Software:TPP

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The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
-[[image:TPP_overview.gif]] 
-Software contained in the TPP:+== Overview ==
 +[[image:TPP.jpg|1200px]]
 +<!-- imagemap>
 +image:TPP.jpg|
 +rect 940 142 760 88 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio]]
 +rect 940 203 760 153 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:XPRESS]]
 +rect 940 273 760 219 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:Libra]]
 +rect 1431 173 1250 88 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:SBEAMS]]
 +rect 454 176 273 134 [[http://tools.proteomecenter.org/wiki/index.php?title=SpectraST]]
 +rect 454 128 273 88 [[http://www.thegpm.org/TANDEM/api/]]
 +rect 1185 273 1010 88 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet]]
 +rect 700 144 515 88 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:PeptideProphet]]
 +rect 700 207 515 152 [[http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial#8._Further_peptide-level_validation_iProphet]]
 +rect 264 333 50 300 [[http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML]]
 +rect 1058 333 425 300 [[http://tools.proteomecenter.org/formats/pepXML/pepXML_xmlspy_docs.html]]
 +rect 1377 333 1168 300 [[http://tools.proteomecenter.org/formats/protXML/protXML_xmlspy_docs.html]]
 +rect 1433 270 1250 185 [[http://pipe2.systemsbiology.net/PIPE2/]]
 +desc none
 +</imagemap -->
 +== Authors and Contributors ==
-==Probability Assignment and Validation==+See [[TPP:Authors and Contributors]]
-[[Software:PeptideProphet|PeptideProphet]]: Statistical validation of spectra-to-peptide sequence, using search engine results.+==Getting the software==
 +The latest TPP version is <b>7.2.0</b>, released November 2024.
-[[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] results.+{| style="border-collapse: separate; border-spacing: 2; border-width: 1px; padding: 4px;"
 +|[[Image:Info.png|middle|left]]
 +| For support both during and after installation, you are encouraged to consult the SPC Tools newsgroups:
 +* The [http://groups.google.com/group/spctools-discuss spctools-discuss discussion group] provides active community support and discussion for the tools.
 +* Subscribing to the low-volume mailing list [http://groups.google.com/group/spctools-announce spctools-announce discussion group] will keep you up to date with the latest news on new releases and software updates for TPP.
 +|}
 +===Installing on a Windows System===
-==Protein Quantification==+The Windows version of TPP is provided as a pre-built binary self-installing executable which can be downloaded from the SourceForge site [https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%200/TPP_Setup_7.0.0.exe/download here]. There are also detailed instructions on how to install the latest version of TPP in the [[TPP:5.2_Installation | TPP 5.2.0 Windows installation guide]]. (instructions also apply to 6.x and 7.x versions)
-[[Software:XPRESS|XPRESS]]: Calculation of relative abundance of proteins from MS/MS data.+===Source Code Installation (For Linux and Android systems)===
 +The latest source code package can be found [https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%200/TPP_7.0.0-src.tgz/download here], on the Sashimi project site on SourceForge. This is gzipped tar archive that can be unpacked using tools such as tar, 7-zip, or WinZip. Details on how to compile TPP can be found in the '''README''' and '''INSTALL_LINUX''' files found in the top level directory of the package. There is also a series of installation guides, which are more detailed and contain information specific to certain distributions: [[Linux Installation Guides|Linux Installation Guides]].
-[[Software:ASAPRatio|ASAPRatio]]: Automated Statistical Analysis on Protein Ratio.+===Advanced Topic: building the TPP from source on Windows===
 +'''NOTE:''' These advanced topics are for developers. Windows users can download and run the TPP Windows installer, which includes everything needed to run the TPP.
-[[Software:Libra|Libra]]: Four channel quantification software.+* [[TPP:Building Windows-native binaries with Mingw]]
 +* [[TPP:Building Windows-native binaries with Visual Studio 2005]]
-==Graphical User Interface (GUI)==+===Mac OSX===
 + 
 +'''Please Note:''' The TPP 7.0.0 is officially supported on Mac OSX. Please download the MacOS [https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%200/TPP-7.0.0-Arafel-macosx-pkg.pkg/download package!]
 + 
 +==Software contained in the TPP==
 + 
 + 
 +===Probability Assignment and Validation===
 + 
 +[[Software:PeptideProphet|PeptideProphet]]: Statistical validation of PSMs using search engine results.
 + 
 +[[Software:iProphet|iProphet]]: Distinct peptide sequence validation, using [[Software:PeptideProphet|PeptideProphet]] results; can also combine the results of multiple search engines.
 + 
