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.

Overview

Authors and Contributors

See TPP:Authors and Contributors

Getting the software

The latest TPP version is 6.3.3, released September 2023.

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

The spctools-discuss discussion group provides active community support and discussion for the tools.
Subscribing to the low-volume mailing list 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

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 versions)

Source Code Installation (For Linux 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.

Mac OSX

Please Note: The TPP is not currently officially supported on Mac OSX. This means that we cannot respond to installation or usage help requests. Users, however, are encouraged to post to the spctools-discuss newsgroup to seek help from the community, or to contact the author of the corresponding post directly.

Mac OSX Installation guide by Ulrich auf dem Keller

Installing TPP 4.6.2 on Mountain Lion Mac OSX by Bosco Ho

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.

Using the TPP web interface ("Petunia")

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

Frequently Asked Questions

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.

 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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+== Overview ==
+[[image:TPP.jpg|1200px]]
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 == Authors and Contributors ==
 ==Getting the software==
+The latest TPP version is <b>6.3.3</b>, released September 2023.
-===Support Note===
+{| style="border-collapse: separate; border-spacing: 2; border-width: 1px; padding: 4px;"
-For support both during and after installation, you are strongly encouraged to consult the SPC Tools newsgroups:
+|[[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.
-* 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.
+* 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===
-[http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/ Latest download (4.7.1)]
-[[Windows Installation Guide | Detailed Windows installation guide]]
-===Source code Installation (For Linux systems)===
+The Windows version of TPP is provided as a pre-built binary self-installing executable which can be downloaded from the SourceForge site [http://sourceforge.net/projects/sashimi/files/latest/download?source=files 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 versions)
-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. These community-contributed notes are a guide to installing on the Ubuntu distribution but should be similar to other linux systems.
-* [[TPP:Installing on Ubuntu 7.04]]
+===Source Code Installation (For Linux systems)===
-* [[TPP:Installing on Ubuntu 8.10]]
+The latest source code package can be found [http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/ 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]].
-* [[TPP 4.2.1: Installing on Ubuntu 9.04]]
-* [[TPP 4.3.1: Installing on Ubuntu 10.04]]
-* [[TPP 4.5.2: Installing on Ubuntu 10.04.3]]
 ===Advanced Topic: building the TPP from source on Windows===
 [[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)===
 ===Input Processing: mzXML Tools===
-[[Software:readmzXML|readmzXML]]: mzXML parser based on RAMP
+[[Software:readmzXML|readmzXML]]: mzML/mzXML parser based on RAMP
 [[Software:MzXML2Search|MzXML2Search]]: Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files
 [[Software:MZIdentML|MZIdentML]]: Handling MZIdentml
+[[Software:DidIScanThat|DidIScanThat]]: Interrogating MS/MS spectra of mzML files.
 RAMP: mzXML data parser