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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, log in before you start editing pages. Thanks! | + | *SPC/TPP course: |
| - | * The tools change rapidly, so make a note of what version you are using if you edit information. | + | ** No courses scheduled at the moment. Please check back soon! |
| + | ** [https://moritz.isbscience.org/courses/proteomics-informatics-course/ Information and materials from previous courses] | ||
| - | '''Latest TPP version: 3.4.0 (November 27, 2007)''' | + | *Outreach at conferences: |
| + | ** None scheduled at the moment | ||
| - | '''News:''' | + | *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. |
| - | *Bryan Prazen of [http://www.insilicos.com InSilicos] has contributed his excellent [[TPP Tutorial]] to our wiki. Thanks, Bryan! | + | ** Please also see [http://groups.google.com/group/spctools-announce spctools-announce group] for important notifications of updates to our software. |
| - | *'''New wiki accounts are temporarily disabled'''. Due to high levels of spam we've temporarily halted creation of new accounts. We will open the wiki again when we have stronger anti-spam measures in place. In the meanwhile, anyone who wants an account can contact Josh (you should be able to find email contact through the spctools-discuss newsgroup website, see below.) | + | |
| - | Please see the TPP [[TPP:Recent_Updates|Recent Updates]] page for more news items. | ||
| - | </div> | + | ==[[Formats:Overview|SPC open proteomics data formats]]: mzXML, pepXML, protXML== |
| + | 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. | ||
| - | == SPC Software== | ||
| - | The SPC is committed to providing open-source, free software to support proteomics research. The | + | ==[[Software:TPP|Trans-Proteomic Pipeline (TPP)]]: MS2 proteomics validation and analysis== |
| - | [[Software:Overview| SPC Software Overview]] page lists (almost) all of the open-source software projects produced at the SPC. Major projects include: | + | The Trans-Proteomic Pipeline (TPP) is a completely free software |
| - | * '''[[Software:TPP|TPP]]''': our proteomics pipeline software is described on the [[Software:TPP|Trans-Proteomic Pipeline (TPP)]] page. | + | solution for MS/MS-based shotgun proteomics analysis with a well-established |
| - | **For information about 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, please see the [[TPP:Related Tools]] page. | + | worldwide user community. TPP is |
| - | * '''[[Formats:Overview|Open Data Formats]]''': You can 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. | + | available on Linux and Windows systems and builds on Mac OS X as well. TPP spans |
| - | * [[Software:SBEAMS|SBEAMS Project]]: SPC's high-powered LIMS database system. | + | * 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]] | ||
| - | ==Links== | ||
| - | ===SPC Links=== | ||
| - | *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://www.proteomecenter.org/course.php SPC Proteomics Course]: Next course is '''November 5-9, 2007''' | ||
| - | *[http://tools.proteomecenter.org/software.php Seattle Proteome Center (SPC) general website]: about our organization. | ||
| - | *[http://sashimi.sourceforge.net Sashimi Website]: an older documentation site, mainly containing useful information about the [[Formats:mzXML|mzXML]] format. | ||
| - | ===Non-SPC, related links=== | + | ==[[Software:PeptideAtlas|PeptideAtlas]]== |
| - | *[http://gaggle.systemsbiology.org The Gaggle project]: The ISB's data interaction, visualization, and exploration system, increasingly integrated with the [[Software:TPP|TPP]] | + | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides |
| - | *[http://www.cytoscape.org Cytoscape Project]: Network visualization tool, integrated with the Gaggle. | + | identified in a large set of tandem mass spectrometry proteomics |
| - | *[http://www.peptideatlas.org PeptideAtlas]: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB. | + | experiments. Mass spectrometer output files are collected for human, mouse, |
| - | *[http://www.systemsbiology.org/Resources_and_Development/Current_Course_Offerings/Introduction_to_Systems_Biology Intro to Systems Biology course] offered at the ISB | + | yeast, and several other organisms, and searched using the latest search |
| - | + | engines and protein sequences. All results of sequence and spectral library | |
| - | == Wiki Guidlines == | + | searching are subsequently processed through the Trans Proteomic Pipeline to |
| - | # These tools change rapidly. Please include the version when describing anything. | + | derive a probability of correct identification for all results in a uniform |
| - | # These pages should '''not''' be used to report bugs. Please use the appropriate support avenues | + | 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 | |
| - | 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. | + | 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.
