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| - | __NOTOC__ | + | The '''Seattle Proteome Center (SPC)''' is committed to providing free, open-source, software projects in support of cutting-edge proteomics research. The SPC maintains active support and education for the open-source proteomics community. |
| - | == Seattle Proteome Center Software Tools Wiki == | + | |
| - | Welcome to the Seattle Proteome Center (SPC) software tools wiki. This wiki is primarily intended as means of sharing user documentation for the SPC tools. We encourage outside contribution, but please make your edits responsibly. | + | ==Education, outreach, training and support== |
| - | <div class="MainPageBG" style="border: 4px solid #ffad08; padding: .5em 1em; color: #000; background-color: #ffffff; margin: 3px 3px 0; text-align: left"> | + | |
| - | * To edit or create pages, simply create an account (link on the top right of the page) before you start editing pages. Thanks! | + | |
| - | * The tools change rapidly, so make a note of what version you are using if you edit information. | + | |
| - | '''Latest TPP version: 3.0.3 (May 8, 2007)''' | + | *SPC/TPP course: |
| - | </div> | + | ** No courses scheduled at the moment. Please check back soon! |
| + | ** [https://moritz.isbscience.org/courses/proteomics-informatics-course/ Information and materials from previous courses] | ||
| - | == SPC Software== | + | *Outreach at conferences: |
| + | ** None scheduled at the moment | ||
| - | The SPC is committed to providing open-source, free software to support proteomics research. The | + | *Active support: all users, both new and experienced, are encouraged to participate in our active [http://groups.google.com/group/spctools-discuss spctools-discuss discussion group]. Discussions range from installation support to advanced data processing questions and feature requests. |
| - | [[Software:Overview| SPC Software Overview]] page lists (almost) all of the open-source software projects produced at the SPC. Major projects: | + | ** Please also see [http://groups.google.com/group/spctools-announce spctools-announce group] for important notifications of updates to our software. |
| - | * '''TPP''': our proteomics pipeline software is described on the [[TPP:Documentation|Trans-Proteomic Pipeline (TPP) Overview]] page. | + | |
| - | * '''Open Data Formats''': You can learn more about the SPC-developed open-formats on the [[Formats:Overview|Formats]] page. | + | |
| - | * [[Prequips:Documentation|Prequips]] project documentation. | + | |
| - | ==Links== | ||
| - | *[http://www.proteomecenter.org Seattle Proteome Center (SPC) general website]: about our organization. | ||
| - | *newsgroups: '''subscriptions highly recommended for SPC Tools users''' | ||
| - | **[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. | ||
| - | **[http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | ||
| - | *[http://www.sourceforge.net/projects/sashimi Sashimi Project Page on SourceForge]: Of interest to developers-- our code repository and software distribution site. | ||
| - | *[http://sashimi.sourceforge.net Sashimi Website]: an older documentation site, mainly containing useful information about the [[Formats:mzXML|mzXML]] format. | ||
| - | *[http://www.sbeams.org SBEAMS Project]: SPC's high-powered LIMS database system. | ||
| - | *[http://gaggle.systemsbiology.org The Gaggle project]: The ISB's data interaction, visualization, and exploration system, increasingly integrated with the [[Software:TPP|TPP]] | ||
| - | *[http://www.cytoscape.org Cytoscape Project]: Network visualization tool, integrated with the Gaggle. | ||
| - | *[http://www.peptideatlas.org PeptideAtlas]: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB. | ||
| - | == Wiki Guidlines == | + | ==[[Formats:Overview|SPC open proteomics data formats]]: mzXML, pepXML, protXML== |
| - | # These tools change rapidly. Please include the version when describing anything. | + | Learn more about the SPC-developed open formats, which include [[Formats:mzXML|mzXML]], [[Formats:pepXML|pepXML]], and [[Formats:protXML|protXML]] on the [[Formats:Overview|Formats]] page. |
| - | # These pages should '''not''' be used to report bugs. Please use the appropriate support avenues | + | |
| - | Refer to [http://meta.wikimedia.org/wiki/MediaWiki_User's_Guide#For_editors MediaWiki user's guide] for an introduction to formatting and editing pages. | ||
| - | == List of all articles == | + | ==[[Software:TPP|Trans-Proteomic Pipeline (TPP)]]: MS2 proteomics validation and analysis== |
