tutorial_wiki.exe.

mzXML is a instrument independent data format and the rationale is to provide a standard format that can used by various data analysis software like TPP. Various raw, proprietary file format from vendors of mass spectrometer can be converted to mzXML


Other pages containing useful information:

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tandem_search"
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