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

Exercise PMF2


A more difficult PMF search. Learn to expect the unexpected!


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


A protein (not alkylated) from a 2D gel spot, digested with trypsin, and analysed on a MALDI-TOF instrument. The instrument is supposed to be capable of 25ppm accuracy, but it has not been used for a long time and the person who ran the spectrum is a novice. The gel was run as part of a study of baker’s yeast, (Saccharomyces Cerevisiae). The data file contains a list of MH+ values.


Right-click this link: PMF2.txt, and choose Save target as or Save link as


  • Take the settings from the first exercise (PMF1) as a starting point
  • The protein sequence is in SwissProt
  • A strong match


  1. What can we learn from this result?
  2. What advice would you give to the person who ran the spectrum?


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