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

Exercise DM1


Setting up a data dependent follow-up task


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

Install Mascot Daemon on your laptop by following this procedure.

If you want to use the Matrix Science public web site, you will need to enter a user name and password for Mascot security because guest users are not allowed to submit searches from Mascot Daemon. The user name is web_training and the password is Pep71de.

daemon configuration


Follow the tutorial in Mascot Daemon. If you are new to Daemon, start at the beginning. If you have used Daemon before, then jump down to the section starting with "Example of a data dependent follow-up task".

The login for the public web site has very limited privileges. You can only search SwissProt using small data files, which is sufficient to work through the tutorial.


  • The free public Mascot Server requires a valid email address, which has to be entered in the Daemon parameter set
  • Remember that on-line HELP is available for Daemon, just press F1


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