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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.

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.

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.

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

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.