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

Exercise DIS2


Submit a search of LC-MS/MS data from Distiller and use de novo on a spectrum that failed to get a match


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. Use this serial number to register: 38EL-C6E7-U73R


The Masslynx raw file qtof10348.raw and the Distiller project file qtof10348.rov need to be in the same directory. Open the project file in Distiller.

Submit a Mascot search of all the peak lists and browse the results in Distiller. Use SwissProt, Trypsin, 2 missed cleavages, 0.5 Da / 0.5 Da, no modifications, and the ESI-QUAD-TOF instrument


Right-click this link: qtof10348.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 called qtof10348.raw)

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


  • To save time, you are starting from a project file where peak picking has been completed. You do not need to create a new Distiller project from the raw file (unless you wish to do so).
  • At the end of this exercise, save the project for use with exercise SQ3


  1. Try to find a peptide match for the summed spectrum of scans 1616-1624 using denovo
  2. How can you decide whether to accept the de novo solution?


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