 +[[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] OR [[Software:iProphet|iProphet]] results.
 + 
 +[[Software:Mayu|Mayu]]: Decoy-estimated FDRs (false discovery rate) for [[Software:PeptideProphet|PeptideProphet]] results.
 + 
 +===Protein Quantification===
 + 
 +[[Software:XPRESS|XPRESS]]: Calculation of relative abundances of peptides and proteins from isotopically labeled MS/MS samples.
 + 
 +[[Software:ASAPRatio|ASAPRatio]]: Automated Statistical Analysis on Protein Ratio; an alternative to XPRESS.
 + 
 +[[Software:Libra|Libra]]: Quantification of isobarically-labeled samples (e.g. iTraq, TMT, etc) for any number of channels
 + 
 +[[Software:StPeter|StPeter]]: Label-free Quantification of Shotgun-MS using Normalized Spectral Indexes, Spectral Counts, or Normalized Spectral Abundance Factors.
 + 
 +===Graphical User Interface (GUI)===
[[Software:Petunia|Petunia]]: Petunia is the name of the TPP's web-based GUI, which presents the tools in an organized and logical manner for those who do not wish to use the command-line. [[Software:Petunia|Petunia]]: Petunia is the name of the TPP's web-based GUI, which presents the tools in an organized and logical manner for those who do not wish to use the command-line.
-==Protein ID Curation==+*[[TPP:Using Petunia|Using the TPP web interface ("Petunia")]]
 + 
 +===Spectral Library Building and Searching===
 +[[Software:SpectraST|SpectraST]]: Searches spectral libraries (including publicly available ones from [http://peptide.nist.gov/ NIST] and [http://www.thegpm.org/hunter/index.html GPM]) to identify peptide MS/MS spectra. Builds spectral libraries from sequence search results.
 + 
 +===Protein ID Curation===
Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT
[[Software:Pep3D|Pep3D]]: Viewer for LC-MS and LC-MS/MS results. [[Software:Pep3D|Pep3D]]: Viewer for LC-MS and LC-MS/MS results.
-==Input Processing: mzXML Tools==+===Input Processing: mzXML Tools===
-readmzXML: mzXML parser based on RAMP+[[Software:readmzXML|readmzXML]]: mzML/mzXML parser based on RAMP
-MsXML2Other: mzXML to SEQUEST dta, MASCOT generic and Micromass pkl converter+[[Software:MzXML2Search|MzXML2Search]]: Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files
[[Software:mzStar|mzStar]]: SCIEX/ABI Analyst format to mzXML converter [[Software:mzStar|mzStar]]: SCIEX/ABI Analyst format to mzXML converter
[[Software:ReAdW|ReAdW]]: ThermoFinnigan Xcalibur format to mzXML converter [[Software:ReAdW|ReAdW]]: ThermoFinnigan Xcalibur format to mzXML converter
 +
 +[[Software:MZIdentML|MZIdentML]]: Handling MZIdentml
 +
 +[[Software:DidIScanThat|DidIScanThat]]: Interrogating MS/MS spectra of mzML files.
RAMP: mzXML data parser RAMP: mzXML data parser
 +
 +===Input Processing: Search-Engine to pepXML converters===
 +*Sequest results: [[Software:Out2XML|Out2XML]]
 +*Mascot results: [[Software:Mascot2XML|Mascot2XML]]
 +*Tandem results: [[Software:Tandem2XML|Tandem2XML]]
 +
 +===Database Search Tools===
 +*[[TPP:X!Tandem_and_the_TPP|X!Tandem]]: Open source peptide search engine from [http://www.thegpm.org GPM]
 +*[[TPP:Comet_and_the_TPP|Comet]]: Open source peptide search engine from [http://comet-ms.sourceforge.net/ Comet-MS]
 +
 +==Working with supported search engines==
 +The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF+, Inspect, MyriMatch, and Phenyx. Please see the [[TPP:Supported Search Engines|supported search engines]] page for more information.
 +
 +==Example Data Analysis==
 +*[[TPP:Example data analysis|Example Data Analysis]]
 +*Try our [[TPP Tutorial]]
 +*You can also see the older [[TPP Tutorial v2]] and [[TPP Tutorial v1]]
 +
 +
 +
 +==TPP and Related Software Tools==
 +
 +[[TPP:Related Tools|This page]] describes the (sometimes confusing!) relationship between the many software projects that integrate with the TPP, either as compatible search engines, or as projects that repackage and redistribute the TPP itself.
 +
 +==Additional help==
 +===FAQ===
 +[[TPP:Frequently Asked Questions|Frequently Asked Questions]]
 +
 +===Newsgroups===
 +'''subscriptions highly recommended for SPC Tools users'''
 +
 +====spctools-discuss====
 +[http://groups.google.com/group/spctools-discuss spctools-discuss discussion group]: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate.
 +
 +====spctools-announce====
 +[http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software
 +
 +===TPP Demo and Tutorial===
 +Try or end-to-end analysis of Orbitrap SILAC data in our [[TPP Tutorial]].
 +
 +==Developer Documentation==
 +*[[TPP:Developer Documentation|Developer Documentation]]
 +*[[Developer: Boost CPP libraries|Boost CPP libraries]]
 +*[[Debugging:Understanding XSL-Generating Code in Perl]]
 +*[[Debugging:Working with boost::shared ptr]]
 +
 +===Links===
 +*[http://sashimi.sourceforge.net Sashimi Project Page on SourceForge]

Current revision

The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.


