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:

SearchGUI

• 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.

PeptideShaker

• 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.