TPP:Related Tools

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Revision as of 00:58, 12 September 2007 Jtasman (Talk | contribs) (→Other tools) ← Previous diff		Current revision Dshteynb (Talk | contribs) (→Compatible Sequence Search Engines)
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	==Introduction==		==Introduction==
-	The TPP has many relationships with other software programs and projects. Some of these, like the TPP itself, are freely-available open-source projects, while others are commercial. Some of these tools provide compatiable data formats that can be used as input to the TPP, while others repackage or redistribute the TPP itself.	+	The TPP has many relationships with other software programs and projects. Some of these, like the TPP itself, are freely-available open-source projects, while others are commercial. Some of these tools provide compatible data formats that can be used as input to the TPP, while others repackage or redistribute the TPP itself, or work with the data produced by the TPP.
-		+
	==Compatible Mass-Spectrometer Instrument-Specific Software and File Formats==		==Compatible Mass-Spectrometer Instrument-Specific Software and File Formats==
		+	===Thermo (Xcalibur) .RAW files===
		+	===Waters (MassLynx) .RAW directories===
		+	===MDS/Sciex (Analyst) .wiff files===
		+	===Agilent (MassHunter) .d directories===
		+
	The TPP aims to support a wide variety of mass-spec instrument formats; the TPP provides tools to convert their proprietary formats into our open mzXML format. Please see [[Formats:mzXML]] for an overview of compatible formats and converter software.		The TPP aims to support a wide variety of mass-spec instrument formats; the TPP provides tools to convert their proprietary formats into our open mzXML format. Please see [[Formats:mzXML]] for an overview of compatible formats and converter software.
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	==Compatible Mass-Spectroscopy Input File Formats==		==Compatible Mass-Spectroscopy Input File Formats==
-		+	===mzXML===
		+	===mzData===
		+	===mzML===
	In addition to the SPC-developed open MS format [[Formats:mzXML|mzXML]], the TPP can also read the HUPO Proteome Standards Initiative (PSI) [http://www.psidev.info/index.php?q=node/80#mzdata mzData] format. Support is ongoing for the next-generation format called [http://www.psidev.info/index.php?q=node/257 mzML], developed through collaboration between PSI, instrument vendors, the SPC, and other proteomics software companies.		In addition to the SPC-developed open MS format [[Formats:mzXML|mzXML]], the TPP can also read the HUPO Proteome Standards Initiative (PSI) [http://www.psidev.info/index.php?q=node/80#mzdata mzData] format. Support is ongoing for the next-generation format called [http://www.psidev.info/index.php?q=node/257 mzML], developed through collaboration between PSI, instrument vendors, the SPC, and other proteomics software companies.
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	All of the programs attempt to assign an amino acid peptide identification to a MS2 spectra. The TPP includes tools to convert the proprietary search engine output file into the TPP's native, open format called [[Formats:pepXML|pepXML]]. We always welcome opportunities to add support for additional search engines. For information about working with these search engines please see [[TPP:Supported Search Engines]]		All of the programs attempt to assign an amino acid peptide identification to a MS2 spectra. The TPP includes tools to convert the proprietary search engine output file into the TPP's native, open format called [[Formats:pepXML|pepXML]]. We always welcome opportunities to add support for additional search engines. For information about working with these search engines please see [[TPP:Supported Search Engines]]
-	Compatible search engines, added in order of support:	+	Compatible search engines:
-	*[http://fields.scripps.edu/sequest/ SEQUEST]: commercial search engine	+	===COMET===
-	*Comet: SPC developed search engine	+	[http://comet-ms.sourceforge.net/ COMET] open-source database search engine provided with TPP (as of version 4.7.1)
