Mascot Server Support

For help with search submission and result interpretation, either click on Help in the main menu or follow this link for an overview.

Version information

• Microsoft Windows 2008 / Vista / 2003 / XP / 2000 / NT4 2.2.04
• Mascot version 2.2 will be the final version to include support for Windows NT4
• Solaris 2.2.01
• Tru64 (HP Alpha) 2.1.03
• Mascot version 2.1 was the final version to include support for Tru64
• Irix (SGI MIPS) 2.1.03
• Mascot version 2.1 was the final version to include support for Irix
• Linux (i86) 2.2.04
• AIX (IBM Power 4, 5) 2.2.01

Updates

Updating Mascot from version 2.1.x or earlier to version 2.2 requires a full installation CD-ROM. Customers who are under warranty, or who have purchased extended support, receive new versions as soon as they are available. If you have allowed your support contract to lapse, please contact us for information on how to get back on track.

If you are running Mascot under Windows, patches and file updates can be downloaded from the links on this page.

If you are running Mascot under Unix, and see that a more recent version is available, please send an email to support@matrixscience.com containing sufficient information for us to verify that you are a licensed Mascot user, and we will email you a download link for the update for your specific platform.

Windows version 2.2.x

Installation Tips

Installation troubleshooter for Windows version 2.2.01 only.

Available Fixes

• 2191: Add /LARGEADDRESSAWARE flag for Windows
• 2233: Installer fails to set permissions on all files
• 2443: Progress reports are slightly off for NA searches with FRAMES
• 2444: Various minor Configuration Editor bugs
• 2447: Confusing error message from Daemon with security and Integra user
• 2448: get_params.pl fails with Integra system user when security is enabled on Linux
• 2452: More minor Configuration Editor bugs
• 2454: mod_file should be re-written whenever a process changes it
• 2457: Installer fails if IIS web site is bound to a specific interface or URL contains an IP address
• 2458: Need to set correct permissions on unimod.xml and quantitation.xml
• 2465: Mascot Daemon 2.2 no longer works with IIS integrated authentication (2.1 was OK)
• 2466: Need to leak bytes in additional place for quant reports to keep connection alive
• 2467: ms-monitor fails when shutting down under Windows with ms-lockmem enabled
• 2471: PMF speed improvements
• 2472: Multiple instances of too many ions error in mzData causes nph-mascot.exe to crash
• 2473: Cannot have space in lcq_dta.exe path name in Daemon
• 2477: Modifications defined locally in one spectrum being used for match in other spectra
• 2478: Perl scripts outputting http headers with charset=ISO-8859-1. Should be utf-8
• 2479: Matches being reported for invalid etags
• 2481: Peptide view and master results might show different set of potential modifications fro error tolerant match when 13C>0
• 2482: Speed improvements for etag searches
• 2484: Export help not clear
• 2485: getseq.pl takes a sessionID parameter, but doesn't pass it on to ms-getseq.exe
• 2486: New configuration file to support modification name aliases
• 2487: Improve support for Vista
• 2488: Installer needs to configure IIS 6 to enable cgi and x-cgi executables and Perl scripts
• 2489: The Mascot paths in the registry now have a trailing slash.
• 2494: Daemon fails to pass through Distiller error messages
• 2497: Mysterious crash while writing results file for nucleic acid search
• 2498: Improve error reporting in scripts when something goes wrong and a graphic is missing
• 2506: URL arguments for quant formatting not being passed to export script
• 2507: Problems with drag and drop to repeat a search in Daemon
• 2511: MS/MS search speed improvements
• 2512: primary_nl string could be incorrect if multiple peptide matches with identical scores
• 2519: State of hide error tolerant checkbox not passed to protein view
• 2520: Protein view and enzymes created by config editor are incompatible
• 2522: Increase range of charge states available in lcq_dta_shell
• 2524: Intermittent crash with integrated ET search and sequences with ambiguous residues
• 2525: Not pulling new files for 2007 ASMS workshop
• 2528: Could get memory overrun causing a repeat search to crash under Windows
• 2529: Table of matches at bottom of peptide view doesn't always agree with pop-up in master results
• 2530: Scripts and parser had different upper limit on significance threshold
• 2536: Added support for "Big" Mascot.
• 2542: Fixed performance issue in "master_results.pl" resulting from fix for CR#2529.
• 2543: Remove legacy uninstall entry for Mascot in "Add/Remove Programs".
• 2550: Isotope correction for multiplex quantitation was not implemented correctly.
• 2551: Modified AB correction code in "quant_subs.pl".
• 2562: Protein View report returns an error for hits without any significant peptide matches.
• 2563: Submitting a search from clients such as Mascot Distiller and Mascot Daemon results in spurious "Failed to lock file" messages in the error log.
• 2572: Database maintenance utility corrupts a Windows group name that includes non-ASCII characters, which causes "SetEntriesInAcl" errors.
• 2584: In cluster mode, automatic decoy search only performed decoy part on the first node.

Windows update procedure

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. In most cases, this will only affect two files: (i) quantitation.xml, if you modified or added any quantitation methods, (ii) enzymes, if you modified or added any enzyme definitions.

