Software:Overview

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(The Trans-Proteomic Pipeline (TPP) Project)
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==The Trans-Proteomic Pipeline (TPP) Project== ==The Trans-Proteomic Pipeline (TPP) Project==
-'''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these components.'''+'''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these components and installation instructions.'''
-This software distribution integrates the following programs:+The TPP software distribution integrates the following programs:
-*[[Software:Petunia|Petunia (TPP GUI)]]+[[Software:Petunia|Petunia (TPP GUI)]], [[Software:PeptideProphet|PeptideProphet]], [[Software:ProteinProphet|ProteinProphet]], [[Software:XPRESS|XPRESS]], [[Software:ASAPRatio|ASAPRatio]], [[Software:Libra|Libra]], [[Software:Pep3D|Pep3D]], [[Software:SpectraST|SpectraST]], [[Software:Out2Summary|Out2Summary]], [[Software:MzXML2Search|MzXML2Search]], [[Software:MsXML2Other|MsXML2Other]],
-*[[Software:PeptideProphet|PeptideProphet]]+[[Software:readmzXML|readmzXML]], [[Software:mzStar|mzStar]]
-*[[Software:ProteinProphet|ProteinProphet]]+[[Software:ReAdW|ReAdW]], [[Software:QualScore|QualScore]], [[Software:RAMP|RAMP]],
-*[[Software:XPRESS|XPRESS]]+[[Software:Out2XML|Out2XML]], [[Software:Mascot2XML|Mascot2XML]], [[Software:Tandem2XML|Tandem2XML]]
-*[[Software:ASAPRatio|ASAPRatio]]+ 
-*[[Software:Libra|Libra]]+Again, please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these components and installation instructions.
-*[[Software:Pep3D|Pep3D]]+ 
-*[[Software:Out2Summary|Out2Summary]]+==Data Conversion==
-*[[Software:MsXML2Other|MsXML2Other]]+===raw MS / MS2 to mzXML converters===
-*[[Software:readmzXML|readmzXML]]+Please see the [[Formats:mzXML|mzXML]] page for info on ReAdW (Thermo), mzStar (ABI/MDS Sciex Analyst), massWolf (Waters MassLynx), and compassXport (Bruker).
-*[[Software:mzStar|mzStar]]+
-*[[Software:ReAdW|ReAdW]]+
-*[[Software:Qualscore|Qualscore]]+
-*[[Software:RAMP|RAMP]]+
==LC-MS Analysis== ==LC-MS Analysis==
[[Software:SpecArray|SpecArray]]: tool for analyzing and comparing LC-MS runs [[Software:SpecArray|SpecArray]]: tool for analyzing and comparing LC-MS runs
-[[Software:MSAnalyzer|MSAnalyzer]]: alternate tool for MS Level 1 analysis.+[[Software:msBID|msBID]]: alternate tool for MS Level 1 analysis.
[[Software:Pep3D|Pep3D]]: Visualization tool for viewing MS and MS/MS runs; integrated into the [[Software:TPP|TPP]]. [[Software:Pep3D|Pep3D]]: Visualization tool for viewing MS and MS/MS runs; integrated into the [[Software:TPP|TPP]].
 +
 +[[Software:QualScore|QualScore]]: reevaluating unassigned high-quality unassigned spectra.
 +
 +[[Software:SuperHirn|SuperHirn]]: software for quantitative analysis of LC-MS data by a combined MS1 and MS2 approach
 +
 +==MS-MS Spectral Assignment==
 +[[Software:ProbID|ProbID]]: open-source search engine
 +
 +==SWATH (DIA) anlaysis tools==
 +[[Software:SWATHProphet|SWATHProphet]]: A tool for statistical analysis of SWATH data and discovery of modifications
==Interpretation== ==Interpretation==
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[[Software:Cytoscape|Cytoscape]]: platform for visualizing and integrating molecular interaction networks [[Software:Cytoscape|Cytoscape]]: platform for visualizing and integrating molecular interaction networks
 +
 +[[Software:Firegoose, Gaggle, and PIPE|Firegoose, Gaggle, and PIPE]]: a suite of tools for analysis and visualization of biological data
==Protein Crosslinking== ==Protein Crosslinking==
 +
 +Kojak http://www.kojak-ms.org/
 +
 +
[[Software:XLink|XLink]]: XLink suite [[Software:XLink|XLink]]: XLink suite
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CGIs - a bundle of useful CGI scripts CGIs - a bundle of useful CGI scripts
-massWolf+[[Software:massWolf|massWolf (wolf.exe)]]: Micromass MassLynx to mzXML converter
-mzBruker+[[Software:mzBruker|mzBruker]]: Bruker to mzXML converter
validateXML validateXML
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InsilicosViewer InsilicosViewer
 +
 +Tomcat

Current revision

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

The Trans-Proteomic Pipeline (TPP) Project

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

The TPP software distribution integrates the following programs:

Petunia (TPP GUI), PeptideProphet, ProteinProphet, XPRESS, ASAPRatio, Libra, Pep3D, SpectraST, Out2Summary, MzXML2Search, MsXML2Other, readmzXML, mzStar ReAdW, QualScore, RAMP, Out2XML, Mascot2XML, Tandem2XML

Again, please see the TPP page for descriptions of the pipeline and these components and installation instructions.

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

msBID: alternate tool for MS Level 1 analysis.

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

QualScore: reevaluating unassigned high-quality unassigned spectra.

SuperHirn: software for quantitative analysis of LC-MS data by a combined MS1 and MS2 approach

MS-MS Spectral Assignment

ProbID: open-source search engine

SWATH (DIA) anlaysis tools

SWATHProphet: A tool for statistical analysis of SWATH data and discovery of modifications

Interpretation

SBEAMS: Systems Biology Experiment Analysis Management System

Cytoscape: platform for visualizing and integrating molecular interaction networks

Firegoose, Gaggle, and PIPE: a suite of tools for analysis and visualization of biological data

Protein Crosslinking

Kojak http://www.kojak-ms.org/


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

Tomcat

Personal tools