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

Mascot Server version 2.0

Known Issues

Two of the taxonomy files on the initial release CD (2.0.0) are old versions. If you are upgrading Mascot, and have existing databases other than MSDB that use taxonomy, (e.g. NCBInr), this will make taxonomy filtering less accurate. For example, if you choose human, you won’t miss any entries, but you may see additional entries in the results that are clearly not human. If this is a concern, please download the latest files from NCBI: Note that these files need to be unpacked into the taxonomy directory, not into the sequence database directory. Under Windows, you can use Winzip to uncompress and untar the files.

Installation Tips

Windows NT4 and 2000 (not XP or 2003) If the operating system is a clean install, the following error may be reported when you try to view any search result report:

Can’t load ‘../bin/auto/msparser/msparser.dll’ for module msparser: load_file:The specified module could not be found at C:/Perl/lib/ line 229.
at ../bin/ line 7
Compilation failed in require at D:\INETPUB\MASCOT\cgi\ line 105.
BEGIN failed–compilation aborted at D:\INETPUB\MASCOT\cgi\ line 105.

This problem is caused by a missing dynamic link library. The fix is platform dependent.

For Windows 2000, download msvcp60.dll by clicking on the following link. The file must be saved or copied to the directory C:\inetpub\mascot\bin\auto\msparser (assuming Mascot was installed on the default path).

For Windows NT4, download Vcredist.exe using the following link and execute it. The file size is approximately 1.8 Mb. Installation does not require any user input or actions other than re-booting the system on completion.

Windows update procedure

All version 2.0.x patches have been collected into a single executable file. This will update version 2.0.x to the latest revision. N.B. this executable will not update files from earlier versions.

Note that Windows NT must be updated using service pack 6a before applying this patch.

Modified scripts will not be patched. If you have modified any of the Mascot 2.0 Perl scripts, e.g., you must revert to the original scripts before applying this patch. The original scripts can be found on the Mascot installation CD, in the unpacked\cgi directory. After copying a file, right click it, choose Properties, and clear the Read-only checkbox.

  • Download and save the update program MascotPatch_20040823.exe (7.5 Mb) to the PC running Mascot Server.
  • As a user with Administrator privileges, start the update program.
  • Ensure that the Mascot directory has been correctly identified.
  • You can choose to apply all patches, (recommended), or just selected patches.
  • After the patches have been installed you can delete the executable.

Available Fixes

  • IgnoreDupeAccessions parameter enabled, allowing duplicate accessions in badly formed fasta files.
  • Fix for ‘permission denied’ error when multiple Daemon searches running concurrently.
  • Fix for sole etag() search reporting error and exiting.
  • Could report Pyro-glu (Q) when the N terminus was not Q.
  • Fixed problem if enzyme was Semi-trypsin and no modifications specified.
  • Don’t allow users to set priority above 0 because this can cause problems on some systems.
  • Lcq_dta shell script: Don’t submit ms-ms spectra without any fragment ion peaks to Mascot.
  • Lcq_dta shell script: Support -P argument in extract_msn.exe.
  • Fixed bugs relating to reporting of matches to ambiguous residues (B,X,Z).
  • Pass IgnoreIonsScoreBelow from to
  • Add user interface to for formatting options.
  • Tooltips problem with KDE browser resolved.
  • New Select report for very large searches
  • Fixed error message about using consistent syntax when trying to create archive report from a search where one or more of the USER parameters were not empty
  • Fixed spurious warnings about syntax errors in mascot.dat when URL or path name in WWW section contained underscore.
  • Firewall changes in XP SP2 would have stopped Mascot cluster mode.
  • Missing .ref (or .dat) file was fatal error.
  • Increase maximum number of tags and etags.
  • Not all modifications were iterated in error-tolerant search
  • Fixed problem with incomplete results from mixed tag / etag search.