• 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_2_04.exe (18.5 Mb)
• x64 for 64 bit Windows: MascotServer_x64_SvcPack_2_2_04.exe (19.2 Mb)
• If your Microsoft Windows Installer is an out-of-date version, you will get the following error message: This patch package could not be opened. Contact the application vendor to verify that this is a valid Windows Installer patch package. (0x80070664). Usually, this will only be encountered on a system isolated from the Internet or where Windows Automatic Update is disabled. The fix is to update Windows Installer by downloading the Windows Installer 3.1 Redistributable from Microsoft.
• After the patches have been installed you can delete the executable.
• This self-extracting patch archive was created using 7-Zip, which is licensed under the GNU LGP Licence. The source code for 7-Zip can be downloaded here.

Windows version 2.1.x

Installation Tips

Configuration Files

• mascot.dat
  • If you are using NCBI nr, the taxonomy index should point to a block labeled "TAXONOMY FOR NCBInr using GI2TAXID" If you are using NCBI EST_others, the taxonomy index should point to a block labeled "TAXONOMY FOR dbEST using GI2TAXID".
• mod_file
  • There should be two entries for phosphorylation:
    Title:Phospho (Y)
    Residues:Y 243.02967 243.155
    *
    Title:Phospho (ST)
    Residues:S 166.99836 167.058
    Residues:T 181.01401 181.085
    NeutralLoss:97.97690 97.995
    *
    Earlier phosphorylation entries can be left in place for backward compatibility, but they should be marked hidden, so as not to appear in search forms. For Mascot 2.1 and later, see here for details of how to specify multiple neutral losses for phosphopeptides.
  • One release had small errors (~0.01 Da) in the mass values for carbamidomethyl cysteine. Verify that you now have the correct entry:
    Title:Carbamidomethyl (C)
    Residues:C 160.03065 160.190
    *
    

  • The list of modifications used by Mascot is taken directly from the Unimod database. For further details of individual modifications, please refer to Unimod. A Mascot mod_file containing all the modifications in Unimod can be downloaded from the help page, (updated weekly). Note that only selected modifications are displayed by default in the Mascot search form. If you want to see the complete list, you must go to the search form defaults page and tick the checkbox for 'Show all mods.'

• masses
  • Ensure the electron mass is correctly defined:
    ELECTRON: 0.000549, 0.000549
• enzymes
  • Upgrades and patches do not modify or replace the enzymes file. If you have upgraded to version 1.9, you'll probably want to replace your original enzymes file or merge in the additional entries for semiTrypsin and CNBr+Trypsin. You can find the latest enzymes file on the Mascot CD, in the unpacked\config directory
• taxonomy files
  • It is very important that the taxonomy indexes are kept up to date. This is particularly critical for the new NCBI indexes, gi_taxid_prot.dmp and gi_taxid_nucl.dmp. Ensure that you download new indexes each time you update the corresponding databases.

Available Fixes

• 2027: Crash if compressed sequence file exceeds 4 GB
• 2028: Benign error message removed: Invalid response (Error) to IPC command: SET_STATE NCBInr 0 1
• 2030, P263: Search parameter Monoisotopic needs to be non-case sensitive (problem with repeating searches submitted from GPS)
• 2031: Entrez links broken again in Protein View
• 2048: Allow any mixture of charge states. MzData files now properly supported with multiple charge states.
• 2051: Bruker XML format is broken for PMF
• 2056: Add support for --result_file_mime and --result_file_ini to client.pl
• 2060: Archive report can select incorrect protein
• 2067: Corruption caused by RTINSECONDS having a long list. (Distiller 2.0 client only)
• 2068: Add Bruker Biotools batch searching task to Mascot Security.
• 2074: No results if user chooses protein summary (rather than peptide summary) for a large search.
• 2086: Add SHOWALLMODS flag to search form for client applications such as Mascot Distiller
• 2089: Support AMD Opteron dual core processors.
• 2093: Uncompress results file before trying to return xml_results for Distiller
• 2094: Add support for retrieving query data to client.pl and export_dat.pl
• 2103: ms-gettaxonomy.exe was slow
• 2104: Setting search priority in Mascot Daemon used to fail sometimes and the search would run at normal priority
• 2108: Titles in significant hits list at top of report can get out of step with accessions if some titles are missing
• 2110: nph-mascot.exe no longer adds a spurious CR to the _name line result file
• 2112: Search form script in endless loop if final * character missing from enzymes file
• 2113: description details provided in mzData files are now passed through as user parameters
• 2146: Monitor log only shows first 10 instances of any particular message
• 2148: ms-makesearchlog doesn't add the userid
• 2220: MS/MS ions score lower than it should be for matches with many internal fragments and/or immonium ions
• P271, P281, P290: Various problems with "require bold red", e.g. could still get proteins that didn't have any bold red matches
• P283: Ignore electron mass in configuration file if value is clearly wrong.

Windows update procedure

Modified scripts will not be patched. If you have modified any of the Mascot 2.1 Perl scripts, e.g. lcq_dta_shell.pl, 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_20060315.exe (14 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.