Contents

[edit]

Overview

[edit]

Authors and Contributors

See TPP:Authors and Contributors

[edit]

Getting the software

The latest TPP version is 7.2.0, released November 2024.

middle
 For support both during and after installation, you are encouraged to consult the SPC Tools newsgroups:
[edit]

Installing on a Windows System

The Windows version of TPP is provided as a pre-built binary self-installing executable which can be downloaded from the SourceForge site here. There are also detailed instructions on how to install the latest version of TPP in the TPP 5.2.0 Windows installation guide. (instructions also apply to 6.x and 7.x versions)

[edit]

Source Code Installation (For Linux and Android systems)

The latest source code package can be found here, on the Sashimi project site on SourceForge. This is gzipped tar archive that can be unpacked using tools such as tar, 7-zip, or WinZip. Details on how to compile TPP can be found in the README and INSTALL_LINUX files found in the top level directory of the package. There is also a series of installation guides, which are more detailed and contain information specific to certain distributions: Linux Installation Guides.

[edit]

Advanced Topic: building the TPP from source on Windows

NOTE: These advanced topics are for developers. Windows users can download and run the TPP Windows installer, which includes everything needed to run the TPP.

[edit]

Mac OSX

Please Note: The TPP 7.0.0 is officially supported on Mac OSX. Please download the MacOS package!

[edit]

Software contained in the TPP

[edit]

Probability Assignment and Validation

PeptideProphet: Statistical validation of PSMs using search engine results.

iProphet: Distinct peptide sequence validation, using PeptideProphet results; can also combine the results of multiple search engines.

ProteinProphet: Protein identification and validation, using PeptideProphet OR iProphet results.

Mayu: Decoy-estimated FDRs (false discovery rate) for PeptideProphet results.

[edit]

Protein Quantification

XPRESS: Calculation of relative abundances of peptides and proteins from isotopically labeled MS/MS samples.

ASAPRatio: Automated Statistical Analysis on Protein Ratio; an alternative to XPRESS.

Libra: Quantification of isobarically-labeled samples (e.g. iTraq, TMT, etc) for any number of channels

StPeter: Label-free Quantification of Shotgun-MS using Normalized Spectral Indexes, Spectral Counts, or Normalized Spectral Abundance Factors.

[edit]

Graphical User Interface (GUI)

Petunia: Petunia is the name of the TPP's web-based GUI, which presents the tools in an organized and logical manner for those who do not wish to use the command-line.

[edit]

Spectral Library Building and Searching

SpectraST: Searches spectral libraries (including publicly available ones from NIST and GPM) to identify peptide MS/MS spectra. Builds spectral libraries from sequence search results.

[edit]

Protein ID Curation

Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT

Pep3D: Viewer for LC-MS and LC-MS/MS results.

[edit]

Input Processing: mzXML Tools

readmzXML: mzML/mzXML parser based on RAMP

MzXML2Search: Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files

mzStar: SCIEX/ABI Analyst format to mzXML converter

ReAdW: ThermoFinnigan Xcalibur format to mzXML converter

MZIdentML: Handling MZIdentml

DidIScanThat: Interrogating MS/MS spectra of mzML files.

RAMP: mzXML data parser

[edit]

Input Processing: Search-Engine to pepXML converters

[edit]

Database Search Tools

[edit]

Working with supported search engines

The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF+, Inspect, MyriMatch, and Phenyx. Please see the supported search engines page for more information.

[edit]

Example Data Analysis


[edit]

TPP and Related Software Tools

This page describes the (sometimes confusing!) relationship between the many software projects that integrate with the TPP, either as compatible search engines, or as projects that repackage and redistribute the TPP itself.

[edit]

Additional help

[edit]

FAQ

Frequently Asked Questions

[edit]

Newsgroups

subscriptions highly recommended for SPC Tools users

[edit]

spctools-discuss

spctools-discuss discussion group: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate.

[edit]

spctools-announce

spctools-announce discussion group: infrequent, important notifications of updates to our software

[edit]

TPP Demo and Tutorial

Try or end-to-end analysis of Orbitrap SILAC data in our TPP Tutorial.

[edit]

Developer Documentation

[edit]

Links

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"
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