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

Mascot Server version 2.6

Updating and upgrading procedures

Known Issues

Installing on Windows 10 and Server 2019

Mascot Server 2.6 is fully compatible with most versions of Windows 10 and Server 2019.

We have had reports that when you install the October 2023 update to Server 2019 (KB5031361), Mascot may stop working. The symptoms are exactly the same as described below for Windows Server 2022. Please either update to Mascot Server 2.8 or later, or uninstall Windows update KB5031361.

Installing on Windows 11 and Server 2022

Mascot Server 2.6 is not fully operational on Windows 11 and Windows Server 2022. Functionality that fails:

  • Perl scripts fail immediately with HTTP error 502.
  • Downloading files from HTTPS URLs using in Database Manager fails with SSL error.

If Perl scripts fail immediately on your system, please install the September 2022 cumulative update for Windows. For Windows 11, this is KB5017328. For Windows Server 2022, this is KB5017316. We have observed that the cumulative update fixes the issue, but we do not have enough information to say what specifically caused the fault.

After installing the Windows cumulative update, you may find that downloading files from HTTPS URLs using Database Manager may succeed with some servers and fail with others. The cause of the fault is in a third-party Perl module, Net::SSLeay, shipped with Mascot. The fault appears as a warning or error in Database Manager similar to the below: 

Could not fetch file (type: taxonomy).
https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz: proxy=[proxy strategy "automatic" [...]]:
500 SSL upgrade failed: SSL connect attempt failed with unknown error 
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed

At present, the only solution is to update to Mascot Server 2.8 or later.

Updating a NIST library after July 2018

NIST revised the contents of all spectral libraries in July 2018. Unfortunately, library version numbers remained the same. The revised MSP files use a syntax for modifications and peak annotations that is at odds with the MSP specification. If you enable or update a NIST spectral library in Mascot 2.6, there are two separate issues:

  1. Existing library searches: Peptide View will fail to show the library spectrum in Spectrum Viewer even if the library is online. Results report is otherwise unaffected.
  2. New library searches: Library modifications are missing in the search results and in Protein Family Summary. View a match in Peptide Summary to see the full library metadata, which contains the modification information.

The issues will be fixed in Mascot 2.7. A workaround is to avoid updating NIST libraries. If you updated a library by accident, please contact Stephen Stein at NIST for a download link to the old-format MSP files.

Documentation updates

Installation & setup manual, chapter 12, pages 177-8: The commands to enable and disable security should read:

Windows
  ..\perl64\bin\perl enable_security.pl
  ..\perl64\bin\perl disable_security.pl

Linux
  ../perl64/bin/perl enable_security.pl
  ../perl64/bin/perl disable_security.pl

Updating from 2.4 or earlier

The list of modifications used by Mascot is taken from Unimod by downloading the database contents in XML format (unimod.xml). In Mascot 2.4 and earlier, if you wanted to change a modification or add a new one, this could be done using the Mascot Configuration Editor or, if you were very brave, by editing unimod.xml. The unsatisfactory aspect of this was that any changes were lost if you downloaded a fresh copy of unimod.xml.

This was improved in 2.5 by saving all changes to a separate file and merging this with the downloaded file to create the working copy of unimod.xml. The Modifications module of the Configuration Editor has a button (Check Unimod) which looks to see whether a newer unimod.xml file is available. If so, you can choose to download it. The downloaded file is re-named to master.xml and saved to the mascot/config/unimod directory. Any local changes you make using the Configuration Editor are saved to a separate file called usermod.xml in the same directory. When the Mascot Monitor service sees that either file has changed, it merges the two files to create a new unimod.xml in the mascot/config directory. (Note that this means you should never edit or update unimod.xml … your changes could disappear at any time.)

If you are updating to Mascot 2.6 from Mascot 2.4 or earlier, and only have a small number of changes to your local list of modifications, the easiest solution is to re-enter them one final time using the Configuration Editor. If you have a large number of changes, rename your old unimod.xml file to usermod.xml and copy it to mascot/config/unimod, over-writing the existing file. A few seconds later, a new unimod.xml will be created automatically in mascot/config. The only time this won’t work is if you had edited unimod.xml to create a new entry in the elements or mod_bricks sections. If this is the case, please contact support for guidance.

Installation Tips

Windows: It is essential that IIS is correctly configured before installing Mascot. Refer to Chapter 3 of the Mascot Server Installation & Setup Manual for details.

Linux: If you are unsure how to mount the ISO file, try something like this:

sudo mkdir /mnt/mount_point
sudo mount -o loop mascot_2_6_0_linux.iso /mnt/mount_point

Windows update procedure

All 2.6 patches have been collected into a single executable file. This will update from 2.6.0 or 2.6.1 to 2.6.2. It will not update version 2.5 or earlier to version 2.6.

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.

  • On the Mascot Server PC, as a user with Administrator privileges, click on the download link and either choose Run or Save the file to your local hard drive and then execute it.
    MascotServer_x64_SvcPack_2_6_2.exe (23 Mb)
  • After the patches have been installed you can delete the executable.

Linux update procedure

All 2.6 patches have been collected into a single archive. This will update from 2.6.0 or 2.6.1 to 2.6.2. It will not update version 2.5 or earlier to version 2.6.

