Software:Overview

From SPCTools

The Seattle Proteome Center (SPC) at the ISB has produced many open-source proteomics tools, many of which are integrated into the TPP project.

Contents 1 The Trans-Proteomic Pipeline (TPP) Project 2 Data Conversion 2.1 raw MS / MS2 to mzXML converters 3 LC-MS Analysis 4 Interpretation 5 Protein Crosslinking 6 Miscellaneous

The Trans-Proteomic Pipeline (TPP) Project

Please see the TPP page for descriptions of the pipeline and these components.

This software distribution integrates the following programs:

• Petunia (TPP GUI)
• PeptideProphet
• ProteinProphet
• XPRESS
• ASAPRatio
• Libra
• Pep3D
• Out2Summary
• MzXML2Search
• MsXML2Other
• readmzXML
• mzStar
• ReAdW
• Qualscore
• RAMP

Data Conversion

raw MS / MS2 to mzXML converters

Please see the mzXML page for info on ReAdW (Thermo), mzStar (ABI/MDS Sciex Analyst), massWolf (Waters MassLynx), and compassXport (Bruker).

LC-MS Analysis

SpecArray: tool for analyzing and comparing LC-MS runs

MSAnalyzer: alternate tool for MS Level 1 analysis.

Pep3D: Visualization tool for viewing MS and MS/MS runs; integrated into the TPP.

Interpretation

SBEAMS: Systems Biology Experiment Analysis Management System

Cytoscape: platform for visualizing and integrating molecular interaction networks

Protein Crosslinking

XLink: XLink suite

Miscellaneous

SPE: SEQUEST Parameter Editor tool

SubsetDB: tools for handling FASTA formatted databases

PeptideSieve: A tool for predicting proteotypic peptides

INTERACT - large dataset curation

CGIs - a bundle of useful CGI scripts

massWolf (wolf.exe): Micromass MassLynx to mzXML converter

mzBruker: Bruker to mzXML converter

validateXML

mzXMLViewer

InsilicosViewer