| - | [[Special:Allpages|all articles]] | + | The Trans-Proteomic Pipeline (TPP) is a completely free software |
| + | solution for MS/MS-based shotgun proteomics analysis with a well-established | ||
| + | worldwide user community. TPP is | ||
| + | available on Linux and Windows systems and builds on Mac OS X as well. TPP spans | ||
| + | * conversion of raw data to open formats; | ||
| + | * support for searching spectra and peptide identification with various popular search engines, including the bundled X!Tandem search software (from The GPM) and [http://comet-ms.sourceforge.net/ Comet], as well as spectral library searching with [[SpectraST]], and cross-linking data with [http://www.kojak-ms.org/ Kojak]; | ||
| + | * conversion of search engine results to a unified format; | ||
| + | * statistical validation of peptide and protein identifications; | ||
| + | * quantitative proteomics analysis tools; | ||
| + | * and tools for interaction with and visualizing results. | ||
| + | * '''The latest TPP version is ''7.3.0,'' released ''April 2025''.''' | ||
| + | ** Download directly at: [https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.3%20%28Trade%20Wind%29%20rev%200/ Sourceforge] | ||
| + | ** Release Notes: [[TPP:7.3.0_Release_Notes]] | ||
| + | *Additional [[Software:TPP | TPP documentation]] | ||
| + | |||
| + | |||
| + | ==[[Software:PeptideAtlas|PeptideAtlas]]== | ||
| + | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides | ||
| + | identified in a large set of tandem mass spectrometry proteomics | ||
| + | experiments. Mass spectrometer output files are collected for human, mouse, | ||
| + | yeast, and several other organisms, and searched using the latest search | ||
| + | engines and protein sequences. All results of sequence and spectral library | ||
| + | searching are subsequently processed through the Trans Proteomic Pipeline to | ||
| + | derive a probability of correct identification for all results in a uniform | ||
| + | manner to insure a high quality database, along with false discovery rates | ||
| + | at the whole atlas level. Results may be queried and browsed at the | ||
| + | PeptideAtlas web site. The raw data, search results, and full builds can | ||
| + | also be downloaded for other uses. | ||
Current revision
The Seattle Proteome Center (SPC) is committed to providing free, open-source, software projects in support of cutting-edge proteomics research. The SPC maintains active support and education for the open-source proteomics community.
Contents |
[edit]
Education, outreach, training and support
- SPC/TPP course:
- No courses scheduled at the moment. Please check back soon!
- Information and materials from previous courses
- Outreach at conferences:
- None scheduled at the moment
- Active support: all users, both new and experienced, are encouraged to participate in our active spctools-discuss discussion group. Discussions range from installation support to advanced data processing questions and feature requests.
- Please also see spctools-announce group for important notifications of updates to our software.
[edit]
SPC open proteomics data formats: mzXML, pepXML, protXML
Learn more about the SPC-developed open formats, which include mzXML, pepXML, and protXML on the Formats page.
[edit]
Trans-Proteomic Pipeline (TPP): MS2 proteomics validation and analysis
The Trans-Proteomic Pipeline (TPP) is a completely free software solution for MS/MS-based shotgun proteomics analysis with a well-established worldwide user community. TPP is available on Linux and Windows systems and builds on Mac OS X as well. TPP spans
- conversion of raw data to open formats;
- support for searching spectra and peptide identification with various popular search engines, including the bundled X!Tandem search software (from The GPM) and Comet, as well as spectral library searching with SpectraST, and cross-linking data with Kojak;
- conversion of search engine results to a unified format;
- statistical validation of peptide and protein identifications;
- quantitative proteomics analysis tools;
- and tools for interaction with and visualizing results.
- The latest TPP version is 7.3.0, released April 2025.
- Download directly at: Sourceforge
- Release Notes: TPP:7.3.0_Release_Notes
- Additional TPP documentation
[edit]
PeptideAtlas
PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. Results may be queried and browsed at the PeptideAtlas web site. The raw data, search results, and full builds can also be downloaded for other uses.
