TPP:Related Tools

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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.

 ==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==
+===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.
+{| class="wikitable" style="text-align:center;" border="2" cellpadding="2"
+|+ Compatible Mass-Spec file formats
+|-
+! Vendor !! Instrument Acquisition Software !! File Type !! TPP mzXML converter
+|-
+| [http://www.thermo.com/ Thermo] || [http://www.thermo.com/com/cda/product/detail/1,,1000001009250,00.html XCalibur ]|| .RAW file|| [[Software:ReAdW|ReAdW]]
+|-
+| [http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5KEKAJ  Waters] || [http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5WQP7W MassLynx] || .RAW directory || [[Software:massWolf|wolf]]
+|-
+| [http://www.mdssciex.com/ MDS/Sciex] for [https://products.appliedbiosystems.com/ab/en/US/adirect/ab;jsessionid=Gn0ZFF66S2ZTv1cfLTLn2nGxCH5L1gYVGv39d92hdr4PqSBglGVG!1672817600?cmd=catNavigate2&catID=600832 ABI] and [http://www.chem.agilent.com/Scripts/PCol.asp?lPage=38192 Agilent] || [https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600927 Analyst], [https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600910 AnalystQS] || .wiff file|| mzWiff (beta, not yet released)
+|-
+| [http://www.chem.agilent.com/Scripts/PCol.asp?lPage=38192 Agilent] || [http://www.chem.agilent.com/scripts/pds.asp?lpage=40460 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 [[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.
 ==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 [[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:
+===COMET===
+[http://comet-ms.sourceforge.net/ COMET] open-source database search engine provided with TPP (as of version 4.7.1)
+===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.
+===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.
+===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.
-*Sequest
+===YPED===
-*Comet
+The [http://info.med.yale.edu/proteome/current_status.htm Yale Protein Expression Database] uses the TPP for data processing.
-*ProbID
-*Mascot
-*X!Tandem
-*Phenyx

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)

TPP:Related Tools

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Contents

Introduction

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

Compatible Mass-Spectroscopy Input File Formats

mzXML

mzData

mzML

Compatible Sequence Search Engines

COMET

X!Tandem

SEQUEST

MSGF+

Inspect

OMSSA

MyriMatch

ProbID

Mascot

Phenyx

Other tools and projects

SBEAMS

PeptideAtlas

The Gaggle

Cytoscape

IPP (InSilicos)

CPAS (LabKey)

Proteus (Genologics)

YPED

Views

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