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Major update to SearchGUI and PeptideShaker

After 3 years of work, SearchGUI (SG), a tool that performs protein identification using various search engines, and PeptideShaker (PS) for protein identification (which uses SearchGUI results) have been deeply updated and released in new major versions: 4.0.7 and 2.0.5, respectively. Furthermore, two new utility tools have been added to make the overall workflow more flexible:

  • Identification parameters for creating parameter files reusable by both SG and PS.
  • FastaCLI, which appends decoy sequences to a FASTA file in a format readable by SG and PS.

The number of changes and improvements made is large, a few highlights:


  • Support for spectrum files in mzML format.
  • Search engines updated to the most recent versions. Options updated accordingly.
  • FASTA file is now out of the search parameters.
  • Many more supported search engines parameters.
  • More detailed release notes.


  • Support for spectrum files in mzML format.
  • Internal refactoring, new internal database and more efficient data management.
  • Reduced file sizes and memory load.
  • More detailed release notes.

Thanks, Carlos Horro Marcos for your awesome work on the Galaxy integration.