This is the home page for your in-house Mascot Server, a powerful search engine that uses mass spectrometry data to identify and characterise proteins from sequence databases. To assist you, the help text for Mascot forms a substantial knowledge base concerning protein identification by MS.

If this is your first visit, start here. If you include results from Mascot in a publication, please cite either www.matrixscience.com or Electrophoresis, 20(18) 3551-67 (1999) (abstract).


Mascot incorporates a role based security model, which allows the system administrator to control which functionality is available to individual users. If security has been enabled, you may be prompted to log in if you attempt to access a page or perform a task that requires authorisation. If security is not enabled, which is the default, the following links will simply confirm this.

Whether or not Mascot security is enabled, in order to comply with the licensing conditions, access to this Mascot server must be restricted to authorised users. We strongly recommend that your server is protected by a secure firewall.

Mascot Utilities

Your system administrator may have restricted access to these utilities

Database Status
View the status of all the sequence databases. Links to database statistics, search status, log files, etc.
Search Log
A tabular view of the search log. Can be filtered to find specific search results.
Configuration Editor
Browser-based configuration editors, including security administration and sequence database management.

Mascot Daemon

Mascot Daemon is a client application which automates the submission of data files to a Mascot server. It runs under Microsoft Windows 2000 and later.
Install | Upgrade | Troubleshoot

Mascot Documentation

Help on using Mascot and understanding the results is contained in these HTML pages. Click on Help at the top of the page to browse the help topics or use the keyword search facility. The following documents are mainly of interest to system administrators.

Setup & Installation Manual Adobe Acrobat pdf
Release Notes Adobe Acrobat pdf