TPP Tandem search

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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)

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

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 proprietary and raw file format from mass spectrometer vendors can be converted to mzXML.

Setting up an account

The TPP GUI comes with one user account. This account has ‘guest’ as both the user name and password. It is useful to create another account for this tutorial.

Open the DOS shell by selecting Run under the Start menue and typing cmd. In the shell type:

cd c:\Inetpub\tpp-bin\users\

mkdir tandem

cd tandem

crypt isbTPPspc TPP > .password

and

chmod -R 777 C:\Inetpub\tpp-bin\users\tandem

You have just created the password ‘TPP’ for the user ‘tandem.’

In order to add a different username, create a tpp-bin/users/NEWUSER/ directory and run crypt isbTPPspc NEWPASSWORD > .password from this directory. In these examples "isbTPPspc" is the crypt key. This can be changed.