-	*[[Software:ProbID|ProbID]]: SPC developed search engine	+
-	*[http://www.matrixscience.com/ Mascot]: commercial search engine	+
-	*[http://www.thegpm.org/TANDEM/ X!Tandem]: open-source, free search engine	+
-	*[http://www.phenyx-ms.com/ Phenyx]: commercial search engine	+
-	==Other tools==	+	===X!Tandem===
		+	[http://www.thegpm.org/TANDEM/ X!Tandem] is a open-source, free search engine. X!Tandem with the K-Score plugin is now distributed as part of the Windows TPP (as of version 3.2.1).
		+	===SEQUEST===
		+	[http://fields.scripps.edu/sequest/ SEQUEST] is a commercial search engine, currently sold by Thermo.
		+
		+	===MSGF+===
		+	[http://proteomics.ucsd.edu/software-tools/ms-gf/ MSGF+]
		+
		+	===Inspect===
		+	[http://proteomics.ucsd.edu/software-tools/inspectms-alignment/ Inspect]
		+
		+	===OMSSA===
		+	[http://www.ncbi.nlm.nih.gov/Web/Newsltr/V14N2/index.html OMSSA]
		+
		+	===MyriMatch===
		+	[http://forge.fenchurch.mc.vanderbilt.edu/scm/viewvc.php/*checkout*/trunk/doc/index.html?root=myrimatch MyriMatch] open-source tandem mass spectral peptide identification by multivariate hypergeometric analysis
		+
		+	===ProbID===
		+	[[Software:ProbID|ProbID]]is an open-source, freely-available SPC developed search engine.
		+
		+	===Mascot===
		+	[http://www.matrixscience.com/ Mascot] is a commercial search engine, distributed by Matrix Science.
		+
		+	===Phenyx===
		+	[http://www.phenyx-ms.com/ Phenyx] is a commercial search engine.
		+
		+	==Other tools and projects==
		+
		+	===SBEAMS===
		+	[[Software:SBEAMS|SBEAMS]] is a high-powered, free and open-source SPC-developed LIMS system. The SBEAMS proteomics module was designed for TPP data. SBEAMS is the backend for PeptideAtlas (see below).
		+
		+	===PeptideAtlas===
		+	[http://www.peptideatlas.org PeptideAtlas]: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB.
		+
		+	===The Gaggle===
		+	[http://gaggle.systemsbiology.org The Gaggle project]: The ISB's open-source data interaction, visualization, and exploration system, increasingly integrated with the [[Software:TPP|TPP]].
		+
		+	===Cytoscape===
		+	[http://www.cytoscape.org Cytoscape Project]: Open-source network visualization tool, integrated with the Gaggle, co-developed at the ISB.
		+
		+	===IPP (InSilicos)===
	[http://www.insilicos.com InSilicos] produces the [http://www.insilicos.com/IPP.html InSilicos Proteomics Pipeline], or IPP; this is a native-windows build of the TPP code which is claimed to be faster than the TPP's Windows distribution. InSilicos provides consultant-based support services for the IPP. InSilicos has contributed important code to the TPP's code base and plays a role in TPP support.		[http://www.insilicos.com InSilicos] produces the [http://www.insilicos.com/IPP.html InSilicos Proteomics Pipeline], or IPP; this is a native-windows build of the TPP code which is claimed to be faster than the TPP's Windows distribution. InSilicos provides consultant-based support services for the IPP. InSilicos has contributed important code to the TPP's code base and plays a role in TPP support.
		+	===CPAS (LabKey)===
	[https://www.labkey.org LabKey Software] produces the [https://www.labkey.org/Project/home/cpas CPAS] LIMS system, which incorporates some components of the TPP. The LabKey team has also contributed important code to the TPP's code base and plays a role in TPP support.		[https://www.labkey.org LabKey Software] produces the [https://www.labkey.org/Project/home/cpas CPAS] LIMS system, which incorporates some components of the TPP. The LabKey team has also contributed important code to the TPP's code base and plays a role in TPP support.
		+	===Proteus (Genologics)===
	[http://www.genologics.com Genologics] produces a commerical LIMS systems called [http://www.genologics.com/products/proteomics_solution.php Proteus] which is compatible with the TPP.		[http://www.genologics.com Genologics] produces a commerical LIMS systems called [http://www.genologics.com/products/proteomics_solution.php Proteus] which is compatible with the TPP.
		+
		+	===YPED===
		+	The [http://info.med.yale.edu/proteome/current_status.htm Yale Protein Expression Database] uses the TPP for data processing.