  • Check that there are no searches running on the server
  • Kill ms-monitor.exe
  • Download the archive to /usr/local/mascot (or to wherever Mascot is installed)
    mascot_2_6_02_patch_x86_64-linux.tar.bz2 (96 Mb)
  • Unpack the files, replacing those from the earlier version, (the –backup option creates backups of the files that are overwritten)
    tar -jx --backup -f mascot_2_6_02_patch_x86_64-linux.tar.bz2
  • Ensure that the ownership of the files matches the user ID that your web server is configured to use. The .tar file has been created using root:root. The required ID when Apache is installed from a RedHat RPM will be apache:apache, and when installed on Ubuntu or Debian, it will be www-data:www-data
    find . -user root | xargs chown apache:apache
  • Launch a web browser, and navigate to the URL corresponding to install.html, e.g. http://your.domain/mascot/install.html
  • Follow the instructions on this web page and those that follow to perform some simple system checks and create or update the Mascot configuration file (mascot.dat).
  • Start ms-monitor.exe

Fixes included in this patch

  • 10732: Mascot needs to handle Windows processor groups correctly
  • 11096: Eliminate IgnoreDupeAccessions
  • 11511: Memory leak in ms-monitor.exe
  • 11557: Search crashing for Error Tolerant search
  • 12185: Export library matches in XML and CSV format
  • 12186: Export library matches in mzTab format
  • 12187: Export library matches in mzIdentML format
  • 12287: Loading peptide view from any protein view always reverts to hit 1
  • 12300: Report text search doesn’t work for some matches?
  • 12304: Unassigned tab doesn’t open when _usecache=0
  • 12358: Support HTTPS for database update file downloads
  • 12531: results_cache_status is not fail safe.
  • 12534: Spectral libraries bigger than 2Gb not useable with MSPepSearch
  • 12550: Would be useful to show a line number for error M00057
  • 12563: Crash if a mod has multiple peptide NL
  • 12636: Inhibit search submission until form fully loaded
  • 12574: The path to the compressed files for a SL library is not correct on the nodes
  • 12581: Licence info page (VIEWLIC) doesn’t support wide characters
  • 12595: Possible change of wording for Mascot Warning email to sysadmin
  • 12603: Roll-up of user interface feature requests for building a library from search results
  • 12605: Memory leaks in ms-monitor
  • 12607: Homology threshold or library threshold can be missing from query tooltip
  • 12613: Search log does not display wide characters correctly
  • 12615: dbman_scan_for_library.pl should handle individual files in a child process to improve robustness
  • 12619: IT_MODS at query level that are substitutions cause mass to be miscalculated
  • 12629: lib2nistcl on Linux has limit of 600k entries
  • 12635: Want a message in the log when a user clicks on the re-compress link in ms-status.exe
  • 12637: Highlighting in SVG graphic and table looks wrong
  • 12640: Cannot search a spectral library with no MW line
  • 12644: Build library from search results – taxonomy doesn’t work
  • 12645: If Windows Firewall service is not running, the installer fails to install the exception and rolls back
  • 12653: dbman_add_task.pl broken for predefined databases
  • 12654: Error: …mgf.tsv has an unexpected format: score is not within range (0,990) [M00582]
  • 12668: Roll-up of backend crawler changes (truncation, logging, import tracking)
  • 12671: Show column string in report builder is broken
  • 12680: Fixed mods not being added to library annotations
  • 12687: When downloading a new unimod.xml (using the button in ms-config.exe) also download the schema
  • 12691: Change "/HITS 100" to "/HITS 10" for MSPepSearch
  • 12693: Need to be able to specify wild card path to crawl in addition to date range
  • 12694: Crawler isn’t annotating all ion series
  • 12700: Incorrect p value reported under distribution graph for spectral library search if you change score threshold
  • 12703: Need to save the spectral library fragment tolerance in the results file
  • 12708: Linux installer uses incorrect path to msparser.pm
  • 12711: Don’t log successful calls to utilities as errors
  • 12712: varmods dumped in manual error tolerant search
  • 12713: Cannot display results of manual error tolerant search as protein family summary
  • 12723: Spectral library scoring improvements
  • 12725: Always annotate spectral libraries
  • 12726: Use of uninitialized value within %type in numeric gt (>) at export_dat_2.pl line 12241
  • 12727: Peptide view added fixed modification to spectral library match
  • 12728: Big Mascot search from Daemon with security enabled fails
  • 12741: When exporting search results with a UniGene index, "Argument "None" isn’t numeric in addition (+)"
  • 12742: MinPepLenInSearch should be written to result file
  • 12746: mzIdentML PeptideEvidence id needs to include database index
  • 12748: ms-status.exe returns an HTML-formatted error with Show=MS_DB_PATH
  • 12750: Crash with manual error tolerant search
  • 12751: Crash at start of search
  • 12752: If ResfileCache and ResultsCache are empty, master_results.pl will still try to create cache files
  • 12754: Database Manager may choose the wrong "latest" predefined definitions file if they all have the same last-modified time
  • 12774: Overflow problem when final field of search log contains very large amount of text
  • 12775: Crazy match from error tolerant search
  • 12782: Percolator 3.00 hangs or crashes on some files when PercolatorUseRT is true
  • 12786: Error when sorting unassigned tab by increasing query if unassigned tab contains more than one page
  • 12788: Rebuild the compressed files etc. for Spectral Libraries created with Mascot Server 2.6.0
  • 12789: Remove duplicate warning when adjusting FDR
  • 12794: Don’t show FDR and decoy link in Protein Family Summary if the decoy section is empty
  • 12798: Search crashes if is errorTolerant and against a spectral library
  • 12988: Protein view: Fatal Error protein sequence has changed since the search was performed
  • 13004: In Database Status, avoid autorefresh if user is not logged in
  • 13007: Protein sequence has changed since the search was performed (again)
  • 13036: Use of uninitialized value $delta in multiplication