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Mascot is a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases. Mascot is unique in that it integrates all of the proven methods of searching, including:

  • Peptide Mass Fingerprinting, in which the only experimental data are peptide mass values
  • Sequence Query, in which peptide mass data are combined with amino acid sequence and composition information
  • MS/MS Ion Search, which uses uninterpreted MS/MS data from one or more peptides

For details on the search algorithm as well as a freely accessible web version (with some limitations on the number of queries that can be submitted at any time) please visit the MatrixScience web site.


Mascot is installed on a quad-core Linux server and can be accessed at You will need to obtain a user name and password to access this search engine.

More information

For more information about getting access to Mascot, please contact the license holder, Dr. Ken Greis (UC Genome Research Institute). In case of technical difficulties, please contact BMI Helpdesk