Mascot Server version 2.4

Updating and upgrading procedures

Known Issues

Database Manager

Database Manager cannot download Fasta files generated by Uniprot database queries, such as Uniprot proteomes. The work-around is to download the Fasta file manually, as described here. From November 2021, Database Manager is also unable to download files for most predefined definitions. This is because the download URLs were changed from FTP to HTTP, and some third-party servers such as NCBI redirect HTTP to HTTPS, which Database Manager in Mascot 2.4 does not support. The workaround is to download and extract the files manually. Please refer to sequence database setup for databases of interest.

Perl 5.8 or 5.10

With Perl versions 5.8 or 5.10, if a predefined database definition is enabled in Database Manager but the download is cancelled, it is possible to get the following fatal error

Cannot handle date (00, 00, 00, 01, 0, 2070) at ../bin/modules/Util/Time.pm line 89

In 2.4.01 (but not 2.4.00), the same error may also occur when viewing the Peptide Summary or Protein Family Summary report. If the results file does not store protein taxonomy data (new in 2.4), the report script checks whether the database is online for looking up taxonomy data. This check follows the same code path as the Database Manager functionality.

If you encounter this error, the fix is to update to ActivePerl 5.14, as included on the Mascot Server 2.4 program CD. After updating Perl on Windows, locate Mascot Server in the programs and features section of the Windows control panel and choose Repair. Instructions for installing ActivePerl on Linux can be found on page 6 of the manual. You will also need to follow steps 1 and 2 (only) of the Installation Script, as described on page 11 in the manual, to create a new soft link for the Mascot Parser Perl module.

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: ActivePerl versions 5.8 (build 820) through 5.14 are supported. ActivePerl 5.14 is the recommended version and installers are included on the Mascot program CD.

Windows update procedure

All version 2.4.x patches have been collected into a single executable file. This will update earlier 2.4.x versions to the latest revision. It will not update files from 2.3.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.
  • x86 for 32 bit Windows: MascotServer_SvcPack_2_4_1.exe (17 Mb)
  • x64 for 64 bit Windows: MascotServer_x64_SvcPack_2_4_1.exe (22 Mb)
• After the patches have been installed you can delete the executable.

