mass spectrometry–based proteomics database search algorithm

• Windows: Microsoft .NET Framework 4.0 Client Profile or higher (4.5 or higher recommended)
  • Thermo MSFileReader for Thermo version
• Linux / Mac OS X: Mono 2.8 or later

• In revision 83 and later, sites inducing and preventing cleavage must be separated by commas in proteases.tsv, since multi-amino acid sites are now supported.
• In revision 108 and later, proteome databases may be UniProt XML files in addition to FASTA files to support G-PTM searching.
  • When an XML file is loaded, its modifications will be read (masses are read from ptmlist.txt), added to your variable modifications list, and checked by default.
• In revision 167 and above, an extra column was added to modifications.tsv to allow for neutral loss modification searching.
• In revision 255 and above, mzIdentML support necessitated the need to link every modification to UniMod. Therefore, two extra columns, 'UniMod Accession Number' and 'UniMod Name', were were added to modifications.tsv.