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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 == | + | ==Education, outreach, training and support== |
| - | 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, which include the Trans-Proteomic Pipeline (TPP). We encourage outside contribution, but please make your edits responsibly. The tools change rapidly, so make a note of what version you are using if you edit information. | + | *SPC/TPP course: |
| + | ** No courses scheduled at the moment. Please check back soon! | ||
| + | ** [https://moritz.isbscience.org/courses/proteomics-informatics-course/ Information and materials from previous courses] | ||
| - | <div class="MainPageBG" style="border: 4px solid #ffad08; padding: .5em 1em; color: #000; background-color: #ffffff; margin: 3px 3px 0; text-align: left"> | + | *Outreach at conferences: |
| + | ** None scheduled at the moment | ||
| - | '''General Information''' | + | *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. |
| + | ** Please also see [http://groups.google.com/group/spctools-announce spctools-announce group] for important notifications of updates to our software. | ||
| - | * Please create an account (link on the top right of the page) before you start editing pages. Thanks! | ||
| - | '''Wiki News''' | + | ==[[Formats:Overview|SPC open proteomics data formats]]: mzXML, pepXML, protXML== |
| - | {{Template:News}} | + | 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. |
| - | </div> | + | |
| - | == SPC Software== | ||
| - | The SPC is committed to providing open-source, free software. The | + | ==[[Software:TPP|Trans-Proteomic Pipeline (TPP)]]: MS2 proteomics validation and analysis== |
| - | [[Software:Overview| SPC Software Overview]] page lists '''all''' of the open-source software projects produced at the SPC; our proteomics pipeline software is described on the [[TPP:Documentation|Trans-Proteomic Pipeline (TPP) Overview]] page. | + | 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]] | ||
| - | You can learn more about the SPC-developed open-formats on the [[Formats:Overview|Formats]] page. | ||
| - | Jump to the [[Prequips:Documentation|Prequips]] documentation. | + | ==[[Software:PeptideAtlas|PeptideAtlas]]== |
| - | + | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides | |
| - | ==Links== | + | identified in a large set of tandem mass spectrometry proteomics |
| - | *[http://www.proteomecenter.org Seattle Proteome Center (SPC) general website]: about our organization. | + | experiments. Mass spectrometer output files are collected for human, mouse, |
| - | *newsgroups: '''subscriptions highly recommended for SPC Tools users''' | + | yeast, and several other organisms, and searched using the latest search |
| - | **[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. | + | engines and protein sequences. All results of sequence and spectral library |
| - | **[http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | + | searching are subsequently processed through the Trans Proteomic Pipeline to |
| - | *[http://www.sourceforge.net/projects/sashimi Sashimi Project Page on SourceForge]: Of interest to developers-- our code repository and software distribution site. | + | derive a probability of correct identification for all results in a uniform |
| - | *[http://sashimi.sourceforge.net Sashimi Website]: an older documentation site, mainly containing useful information about the [[Formats:mzXML|mzXML]] format. | + | manner to insure a high quality database, along with false discovery rates |
| - | *[http://www.sbeams.org SBEAMS Project]: SPC's high-powered LIMS database system. | + | at the whole atlas level. Results may be queried and browsed at the |
| - | *[http://gaggle.systemsbiology.org The Gaggle project]: The ISB's data interaction, visualization, and exploration system, increasingly integrated with the [[Software:TPP|TPP]] | + | PeptideAtlas web site. The raw data, search results, and full builds can |
| - | *[http://www.cytoscape.org Cytoscape Project]: Network visualization tool, integrated with the Gaggle. | + | also be downloaded for other uses. |
| - | *[http://www.peptideatlas.org PeptideAtlas]: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB. | + | |
| - | + | ||
| - | == Wiki Guidlines == | + | |
| - | # These tools change rapidly. Please include the version when describing anything. | + | |
| - | # 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 == | + | |
| - | [[Special:Allpages|all articles]] | + | |
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.