Fixes included in this patch

• 10757: ExecAfterSearch bugs relating to repeat arguments and environment variables
• 10759: Need to export site analysis data
• 10862: Upgrade exported mzIdentML to version 1.1.0
• 11013: mzIdentML fails to validate with error: PeptideHypothesis: No match found for key-sequence
• 11057: export_dat_2.pl should not assume results file is in ../data
• 11058: Use Parser in enumerating repeat search parameters
• 11062: ProteinView should take the taxonomy from the .dat file rather than use ms-gettaxonomy.exe
• 11065: Huge PMF score for single large protein with noenzyme
• 11066: Add preferred taxonomy control to all summary reports
• 11067: Boolean expression in Report Builder can have an empty clause
• 11068: “Only error tolerant” should only show ET matches that score higher than non-ET
• 11070: Yellow query background in Protein Family Summary is truncated
• 11072: More intuitive menu structure in Database Manager
• 11073: Better feedback from testing database configuration in DB Manager
• 11075: Untangle Catch-22 in setting up a database with reference file in DB Manager
• 11080: Empty task list has redundant headers in DB Manager
• 11082: Clarify FASTA file name collision rules in DB Manager
• 11085: More logical wizard sequence when synchronising databases in DB Manager
• 11087: Apply predefined definitions updates even when no new FASTA file is available in DB Manager
• 11088: Add UniGene configuration interface in DB Manager
• 11090: Fewer mouse clicks when editing parse rules in DB Manager
• 11091: DB Manager should download if there are no files in current directory
• 11093: Allow editing of filename pattern in DB Manager
• 11095: Database directory displayed incorrectly on occasion in DB Manager
• 11099: More detailed I/O error reporting on Windows for DB Manager
• 11101: If the fasta file being downloaded changes during the download, should retry in DB Manager
• 11113: If CronEnable is 0, no warning is given in task list in DB Manager
• 11115: Provide interface to the tree/hierarchical cluster method of the C Clustering library
• 11117: Confusing error message when FASTA filename case is wrong in DB Manager
• 11118: Site analysis doesn’t handle near isobaric mods correctly
• 11123: Negative mass values in proteins section of result file
• 11124: GET request URLs exceed 2 kB in Report Builder
• 11151: Fix inconsistent case when importing mascot.dat in DB Manager
• 11153: Add the number of proteins used in error tolerant search to the results file
• 11159: Disable option for file URLs when creating custom definition if Internet access is disabled
• 11162: Retry URI in DB Manager points to db_manager.pl, not ms-status.exe
• 11167: client.pl result_file_mime2 creates corrupt gz file
• 11168: “Invalid argument” error when downloading database files
• 11173: Fatal error when click on query number link for query with no matches
• 11179: mascot.dat with errors causes Database Manager initial import to fail
• 11180: DB Manager doesn’t download a missing reference file
• 11182: Add streaming compress mode to ms_zip
• 11185: Support for multiple modifications on one site in ms_aahelper class
• 11186: Manual error tolerant search gives M00323 error
• 11187: “Protein sequence has changed” error for manual ET of NA database
• 11189: PMF search results don’t have protein taxonomy data
• 11190: getProteinTaxonomyIDs() should return taxonomy IDs for PMF results
• 11192: FASTA and reference URL textbox order varies in DB Manager
• 11193: Exporting large data sets very slow possibly due to multiple ms-getseq.exe calls
• 11194: Opening protein family reports fails with “Node.pm line 882″ error when using Perl 5.12
• 11195: Export gets into endless loop if show subsets true and no protein grouping
• 11201: ms_aahelper constructor using a results file needs path(s) to unimod schema
• 11202: In DB Manager, if the remote file doesn’t exist, confusing message “HEAD request succeeded for …, but GET did not; cannot continue”
• 11204: Peptide view link in Protein Family Summary doesn’t have sessionID
• 11207: When no taxonomy defined for NA database, ms-getseq with XML gives an error
• 11212: Illegal value for ‘_sigthreshold’: “0.00000″ when try to set FDR to selected value
• 11221: SwissProt_AC definition in databases_1.xml incorrect
• 11222: Problems with annotation settings in DB Manager
• 11225: DB Manager: Copying a database definition may fail with “taxonomy entry does not exist”
• 11231: Version file parse rule kinks in DB Manager
• 11248: Error tolerant match tooltip in protein view redirects to “Illegal value for mimetype”
• 11251: “Resource not found” error after percolator fails
• 11256: “Length of longest sequence” in stats file and errorlog incorrect when there are sequences longer than MaxSequenceLen
• 11266: Add a function to return the number of proteins used in an error tolerant search
• 11269: If charge is 9+ or more, product ion masses incorrect
• 11271: Predefined definition directory is missing from mascot.dat when download task failed
• 11274: Use old-style mkpath() API when Perl is 5.8.8 or older
• 11275: Additional return values for getThresholdForFDRAboveIdentity and getThresholdForFDRAboveHomology
• 11278: IE 9 and Firefox 10 performance improvements
• 11282: Duplicate group with prettyrank=1 master not expanded when searching by query
• 11284: The sequence directory might not be created during installation
• 11286: Peptide view shows wrong expect value when qmatch < 20
• 11288: Database Manager: cannot set ‘None’ for taxonomy if it has previously been ‘Fasta file’
• 11290: Disable the MIME-sniffing feature of Internet Explorer 8
• 11293: Export script creates invalid MGF with embedded INSTRUMENT= and RULES=
• 11295: Quantitation method editor fails to find mod with name that is substring of another mod
• 11301: ms-gettaxonomy.exe should support –sessionID
• 11305: Error from search: Requested query X, hit -64 in function ms_proteinsummary::getPeptide
• 11306: Protein accession can be different when Peptide View invoked from Protein View
• 11307: HEAD requests to uniprot.org work again in DB Manager
• 11309: ms-getseq.exe refuses to accept 6 parameters, so cannot specify frame number and session_id
• 11316: Add support for neXtProt in database manager.
• 11318: Auto decoy not working correctly for NA database