Mascot, by Matrix Science, is a search engine that can perform peptide mass fingerprinting, sequence query and tandem mass spectra searches. LabKey Server supports using your existing Mascot installation to search an mzXML file against a FASTA database. Results are displayed in the MS2 viewer for analysis.

• Configure Mascot Support
• Site-Wide Configuration
• Project and Folder Configuration
• Test the Mascot Configuration
• Set Up Sequence Database Synchronization
• Supported and Tested Mascot Configurations

Configure Mascot Support

If you are not familiar with your organization's Mascot installation, you will want to recruit the assistance of your Mascot administrator.

Before you configure Mascot support, have the following information ready:

• Mascot Server URL: Typically of the form mascot.server.org
• User: The user id for logging in to your Mascot server (leave blank if your Mascot server does not have security configured)
• Password: The password to authenticate you to your Mascot server (leave blank if your Mascot server does not have security configured)
• HTTP Proxy URL: Typically of the form http://proxyservername.domain.org:8080/ (leave blank if you are not using a proxy server)

Site-Wide Configuration

To configure Mascot support across all projects on the site:

Project and Folder Specific Configuration

You can configure Mascot support for a specific project or folder that overrides any site-wide configuration. To configure project or folder specific Mascot support:

Test the Mascot Configuration

To test your Mascot support configuration:

A window will open to report the status of the testing.

If the test is successful, LabKey displays a message indicating success and displaying the settings used and the Mascot server configuration file (mascot.dat).

If the test fails, LabKey displays an error message, followed by one of the following additional messages to help you troubleshoot.

• Is not a valid user: Check that you have entered the correct user account. Contact your Mascot administrator for help if problem persists.
• You have entered an invalid password: Check that you have entered the right password. Ensure that your CAPS lock and NUM lock settings are correct. Contact your Mascot administrator for help if problem persists.
• Failure to interact with Mascot Server: LabKey cannot contact the Mascot server. Please check that the Mascot server is online and that your network is working.

Set Up Sequence Database Synchronization

The Perl script labkeydbmgmt.pl supports the download of sequence database from your Mascot server. To download the Perl script, click: here. The database is needed to translate the Mascot result (.dat file) to pepXML (.pep.xml file).

• Copy the Perl script labkeydbmgmt.pl to the folder /cgi/
• Open labkeydbmgmt.pl in a text editor and change the first line to refer to your Perl executable full path. (See your copy of /cgi/search_form.pl for the correct path.)
• If your Mascot runs on a *nix system, you need to set the execution attribute. Command:

chmod a+rx labkeydbmgmt.pl

Supported and Tested Mascot Versions

To get your Mascot server version number check with your Mascot administrator. You can use the helper application at /bin/ms-searchcontrol.exe to determine your version. Usage:

./ms-searchcontrol.exe –version

If your Mascot Server version is v2.1.03 or later, LabKey should support it with no additional requirements. If your Mascot Server version is v2.0.x or v2.1.x (earlier than v2.1.03), you must perform the following upgrade:

• Visit the Matrix Science website for the free upgrade (http://www.matrixscience.com/distiller_support.html#CLIENT).
• Ask your Mascot administrator to determine the correct platform upgrade file to use and to perform the upgrade. Remember to back up all files that are to be upgraded beforehand.
• As the Mascot result is retrieved via the MIME format, you must make two sets of changes to client.pl. Insert the section shown from line 143 to line 144, insert the section shown between lines 160 and 161.

140: close(SOCK);
141: print @temp;
142: 
143:# WCH: 28 July 2006
# Added to support the retrieval of Mascot .dat result file in MIME format
# This is necessary if you are using Mascot version 2.0 or 2.1.x (< v 2.1.03) and
# have upgraded to the version 2.1 Mascot daemon
} elsif (defined($thisScript->param('results'))
|| defined($thisScript->param('xmlresults'))
|| defined($thisScript->param('result_file_mime'))) {
# END - WCH: 28 July 2006 
144:
145: if ($taskID < 1) {
146: print "problem=Invalid task ID - $taskIDn";
147: exit 1;
148: }
149:
150: # Same code for results and xmlresults except that the latter requires
151: # reporttop and different command to be passed to ms-searchcontrol
152: my ($cmnd, $reporttop);
153: if (defined($thisScript->param('xmlresults'))) {
154: $cmnd = "--xmlresults";
155: if (!defined($thisScript->param('reporttop'))) {
156: print "problem=Invalid reporttopn";
157: exit 1;
158: } else {
159: $reporttop = "--reporttop " . $thisScript->param('reporttop');
160: } 
# WCH: 28 July 2006
# Added to support the retrieval of Mascot .dat result file in MIME format
# This is necessary if you are using v2.0 Mascot Server and
# have upgraded to the version 2.1 Mascot Daemon
} elsif (defined($thisScript->param('result_file_mime'))) {
$cmnd = "--result_file_mime";
# END - WCH: 28 July 2006 
161: } else {
162: $cmnd = "--results";
163: }
164:
165: # Call ms-searchcontrol.exe to output search results to STDOUT

Related Topics

• View, Filter, and Export Mascot Runs