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| Revision as of 01:08, 20 June 2006 Gehlenbo (Talk | contribs) (Added news and announcements section.) ← Previous diff |
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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. |
| - | <div class="MainPageBG" style="border: 4px solid #ffad08; padding: .5em 1em; color: #000; background-color: #ffffff; margin: 3px 3px 0; text-align: left"> | + | ==Education, outreach, training and support== |
| - | '''Wiki Announcements''' | + | *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] | ||
| - | * Please create an account (link on the top right of the page) before you start editing pages. Thanks! | + | *Outreach at conferences: |
| + | ** None scheduled at the moment | ||
| - | '''Wiki 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. |
| - | {{Template:News}} | + | ** Please also see [http://groups.google.com/group/spctools-announce spctools-announce group] for important notifications of updates to our software. |
| - | </div> | + | |
| - | == Nils' Wiki Structure Proposal == | + | ==[[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. | ||
| - | I assume that this wiki will mostly be used to document specific tools that have been developed by the group. I propose the following structure: | ||
| - | # A standardized template to describe the main properties of a tool could help to provide a quick overview that is not hard to maintain. A good example for this is the [http://en.wikipedia.org/wiki/Template:Infobox_Software infobox software template]: [http://en.wikipedia.org/wiki/GIMP GIMP], [http://en.wikipedia.org/wiki/Microsoft_Office_Excel Excel]. Of course we could change this a little to fit our needs. | + | ==[[Software:TPP|Trans-Proteomic Pipeline (TPP)]]: MS2 proteomics validation and analysis== |
| - | # Each page describing a tool or process should contain a section "Comments" where developers/users can post messages regarding their experience with the tool. This could also include tips on how to use it on a particular operating system etc. but should not be used to report bugs. | + | The Trans-Proteomic Pipeline (TPP) is a completely free software |
| - | # The main page should feature a "News" section where we post latest additions and changes to the wiki. (I know that there are other ways to find out what has been changed but this is the most convenient for people who are not familiar with wikis.) | + | solution for MS/MS-based shotgun proteomics analysis with a well-established |
| - | # A prefix such as for example "Prequips:" should be used so we can have multiple instances of pages such as "FAQ", "Installation" etc. on this wiki. | + | 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]] | ||
| - | Any comments welcome! | ||
| - | === Things that are missing === | + | ==[[Software:PeptideAtlas|PeptideAtlas]]== |
| - | + | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides | |
| - | * file upload | + | identified in a large set of tandem mass spectrometry proteomics |
| - | + | experiments. Mass spectrometer output files are collected for human, mouse, | |
| - | == Getting started == | + | yeast, and several other organisms, and searched using the latest search |
| - | + | engines and protein sequences. All results of sequence and spectral library | |
| - | Consult the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for information on using the wiki software. | + | searching are subsequently processed through the Trans Proteomic Pipeline to |
| - | + | derive a probability of correct identification for all results in a uniform | |
| - | * [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list] | + | manner to insure a high quality database, along with false discovery rates |
| - | * [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | + | at the whole atlas level. Results may be queried and browsed at the |
| - | * [http://mail.wikipedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] | + | 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.
