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

Exercise DIS1


Process a file of MS data in Distiller and submit a PMF search


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

Install Mascot Distiller on your laptop by downloading the appropriate installer.

When Distiller is first launched, you will be prompted to register on-line and get a temporary 30 day licence by email. Please contact us at to get a trial licence.


Create a new project for a Waters Masslynx format file Select maldi-pmf.raw and the M@ldi processing options. Process the file, and submit a search to a Mascot server. Search SwissProt with a tolerance of 0.4 Da, trypsin, 1 missed cleavage, and Carbamidomethyl (C) as a fixed modification.


Right-click this link: maldi-pmf.exe, and choose Save target as or Save link as. The downloaded file is a self-extracting archive, double-click to unpack the data file (which is really a folder): maldi-pmf.raw


  • The data file includes both sample and calibrant scans. Make sure you search the peak list for the sample.
  • Correct match has a score of approximately 200
  • Make sure you choose the correct processing options, which are not the default.


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