Software:TPP
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| Revision as of 00:26, 19 September 2007 Jtasman (Talk | contribs) (→Additional help) ← Previous diff |
Current revision Luis (Talk | contribs) (→Getting the software) |
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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]] | ||
| + | == 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 --> | ||
| - | ==Getting the software== | + | == Authors and Contributors == |
| - | ===Support Note=== | + | See [[TPP:Authors and Contributors]] |
| - | For support both during and after installation, you are strongly encouraged to consult the SPC Tools newsgroups: | + | |
| - | * The [http://groups.google.com/group/spctools-discuss spctools-discuss discussion group] provides active community support and disucussion for the tools. | + | |
| - | * Important information about new releases and software updates can be found on the [http://groups.google.com/group/spctools-announce spctools-announce discussion group]. You are '''highly encouraged''' to subscibe to this low-volume list. | + | |
| - | ===[[TPP:Windows Cygwin Installation|Installing on a Windows System]]=== | + | ==Getting the software== |
| + | The latest TPP version is <b>7.2.0</b>, released November 2024. | ||
| - | ===Source code Installation (For Linux systems)=== | + | {| style="border-collapse: separate; border-spacing: 2; border-width: 1px; padding: 4px;" |
| - | The latest source code package can be found [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 here], on the Sashimi project site on SourceForge. | + | |[[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=== | ||
| - | ====[[TPP:Installing_on_Ubuntu_7.04|Installing on Ubuntu]]==== | + | 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) |
| - | These community-contributed notes are a guide to installing on the Ubuntu distribution but should be similar to other linux systems. | + | |
| - | ===[[TPP:Installing on Mac OSX|Mac OSX Installation guide]]=== | + | ===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]]. | ||
| - | <!-- <P>Download source from local site: <a href="./software/TPP_v2.9.7_GALE.zip">TPP_v2.9.7_GALE.zip</a></P> --> | + | ===Advanced Topic: building the TPP from source on Windows=== |
| - | <!-- <P>Download cygwin binaries: <a href="windows.php">Windows installation</a></P> --> | + | '''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. |
| + | * [[TPP:Building Windows-native binaries with Mingw]] | ||
| + | * [[TPP:Building Windows-native binaries with Visual Studio 2005]] | ||
| - | <!-- <P>Download source from Web: <a href="http://sourceforge.net/project/showfiles.php?group_id=69281">Sourceforge Page</a><br> --> | + | ===Mac OSX=== |
| - | <!-- <em>Note: On the web you might find a newer version of this software.</em></P> --> | + | |
| + | '''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== | ==Software contained in the TPP== | ||
| Line 33: | Line 57: | ||
| ===Probability Assignment and Validation=== | ===Probability Assignment and Validation=== | ||
| - | [[Software:PeptideProphet|PeptideProphet]]: Statistical validation of spectra-to-peptide sequence, using search engine results. | + | [[Software:PeptideProphet|PeptideProphet]]: Statistical validation of PSMs using search engine results. |
| - | [[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] 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=== | ===Protein Quantification=== | ||
| - | [[Software:XPRESS|XPRESS]]: Calculation of relative abundance of proteins from MS/MS data. | + | [[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. | + | [[Software:ASAPRatio|ASAPRatio]]: Automated Statistical Analysis on Protein Ratio; an alternative to XPRESS. |
| - | [[Software:Libra|Libra]]: Four channel quantification software. | + | [[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)=== | ===Graphical User Interface (GUI)=== | ||
| Line 49: | Line 79: | ||
| *[[TPP:Using Petunia|Using the TPP web interface ("Petunia")]] | *[[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=== | ===Protein ID Curation=== | ||
| Line 56: | Line 89: | ||
| ===Input Processing: mzXML Tools=== | ===Input Processing: mzXML Tools=== | ||
| - | [[Software:readmzXML|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 | ||
| Line 70: | Line 107: | ||
| *Mascot results: [[Software:Mascot2XML|Mascot2XML]] | *Mascot results: [[Software:Mascot2XML|Mascot2XML]] | ||
| *Tandem results: [[Software:Tandem2XML|Tandem2XML]] | *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== | ==Working with supported search engines== | ||
| - | The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, and Phenyx. Please see the [[TPP:Supported Search Engines|supported search engines]] page for more information. | + | 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== | ==Example Data Analysis== | ||
| *[[TPP:Example data analysis|Example Data Analysis]] | *[[TPP:Example data analysis|Example Data Analysis]] | ||
| - | *Also see the [[TPP Tutorial]] | + | *Try our [[TPP Tutorial]] |
| + | *You can also see the older [[TPP Tutorial v2]] and [[TPP Tutorial v1]] | ||
| + | |||
| - | ==What's New== | ||
| - | The [[TPP:Recent Updates]] page describes updates to the software. | ||
| ==TPP and Related Software Tools== | ==TPP and Related Software Tools== | ||
| Line 98: | Line 139: | ||
| [http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | [http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | ||
| - | ===TPP Tutorial=== | + | ===TPP Demo and Tutorial=== |
| - | [[TPP Tutorial]] | + | Try or end-to-end analysis of Orbitrap SILAC data in our [[TPP Tutorial]]. |
| ==Developer Documentation== | ==Developer Documentation== | ||
Current revision
The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
Contents |
Overview
Authors and Contributors
See TPP:Authors and Contributors
Getting the software
The latest TPP version is 7.2.0, released November 2024.
 | For support both during and after installation, you are encouraged to consult the SPC Tools newsgroups:
|
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)
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.
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.
- TPP:Building Windows-native binaries with Mingw
- TPP:Building Windows-native binaries with Visual Studio 2005
Mac OSX
Please Note: The TPP 7.0.0 is officially supported on Mac OSX. Please download the MacOS package!
Software contained in the TPP
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.
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.
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.
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.
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.
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
Input Processing: Search-Engine to pepXML converters
- Sequest results: Out2XML
- Mascot results: Mascot2XML
- Tandem results: Tandem2XML
Database Search Tools
- X!Tandem: Open source peptide search engine from GPM
- Comet: Open source peptide search engine from 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 supported search engines page for more information.
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
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
Newsgroups
subscriptions highly recommended for SPC Tools users
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
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
- Developer Documentation
- Boost CPP libraries
- Debugging:Understanding XSL-Generating Code in Perl
- Debugging:Working with boost::shared ptr
