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

Exercise MSMS1


Use an error tolerant search to find unusual modifications, sequence variants, and non-specific cleavage.


User access to any Mascot server, including the Matrix Science public web site


Perform an automatic error tolerant search of the supplied MGF format peak list against Swiss-Prot with a taxonomy filter of Mammalia. Use Trypsin, 2 missed cleavages, 0.5 Da / 0.5 Da, no modifications, and the ESI-QUAD-TOF instrument.


Right-click this link: qtof10348.mgf, and choose Save target as or Save link as.


  • Use the yellow pop-ups to try and decide which modifications or substitutions may have caused the mass deltas


  1. Try to explain as many as possible of the additional error tolerant matches
  2. Are there any that you cannot explain or do not believe?
  3. Which modifications, if any, should have been selected for the first pass search?


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