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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

Education, outreach, training and support

  • SPC/TPP course:
    • A condensed (3-day) version of the course was given as part of the Bioinformatics for Proteomics EuPA course, held at ETH Z├╝rich, November 25th - 29th.
    • A 4 1/2 day course will be given at CINVESTAV in Irapuato, Mexico, February 3rd - 7th, 2014.
    • The next course in Seattle will be given on March 31st - April 4th, 2014. Registration is now open.
    • A four-day course was held prior to the HUPO World Congress in Yokohama, Japan, September 10-13, 2013.
  • Outreach at conferences: SPC Tools developers attended the 61st ASMS Conference in Minneapolis, MN (June 9th through 13th), and the 12th HUPO World Congress in Yokohama, Japan (September 14th - 18th).
  • 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 4.6.3, released July 2013.
  • 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.

SBEAMS-Proteomics is part of the SBEAMS (Systems Biology Experiment Analysis Management System) Project, which is a framework for collecting, storing, and accessing data produced by a variety of different experiments. These experiments can be managed separately but then correlated later under the same framework. This integrated system combines a unified relational database management system (RDBMS) back end, a collection of tools to store, manage, and query experiment information and results in the RDBMS, a web front end for querying the database and providing integrated access to remote data sources, and an interface to existing programs for clustering and other analysis. The knowledge stored while analyzing experiments remains easily accessible at later times and by other investigators to fully capitalize on previous work.

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.

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