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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"> | + | |
| - | '''Latest TPP version: 4.1.1, November 14, 2008. [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 download latest TPP software directly]; read the [[Software:TPP | TPP documentation]]''' | + | *SPC/TPP course: The next '''[http://www.proteomecenter.org/course.php 5-day SPC Tools Course]''' will be held ''April 27 through May 1, 2009'', at the ISB in Seattle. Space is limited so sign up soon! |
| + | *outreach at conferences: The next conference attended by SPC Tools developers will be '''US HUPO, February 22-25 2009''' | ||
| + | *active support: All users, both new and experienced, are encouraged to participate in our very active [http://groups.google.com/group/spctools-discuss spctools-discuss discussion group]. Daily 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 discussion group] for important notifications of updates to our software. | ||
| - | '''News:''' | + | ==[[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. | ||
| - | The TPP release system moved from cygwin to a true '''native Windows installation''' with the 4.0.0 release. We thank Insilicos for their continued major contributions to the project. The 4.0.0 release also brings full support for the new '''mzML 1.0 standard''', a joint effort of the HUPO PSI, SPC, vendors, and others. | + | ==The [[Software:TPP|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. The TPP is | ||
| + | available on Linux and Windows systems and builds on Mac OS X as well. The 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); | ||
| + | * 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 ''4.1.1,'' released ''November 14, 2008''. [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 download latest TPP software directly] | ||
| + | *Additional [[Software:TPP | TPP documentation]] | ||
| - | *The next '''[http://www.proteomecenter.org/course.php SPC Tools Course]''' will be held '''April 27 through May 1, 2009''', at the ISB in Seattle. Space is limited so sign up soon! | + | ==The [[Software:Firegoose, Gaggle, and PIPE|Protein Information and Property Explorer (PIPE)]]== |
| + | After data processing with the TPP, the PIPE is a starting point for the next step in analysis of proteomic experimental results. It is a launching pad from where simple operations can be performed on this data and messages can be passed to other more sophisticated analysis software such as the Gaggle. | ||
| - | *'''Note: 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 Natalie (you should be able to find email contact through the spctools-discuss newsgroup website, see below.) | + | Once protein identifiers have been established with the TPP, the PIPE can perform several different operations on the list of IDs, including: mapping to other IDs (entrez gene, unigene, uniprot, etc.), Gene Ontology enrichment calculations (to see what biological processes are overrepresented in the list), annotation of the list to specific GO terms, and more. The PIPE can also serve as a data management tool, saving lists with user specified metadata (i.e., description of the data). |
| - | Please see the '''TPP [[TPP:Recent_Updates|Recent Updates]]''' page for more news items. | + | ==[[Software:Corra|Corra]]: Label-free MS1-based biomarker discovery pipeline== |
| + | Corra is open source software for discovering biomarkers by detecting differentially expressed features/peptides using a MS1 based processing pipeline. Corra has an extensible software architecture to plug-in new MS1 feature extraction alignment modules as well as statistical packages. | ||
| - | </div> | + | ==[[Software:TIQAM|TIQAM]]: Targeted Identification for Quantitative Analysis by MRM== |
| + | TIQAM supports hypothesis-driven biomarker validation by SRM (Selected Reaction Monitoring) for targeted proteomics. The TIQAM suite is a desktop application which assists in target selection and validation, and contains: | ||
| + | * TIQAM-PeptideAtlas, which interfaces with the public observed MS/MS database, PeptideAtlas; | ||
| + | * TIQAM-Digestor integrates TIQAM-PeptideAtlas output, pepXML files, and other data in order to select transition lists according to user-defined priorities; | ||
| + | * TIQAM-viewer provides a visual aid to analyze SRM-triggered MS/MS experiments, and allow users to catalog the validated transitions. | ||
| - | == SPC Software== | + | ==[[Software:SBEAMS|SBEAMS-Proteomics]]: Multi-experiment data management== |
| + | [[Software:SBEAMS|SBEAMS Project]]: SPC's high-powered LIMS database system has a proteomics module for managing and tracking large amounts (terrabytes) of data. | ||
| - | The SPC is committed to providing open-source, free software to support proteomics research. The | + | ==[[Software:PeptideAtlas|PeptideAtlas]]== |
| - | [[Software:Overview| SPC Software Overview]] page lists (almost) all of the open-source software projects produced at the SPC. Major projects include: | + | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides |
| - | * '''[[Software:TPP|TPP]]''': our proteomics pipeline software is described on the [[Software:TPP|Trans-Proteomic Pipeline (TPP)]] page. | + | identified in a large set of tandem mass spectrometry proteomics |
| - | **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. | + | experiments. Mass spectrometer output files are collected for human, mouse, |
| - | * '''[[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. | + | yeast, and several other organisms, and searched using the latest search |
| - | * [[Software:SBEAMS|SBEAMS Project]]: SPC's high-powered LIMS database system. | + | engines and protein sequences. All results of sequence and spectral library |
| - | + | searching are subsequently processed through the Trans Proteomic Pipeline to | |
| - | ==Links== | + | derive a probability of correct identification for all results in a uniform |
| - | ===SPC Links=== | + | manner to insure a high quality database, along with false discovery rates |
| - | *newsgroups: '''subscriptions highly recommended for SPC Tools users''' | + | at the whole atlas level. Results may be queried and browsed at the |
| - | **[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. | + | PeptideAtlas web site. The raw data, search results, and full builds can |
| - | **[http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | + | also be downloaded for other uses. |
| - | *[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]: The next course is scheduled for '''May 12-16, 2008''' | + | |
| - | *[http://tools.proteomecenter.org/software.php Seattle Proteome Center (SPC) general website]: about our organization. | + | |
| - | + | ||
| - | ===Non-SPC, related links=== | + | |
| - | *[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. | + | |
| - | *[http://www.systemsbiology.org/Resources_and_Development/Current_Course_Offerings/Introduction_to_Systems_Biology Intro to Systems Biology course] offered 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. | + | |
Revision as of 01:30, 29 January 2009
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.
Education, outreach, training and support
- SPC/TPP course: The next 5-day SPC Tools Course will be held April 27 through May 1, 2009, at the ISB in Seattle. Space is limited so sign up soon!
- outreach at conferences: The next conference attended by SPC Tools developers will be US HUPO, February 22-25 2009
- active support: All users, both new and experienced, are encouraged to participate in our very active spctools-discuss discussion group. Daily discussions range from installation support to advanced data processing questions and feature requests. Please also see spctools-announce discussion group for important notifications of updates to our software.
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.
The 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. The TPP is available on Linux and Windows systems and builds on Mac OS X as well. The 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);
- 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 4.1.1, released November 14, 2008. download latest TPP software directly
- Additional TPP documentation
The Protein Information and Property Explorer (PIPE)
After data processing with the TPP, the PIPE is a starting point for the next step in analysis of proteomic experimental results. It is a launching pad from where simple operations can be performed on this data and messages can be passed to other more sophisticated analysis software such as the Gaggle.
Once protein identifiers have been established with the TPP, the PIPE can perform several different operations on the list of IDs, including: mapping to other IDs (entrez gene, unigene, uniprot, etc.), Gene Ontology enrichment calculations (to see what biological processes are overrepresented in the list), annotation of the list to specific GO terms, and more. The PIPE can also serve as a data management tool, saving lists with user specified metadata (i.e., description of the data).
Corra: Label-free MS1-based biomarker discovery pipeline
Corra is open source software for discovering biomarkers by detecting differentially expressed features/peptides using a MS1 based processing pipeline. Corra has an extensible software architecture to plug-in new MS1 feature extraction alignment modules as well as statistical packages.
TIQAM: Targeted Identification for Quantitative Analysis by MRM
TIQAM supports hypothesis-driven biomarker validation by SRM (Selected Reaction Monitoring) for targeted proteomics. The TIQAM suite is a desktop application which assists in target selection and validation, and contains:
- TIQAM-PeptideAtlas, which interfaces with the public observed MS/MS database, PeptideAtlas;
- TIQAM-Digestor integrates TIQAM-PeptideAtlas output, pepXML files, and other data in order to select transition lists according to user-defined priorities;
- TIQAM-viewer provides a visual aid to analyze SRM-triggered MS/MS experiments, and allow users to catalog the validated transitions.
SBEAMS-Proteomics: Multi-experiment data management
SBEAMS Project: SPC's high-powered LIMS database system has a proteomics module for managing and tracking large amounts (terrabytes) of data.
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.