---

Current revision

Contents 1 Introduction 2 Compatible Mass-Spectrometer Instrument-Specific Software and File Formats 2.1 Thermo (Xcalibur) .RAW files 2.2 Waters (MassLynx) .RAW directories 2.3 MDS/Sciex (Analyst) .wiff files 2.4 Agilent (MassHunter) .d directories 3 Compatible Mass-Spectroscopy Input File Formats 3.1 mzXML 3.2 mzData 3.3 mzML 4 Compatible Sequence Search Engines 4.1 COMET 4.2 X!Tandem 4.3 SEQUEST 4.4 MSGF+ 4.5 Inspect 4.6 OMSSA 4.7 MyriMatch 4.8 ProbID 4.9 Mascot 4.10 Phenyx 5 Other tools and projects 5.1 SBEAMS 5.2 PeptideAtlas 5.3 The Gaggle 5.4 Cytoscape 5.5 IPP (InSilicos) 5.6 CPAS (LabKey) 5.7 Proteus (Genologics) 5.8 YPED

Introduction

The TPP has many relationships with other software programs and projects. Some of these, like the TPP itself, are freely-available open-source projects, while others are commercial. Some of these tools provide compatible data formats that can be used as input to the TPP, while others repackage or redistribute the TPP itself, or work with the data produced by the TPP.

Compatible Mass-Spectrometer Instrument-Specific Software and File Formats

Thermo (Xcalibur) .RAW files

Waters (MassLynx) .RAW directories

MDS/Sciex (Analyst) .wiff files

Agilent (MassHunter) .d directories

The TPP aims to support a wide variety of mass-spec instrument formats; the TPP provides tools to convert their proprietary formats into our open mzXML format. Please see Formats:mzXML for an overview of compatible formats and converter software.

Compatible Mass-Spec file formats

Vendor	Instrument Acquisition Software	File Type	TPP mzXML converter
Thermo	XCalibur	.RAW file	ReAdW
Waters	MassLynx	.RAW directory	wolf
MDS/Sciex for ABI and Agilent	Analyst, AnalystQS	.wiff file	mzWiff (beta, not yet released)
Agilent	MassHunter	.d directory	trapper (beta, not yet released)

Compatible Mass-Spectroscopy Input File Formats

mzXML

mzData

mzML

In addition to the SPC-developed open MS format mzXML, the TPP can also read the HUPO Proteome Standards Initiative (PSI) mzData format. Support is ongoing for the next-generation format called mzML, developed through collaboration between PSI, instrument vendors, the SPC, and other proteomics software companies.

Compatible Sequence Search Engines

All of the programs attempt to assign an amino acid peptide identification to a MS2 spectra. The TPP includes tools to convert the proprietary search engine output file into the TPP's native, open format called pepXML. We always welcome opportunities to add support for additional search engines. For information about working with these search engines please see TPP:Supported Search Engines

Compatible search engines:

COMET

COMET open-source database search engine provided with TPP (as of version 4.7.1)

X!Tandem

X!Tandem is a open-source, free search engine. X!Tandem with the K-Score plugin is now distributed as part of the Windows TPP (as of version 3.2.1).

SEQUEST

SEQUEST is a commercial search engine, currently sold by Thermo.

MSGF+

MSGF+

Inspect

Inspect

OMSSA

OMSSA

MyriMatch

MyriMatch open-source tandem mass spectral peptide identification by multivariate hypergeometric analysis

ProbID

ProbIDis an open-source, freely-available SPC developed search engine.

Mascot

Mascot is a commercial search engine, distributed by Matrix Science.

Phenyx

Phenyx is a commercial search engine.

Other tools and projects

SBEAMS

SBEAMS is a high-powered, free and open-source SPC-developed LIMS system. The SBEAMS proteomics module was designed for TPP data. SBEAMS is the backend for PeptideAtlas (see below).

PeptideAtlas

PeptideAtlas: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB.

The Gaggle

The Gaggle project: The ISB's open-source data interaction, visualization, and exploration system, increasingly integrated with the TPP.

Cytoscape

Cytoscape Project: Open-source network visualization tool, integrated with the Gaggle, co-developed at the ISB.

IPP (InSilicos)

InSilicos produces the InSilicos Proteomics Pipeline, or IPP; this is a native-windows build of the TPP code which is claimed to be faster than the TPP's Windows distribution. InSilicos provides consultant-based support services for the IPP. InSilicos has contributed important code to the TPP's code base and plays a role in TPP support.

CPAS (LabKey)

LabKey Software produces the CPAS LIMS system, which incorporates some components of the TPP. The LabKey team has also contributed important code to the TPP's code base and plays a role in TPP support.

Proteus (Genologics)

Genologics produces a commerical LIMS systems called Proteus which is compatible with the TPP.

YPED

The Yale Protein Expression Database uses the TPP for data processing.