From SPCTools

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 1 Performing XTandem search using the Trans Proteomic Pipeline (TPP) Tutorial 1.1 Introduction

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.

Other pages containing useful information:

• Installing TPP
• A list of software that TPP integrates
• converters to mzXML (an open data format for storage and exchange of mass spectroscopy data)
• TPP related tools
• Using Petunia (which is the graphical interface of TPP)
• TPP:X!Tandem and the TPP
• Example data analysis in TPP
• A very comprehensive tutorial on using TPP to analyzed results from a database search