Software:Overview
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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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| [[Software:massWolf|massWolf (wolf.exe)]]: Micromass MassLynx to mzXML converter | [[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
