Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Exercise MSMS2


Investigate the Protein Family report and run a target-decoy search to determine false discovery rate.


User access to any Mascot server, version 2.4 or later, including the Matrix Science public web site.


Data from an Quadrupole TOF instrument for human proteins digested with trypsin. Cysteine residues reduced and alkylated with iodoacetamide (+57), some deamidation at N and Q. Search Swiss-Prot with precursor tolerance of 0.4 Da and fragment tolerance of 0.2 Da. Select a decoy search.


Right-click this link: MSMS2.mgf, and choose Save target as or Save link as


  1. Do you get better sensitivity at a given FDR using the identity threshold or the homology threshold?
  2. Do you get better sensitivity searching the whole of SwissProt or just the human entries?
  3. Do you think there is evidence for both ACTB_HUMAN and ACTA_HUMAN?
  4. How many proteins are you confident are present in this sample?


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