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

Mascot 2.2.03 known issues

The following issues affect Mascot 2.2.03 only.

  1. Message in Mascot error log when search submitted from Mascot Distiller.
    Error message is similar to Error [M00267 - Job -1 - X00875:ms_fileutil] – Wed Oct 17 16:07:27 2007 – Failed to lock file – error Bad file descriptor

  2. (Windows only) In non-English locales, sequence databases fail to reach the "In Use" state and the error log contains messages referring to SetEntriesInAcl.
    Typical error messages: Error setting/getting security rights for file/memory. Error 1788 in SetEntriesInAcl and Error [M00143 - Job -1 - X00510:ms_fileutil] – Tue Nov 13 09:36:38 2007 – Error setting/getting security rights for file/memory. Error 1332 in SetEntriesInAcl

  3. Unable to load a Protein View report for certain hits.
    Error message is: Can’t call method "getAccession" on an undefined value at C:\inetpub\mascot\cgi\protein_view.pl line 465

1. Message in Mascot error log when search submitted from Mascot Distiller.

This is a spurious error message, which can safely be ignored.

2. (Windows only) In non-English locales, sequence databases fail to reach the "In Use" state and the error log contains messages referring to SetEntriesInAcl.

This only affects non-English locales, where the name of the Windows "Guests" group contains an extended character, (code > 127). For example, in French language Windows, the default is Invités. For German language Windows, the default is Gäste. You can see the correct name in the Computer Management Control Panel.

IIS6

The cause is a bug in the Database Maintenance script, db_gui.pl, located in the Mascot x-cgi directory. Open db_gui.pl in a text editor, (e.g. NotePad), and locate the following line. If your editor displays line numbers, this is line 81:

print $thisScript->header( -expires => ‘-1d’, -charset => “utf-8″ );

Change to:

print $thisScript->header( -expires => ‘-1d’ );

Make sure you save the file as plain text, (do not choose Unicode or UTF-8). If you choose Save As…, the editor may add .txt to the end of the file name, which you will need to remove. If you prefer not to edit the script yourself, please email support@matrixscience.com and request a copy of the corrected script.

After fixing the script, open mascot.dat in Notepad, (not Wordpad), and correct the value of the NTIUserGroup. This will have been corrupted, e.g. Invités truncated to Invit. Correct the name and save as ANSI text, (do not choose Unicode or UTF-8). Launch Database Maintenance, and verify that the value of the NTIUserGroup (on the Options page) is displayed correctly.

Finally, stop and re-start the Mascot service. All databases should now reach the "In Use" state.

Note that similar problems can also be caused by editing mascot.dat in WordPad, because the file is automatically converted to UTF-8 encoding. If you want to edit mascot.dat, use NotePad or an editor where you can ensure the file is saved as Western European ANSI text.

3. Unable to load a Protein View report for certain hits.

Affected hits are those without any significant peptide matches.

Go to the Mascot cgi directory and open protein_view.pl in a text editor, (e.g. NotePad or vi), and locate the following line. If your editor displays line numbers, this is line 327:

$objSingleHit = new msparser::ms_peptidesummary($objResFile, $msresFlags, $sigThreshold, 1, "", $ignoreIonsScoreBelow, $minPepLen, $hitNum);

Change to:

$objSingleHit = new msparser::ms_peptidesummary($objResFile, $msresFlags, 0, 1, "", $ignoreIonsScoreBelow, $minPepLen, $hitNum);

That is, replace the letters $sigThreshold with the digit 0. Make sure you save the file as plain ASCII text and that the editor does not add .txt to the end of the file name. If you prefer not to edit the script yourself, please email support@matrixscience.com and request a copy of the corrected script.