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

Mascot Server version 2.3

Known Issues

ActivePerl 5.10 build 1007 and IIS

There appears to be a problem with the installer for ActivePerl 5.10 build 1007. It fails to create a handler mapping for Perl in IIS. In the case of IIS 7, there is a further problem with failing to set the response buffer size, which means that larger searches are prone to fail with HTTP error 400 (Bad Request). Until these issues are resolved, we recommend installing ActivePerl 5.10 build 1006 from the Mascot program CD. (Does not apply to Apache web server.)

AB SCIEX ProteinPilot 3.0 and earlier

For AB SCIEX ProteinPilot 3.0 and earlier, in the options section of mascot.dat, change the value of

ProteinFamilySwitch 300
ProteinFamilySwitch 1000000

This is to prevent the results being returned by default in the new Protein Family Summary report format. If you want to work with the Protein Family Summary report in a web browser, select it from the drop down list in the format controls and choose Format As.

Installation Tips

Windows Vista / 2008 / 7: It is essential that IIS is correctly configured before installing Perl or Mascot. Refer to Chapter 3 of the Installation & Setup Manual for details.

ActivePerl: Perl 5.6 is no longer supported. You cannot perform a single-step upgrade from ActivePerl 5.8 or earlier to ActivePerl 5.10. You must uninstall the earlier version before installing Perl 5.10. As a precaution, it is also worth deleting the Perl application directory after the uninstall step.

Windows update procedure

All version 2.3.x patches have been collected into a single executable file. This will update earlier 2.3.x versions to the latest revision. It will not update files from 2.2.x and earlier versions.

Note: If the service pack needs to replace any configuration files or Perl scripts that you have modified, it will move your modified file to a Mascot sub-directory called _install_backup. Inspect any files placed in this directory to see whether you wish to merge your changes into the updated files.

  • Locate your original Mascot installation CD, which may be required during the update
  • On the Mascot Server PC, as a user with Administrator privileges, click on the appropriate download link and either choose Run or Save the file to your local hard drive and then execute it.
  • After the patches have been installed you can delete the executable.