Windows version 2.0.x

Installation Tips

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

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).

• msvcp60.dll

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.

• Vcredist.exe

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: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz. 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.

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 argument in extract_msn.exe.
• Fixed bugs relating to reporting of matches to ambiguous residues (B,X,Z).
• Pass IgnoreIonsScoreBelow from master_results.pl to protein_view.pl
• Add user interface to master_results.pl 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.

Windows update procedure

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. lcq_dta_shell.pl, 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.

Windows version 1.9.x

Installation Tips

Unfortunately, if the security is too tight, it interferes with the correct operation of Mascot. In particular, a common precaution is to prevent CGI programs executing the command processor (cmd.exe). This causes problems with the Mascot search engine and certain Perl scripts, because CGI processes can no longer create directories on the server. The symptom is a message similar to "Can't open results file: C:/INETPUB/MASCOT/data/20030116/F046466.dat for "w" [M00013]" at the end of a search. The fix is as follows:

Note that the following change will make your server less secure and more open to malicious attack. It is essential that any Mascot server be protected by a secure firewall

• In Windows Explorer, navigate to the c:\windows\system32 directory
• Right click on cmd.exe and choose properties
• Click on the security tab. (If you don't see a security tab, then open "Folder Options" in Control Panel. On the View tab, under Advanced settings, clear "Use simple file sharing [Recommended]")
• Click on the "Internet Guest Account" in the top pane. This is usually in the form "IUSR_MACHINENAME", where "MACHINENAME" is the name of the local machine. If there is no Internet Guest Account, click the "ADD" button You may have to switch to the local machine under "Look In" to find this user.
• Click on "Read & Execute" in the allow column, (Read will automatically be selected, and there will just be a selection for "write" in the deny column).
• Click on OK

Windows Server 2003 The following changes apply to a stand-alone server or the master node (only) of a cluster:

1. Don't install Perl from the Mascot CD. Instead, download and install perl 5.8 from Active State
2. When we last checked, there was no package for the GD library in the Active State repository for Perl 5.8. Fortunately, an alternative source is available. At a command prompt, enter:
   ppm install http://theoryx5.uwinnipeg.ca/ppms/GD.ppd
3. From the Windows Start menu, choose Administrative tools, Internet Information Services Manager. Expand computer name and highlight "Web Service Extension". In the right pane, highlight "All Unknown CGI Extensions" and click on Allow.

Available Fixes

• Several executables would not run on NT4 because of missing procedure entry point in kernel
• Monitor would loop if insufficient memory to lock a database
• Improvements to mixture mode reports
• Ions scores were slightly low for spectra with a large number of matches to neutral loss fragments
• The mass of an electron was incorrect leading to errors of 0.005 Da per charge
• Fixed bug affecting N-term enzyme cleavage
• Daemon would hang if a search produced no results
• Fixed bug affecting semi-specific enzyme cleavage
• Defined U as selenocysteine
• Update of Swiss-prot sometimes swapped out both old and new database files

Windows update procedure

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

• Download and save the update program MascotPatch_20030416.exe (3.3 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.

Windows version 1.8.x

Installation Tips

Vcredist.exe can be downloaded using the following link. The file size is approximately 1.8 Mb. Installation does not require any user input or actions except for rebooting the system on completion.

• Vcredist.exe

Available Fixes

• Creating compressed files for MSDB now significantly faster.
• Cluster mode more tolerant of TCP/IP errors
• Taxonomy changes for NCBI
• Performance improvement for some MS/MS searches
• Larger searches are now possible in a given address space
• Using long file or path names could cause unpredictable behaviour in cluster mode
• Added support for Maldi Quad TOF to fragmentation rules
• Rare crashes in cluster mode fixed
• Molecular weight matches with zero ions score were not being displayed in the Protein Summary report for an MS/MS search
• Peptide mass fingerprint matches with a variable modification on the C-terminus were not being reported correctly

Windows update procedure

• Download and save the update program MascotPatch_20021006.exe (1.5 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, or just selected patches.
• After the patches have been installed you can remove the executable from the Mascot Server hard disk.

Windows version 1.7.x

Available Fixes

• Example result files: Could be loaded, but clicking on "Repeat Search" would always fail.
• Peptide View: Error graph was using units from the peptide tolerance rather than the fragment ion tolerance
• Peptide View: Fixed broken NCBI BLAST links
• Protein View: Fixed broken NCBI BLAST links
• GetError: Failed to show error when called with a single error number; hence Mascot Daemon gave incorrect error descriptions.
• GetTaxonomy: Problem getting taxonomy information from the Swiss-Prot .DAT file; could hang Protein View report.
• Databases Maintenance: Failed to copy required file cksum.exe during upgrade installations
• Databases Maintenance: Incorrectly rejecting database names containing legal punctuation characters, e.g. hyphen
• Databases Maintenance: Could sometimes hang when testing parse rules on new database

Windows update procedure

• Download and save the update program MascotPatch_20010806.exe (398,848 bytes) 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, or just selected patches.
• After the patches have been installed you can remove the executable from the Mascot Server hard disk.