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

Exercise PMF4


To investigate how PMF mixtures are reported


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


MALDI-TOF data from a 2D gel spot. Protein(s) are from yeast. Enzyme trypsin, state of cysteine unimportant, mass tolerance 100 ppm. The data file contains a list of MH+ values


Right-click this link: PMF4.txt, and choose Save target as or Save link as


  • Try searching SwissProt and NCBInr with and without a taxonomy filter


  1. What are the effects of database size?
  2. How many components are you confident are present?
  3. Does the search engine report a choice of mixtures? If so, what does this mean?


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