Available Fixes

  • 2736: Error message unclear for failure to create ‘daily’ result directory
  • 2792: Suspect NA insertion and deletion broken in error tolerant search
  • 2830: Results from ET search of NA database failing to record some NA substitutions
  • 2848: Browser problems in Protein Family Summary (mostly MSIE6)
  • 2849: Modality problems in Protein Family Summary
  • 2853: Performance and memory usage improvements in Protein Family Summary
  • 2854: Minor Daemon layout issues when window resized
  • 2863: Interface details and improvements in Protein Family Summary
  • 2868: Cannot submit multiple variable modifications using search form in MSIE 6
  • 2869: Incorrect modifications reported in Cluster mode with some Quant methods
  • 2871: master_results_2 won’t open data files if InterFileBase/RelPath is outside Mascot install
  • 2872: Test of significance of fold change wrong for weighted average protein ratio
  • 2873: Save as HTML in Protein Family Summary doesn’t work well
  • 2875: nph-mascot opens hundreds of files when search is multi-database
  • 2876: bzip2.exe and percolator.exe don’t work from in Windows XP
  • 2877: URL argument problems in Protein Family Summary
  • 2880: EST crashes with sequences with less than 4 bases
  • 2881: Uploading a file with a file name less than 4 characters can cause a crash
  • 2882: Error when try to search mzML file which references the indexed form of the schema
  • 2883: Family report should split fasta name at first underscore
  • 2884: Peptide view reports unexpected difference between Mr from result file and calculated mass when fixed and variable mods have same specificity
  • 2885: Variable mod in form and fixed mod in quantitation method not allowed
  • 2886: Crash if select variable mod with multiple specificities and fixed mod with one of the same specificities
  • 2889: emPAI not shown in Protein Family Summary if quantitation method in use
  • 2890: Protein Family summary: collapse all doesn’t work in MSIE 8
  • 2892: Daemon reports POST The operation timed out and pauses task
  • 2895: Some scripts are using percolate_use_rt as the URL argument label, should be percolate_rt
  • 2897,P638: MGF parameters scans, rawscans, rtinseconds and index get discarded in a repeat search
  • 2900: In Protein Family Summary, (i) quantitation format options should include unique peptides checkbox, (ii) should list frame number for NA search unless mixed
  • 2901: Implement "Find page N" and "Find hit N" in Protein Family Summary
  • 2907: If REPORT is present but has no value in results file, Protein Family Summary fails to show anything
  • 2908: Mascot Daemon reports "Search did not return any matches" when Percolator=1 in mascot.dat
  • 2909: "matrixMkdir()" fails too easily if one of the directories on the path is not readable but is traversable
  • 2910: Error tolerant NA search does not reject I/L Q/K matches, etc., for substitution, insertion, deletion
  • 2912: In family report, need to cross-reference query peptides above homology to other families
  • 2917: Daemon reports ‘empty document returned’ when retrieving results (timeout)
  • 2920: Narrow taxonomy range causes idle cpus on SMP box / busy cluster Master
  • 2923: Export script needs to support Percolator
  • 2926: Divide by zero error when opening iTRAQ report with normalisation = weighted if all peptide ratios for a protein are negative
  • 2927: Mutex error (WaitForSingleObject) – error code: 6 (cluster mode only)
  • 2929: Cannot perform a repeat search of data with IT_MODS defined at spectrum level
  • 2933: ms-gettaxonomy post request crash with unknown species
  • 2934: Rare exit with error or hang in cluster mode
  • 2935: ms-searchcontrol.exe shouldn’t use or report reptype any more
  • 2936: Export script creates invalid MGF with embedded INSTRUMENT= and RULES=
  • 2937: Mascot Daemon passes unsuitable loglevel to Mascot Distiller.exe for quant
  • 2938: Support for indexed RAWSCANS, SCANS and RTINSECONDS
  • 2939: Error tolerant search not filtering out mods less than TOL – documentation error.
  • 2940: Infinite recursive function call loop if locking errorlog.txt fails
  • 2942,P645: Can’t load family report for an ET search with 0 < ignoreIonsScoreBelow < 1
  • 2943,P641: Family report for Unigne clustered database painfully slow
  • 2944: Export script needs to emulate family report
  • 2945: Internal Mascot error (modifications overflow) pl=10, plmax=9 [M00140]
  • 2946: takes very long time to open report with just one query that happens to be found in over 18,000 proteins.
  • 2947: Family report for database where Unigene enabled but not selected is adding UNIGENE=None to Protein View URL
  • 2948: Daemon merge of MGF can occasionally produce corrupt output
  • 2949: Mascot Daemon needs to support MDRO "MultiFileScanNumbering"
  • 2950,P644: Need tag to pass session_id and task_id to external processes called by ExecAfterSearch
  • 2954,P629: Find facility does not find some peptides when searching by sequence
  • 2955: mzIdentML export fails if select Matched Fragment Ions for search that includes non-metabolic quantitation method
  • 2956: Increase post request upload limit for ms-gettaxonomy.exe and ms-getseq.exe from 10k to 10Mb
  • 2959: Peptide View can display wrong score for non-ET match in ET search
  • 2961: Error tolerant match can have slightly higher score than identical non ET match
  • 2963: If you cut one or more dendrograms, this should persist when swapping to the quantitation tab and back to the proteins tab
  • 2964: Error during Windows installation: ParseIISConfig: Unsupported protocol: net.tcp
  • 2965: MGF with more than 30 kB per spectrum gives error: Missing ion intensity value on line 6800180 of input file [M00430]
  • 2966: should cache protein descriptions
  • 2969: NCBI query.fcgi no longer accepts gi| prefix
  • 2970,P655: Order of MetOx neutral losses make small change to peptide match score
  • 2972: "Error: Can’t find the session file requested" when viewing quantitation tab in Windows 7
  • 2974: If a family has many hundreds of proteins, no dendrogram is shown
  • 2976: Infinite loop in when expanding subsets node for protein with 5045 subsets
  • 2987: Revert to full matrix inversion for reporter isotope correction
  • 2988: Cannot repeat PMF search from ‘Wot no results’
  • P369: No documentation for ms_customproperty
  • P461: ms_umod_configfile getElementByName() hangs if called with null argument
  • P596: Orphaned ms_enzyme lacks will to live
  • P614: ms_aahelper.createPeptide doesn’t support #varmods > 9
  • P624: Family grouping always displays top scoring protein even though it is actually subset
  • P626: Family grouping can treat a protein as a subset when it should be a family member
  • P627: ms-createpip.exe crashes when processing a 15N file (or any other metabolic labelling)
  • P628: Counts of matches and sequences above sig threshold wrong for error tolerant search results
  • P630: Accession strings with spaces in are truncated when loading proteins from cache
  • P632: Add getFlags2 to ms_peptidesummary
  • P633: MinPepLenInPepSummary not used for family grouping
  • P634: Misleading error message that "mascot.dat" file does not exist
  • P635: Support for merging multiple results files
  • P636: Null accession crashes parser when creating summary object
  • P639: add function ms_mascotresfile::enumerateQuerySectionKeys
  • P647: Support for Python under Linux
  • P649: getProteinDescription() and getProteinMass() can be slow
  • P652: aahelper->CreatePeptide fail
  • P653: File where creating from cache is much slower than without using cache
  • P654: Concurrency issue on Windows when using ms_session
  • P656: Parser fails if two processes try to create a cache directory at same time