Mascot database search FAQ

  1. How should I cite Mascot in a publication?
  2. Why are the graphics missing from report print-outs?
  3. Why do I get an error message about "max number of ion values 10,000" when I know that the spectrum has far fewer peaks?
  4. Why is there a long delay after submitting a Mascot search form before the progress report appears?
  5. What is the relationship between Mascot and Mowse?
  6. What limits apply to searches submitted to the public Mascot server?
  7. Can I save search results?
  8. How long are search results retained on the public Mascot server?
  9. What platforms are supported by Mascot?
  10. Is it possible to add a new modification?
  11. What is the public web server hardware and software?
  12. Can I get a demo copy of Mascot?

  1. How should I cite Mascot in a publication?

    The primary publication is Perkins, DN, Pappin, DJ, Creasy, DM and Cottrell, JS, Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20(18) 3551-67 (1999).
    The abstract can be found here.


  2. Why are the graphics missing from report print-outs?

    The usual cause of this problem is that Internet Explorer is configured to Check for newer versions of stored pages on Every visit to the page. To fix this, choose Internet Options from the Tools menu. On the General Tab, in the Temporary Internet Files frame, choose Settings. Under Check for newer versions of stored pages, select Automatically. (If the graphics are missing in the browser, this is a different problem. It probably means you have an in-house Mascot server and the GD graphics library is not installed).


  3. Why do I get an error message about "max number of ion values 10,000" when I know that the spectrum has far fewer peaks?

    You are uploading peak lists, i.e. centroided mass values, aren’t you? Uploading profile data will (i) take a very long time (ii) give unpredictable, usually very bad, results.


  4. Why is there a long delay after submitting a Mascot search form before the progress report appears?

    Are you uploading a data file? If so, this delay may be entirely due to the file upload time. Some browsers are better than others at showing signs of activity during file upload. If the delay doesn’t seem to correlate with data file size, then maybe you’re hitting the server at a very busy time.


  5. What is the relationship between Mascot and Mowse?

    Mascot was developed from Mowse, and incorporates all of its functionality. You can find a brief history of Mowse here.


  6. What limits apply to searches submitted to the public Mascot server?

    The public Mascot server gets very busy, so we have to limit the time taken by individual searches. The current limits are:

    • Maximum of 2 simultaneous searches per user
    • Maximum file upload 20 Mb
    • Maximum of 1200 spectra in a single MS/MS search
    • Cannot select enzyme type ‘None’

    We also request that you do not submit more than one long running search at a time. Long running search means:

    • More than 5 variable modifications or
    • Any search of an EST database

    Once you get the results back, either directly or by email, it’s safe to submit the next search.

    If you really need to perform a no enzyme search, e.g. for endogenous peptides, email support@matrixscience.com and we will provide a log-in that allows no enzyme searches of up to 5 spectra.


  7. Can I save search results?

    See the help page for Sharing Result Reports.


  8. How long are search results retained on the public Mascot server?

    We don’t systematically delete old results files, but we don’t guarantee to keep them, either. They may disappear because of a hardware failure or because we run out of disk space. If your results are important, you should consider licensing Mascot for use in-house. See the Products pages for further information.


  9. What platforms are supported by Mascot?

    The current release of Mascot can be installed under Microsoft Windows (Vista and later) and Linux on Intel and AMD. The operating system must be 64-bit.


  10. Is it possible to add a new modification?

    The list of modifications used by Mascot is taken directly from the Unimod database. If you want to add a new modification to Unimod, you can do so, and you then become the curator of the new record. The Mascot modifications list is updated from Unimod each weekend.

    Note that only selected modifications are displayed by default in the Mascot search form. If you want to see the complete list, you must check ‘Display all modifications’.


  11. What is the public web server hardware and software?

    The Matrix Science web server runs Mascot searches on an IBM eServerTM BladeCenterTM. Twelve blades are used for searches, each containing dual 2.83 GHz quad core E5440 processors and 16 GB memory. The operating system is Debian Linux. Our Apache web server runs on a separate, dual processor PC with a 1.6 TB RAID array for storing search results.


  12. Can I get a demo copy of Mascot?

    We encourage everyone to use the web site for evaluation purposes. The package is fully functional and the databases are updated regularly.