TPP Tutorial v1

From SPCTools

Trans Proteomic Pipeline (TPP) TUTORIAL

TPP V3.2.1, 2007. Note: Screenshots may vary from the TPP build you are using because the application is in development.

This document was originally assembled and edited by Bryan Prazen of Insilicos.

Table of Contents

1 Introduction

1.1 About Trans Proteomic Pipeline

1.2 Systems Requirements

1.3 About this Tutorial

1.4 Who Should Use this Tutorial?

2 Getting Started

2.1 Downloading TPP

2.2 Installing TPP

2.3 DOS reminders

3 Tutorial Data

3.1 Getting the Tutorial Data

4 TPP Tutorial - SEQUEST data

4.1 Creating Summary HTML Files

4.2 Opening the GUI

4.2 Creating pepXML Files

4.3 PepXML Viewer

4.4 Peptide Level Analysis

4.4.1 PeptideProphet

4.4.2 XPRESS

4.4.3 ASAPRatio

4.4.4 Libra

4.4.5 Run Analysis

4.5 Evaluating the Results

4.5.1 PeptideProphet Results

4.5.2 XPRESS Results

4.5.3 ASAPRatio Results

4.5.4 Reviewing Processed Data

4.6 Protein Analysis

4.7 Exporting Data

4.8 Automation

5 X!Tandem/TPP Analysis

5.7 Analyze Peptides

6 Beyond this Tutorial

6.1 Creating mzXML Files

6.2 Setting up a TPP Account

7 Getting Help

8 Glossary

9 References

Introduction

This tutorial will cover the application of the Trans Proteomic Pipeline (TPP) for protein identification and quantitation to LC-tandem MS data. The data used in this tutorial has previously been searched with SEQUEST (Thermo Finnigan). Although this tutorial should be helpful to anyone interested in statistical identification and quantitative analysis of proteins with mass spectrometry, this tutorial was designed for the scientist who is currently running SEQUEST searches on their tandem mass spectrometry data and would like to process their data a step further. This tutorial shows an example of how to run the TPP tools so that searched data can be statistically evaluated, quantified and organized using TPP. This tutorial focuses on the application of TPP and only briefly touches on the bioinformatics behind the tools which are included in TPP.