Software:TPP

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==Getting the software== ==Getting the software==
-===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. * 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=== ===Installing on a Windows System===
-[http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/ Latest download (4.8.0)] 
-[[Windows Installation Guide | Detailed Windows installation guide]]+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 also detailed instructions on how to install all prerequisites for TPP in the [[Windows Installation Guide | Windows installation guide]].
-===Source code Installation (For Linux systems)===+===Source Code Installation (For Linux systems)===
-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. Details on how to build TPP can be found in the [http://sourceforge.net/p/sashimi/code/HEAD/tree/tags/release_4-8-0/trans_proteomic_pipeline/README README] and [http://sourceforge.net/p/sashimi/code/HEAD/tree/tags/release_4-8-0/trans_proteomic_pipeline/INSTALL_LINUX INSTALL_LINUX] files found in the top level directory of the package.+The latest source code package can be found [http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.8%20%28philae%29%20rev%200/TPP_4.8.0-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 [http://sourceforge.net/p/sashimi/code/HEAD/tree/tags/release_4-8-0/trans_proteomic_pipeline/README README] and [http://sourceforge.net/p/sashimi/code/HEAD/tree/tags/release_4-8-0/trans_proteomic_pipeline/INSTALL_LINUX INSTALL_LINUX] files found in the top level directory of the package.
===Advanced Topic: building the TPP from source on Windows=== ===Advanced Topic: building the TPP from source on Windows===

Revision as of 06:27, 14 January 2015

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


Contents

Overview

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Authors and Contributors

See TPP:Authors and Contributors

Getting the software

middle
 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 also detailed instructions on how to install all prerequisites for TPP in the Windows installation guide.

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.

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.

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

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: 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

RAMP: mzXML data parser

Input Processing: Search-Engine to pepXML converters

Database Search Tools

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


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.

Developer Documentation

Links

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