wiki:WorkflowUtilities

Automation of gel-based workflow

Scripts

For database searches for protein identification, it is always a good idea to perform the search in a database which has been expanded with a random or reverse part. Matrix Science provides a free script to generate such a database. Here you can download a modified script which will name modified IPI:IPI entries IPI:IPRNDx.x or IPI:IPREVx.x for easy parsing of accession numbers. Other entries will have a ###RND### or ###REV### prefix. The script should be run with the --append option so that the decoy database is added at the end of the existing database. If you plan to do PMF searches or 'no enzyme' searches, the --random option is preferable. If you use local reference (.dat) files for Mascot IPI databases, the .dat will also need to be expanded using this script

Proteios will import XML output from Mascot, but not the .DAT files. To perform batch export of XML files from a Mascot server, the export_batch.pl script can be used. It has been tested with Mascot Server 2.1. After performing Mascot searches with mzData files find out the number of the first and last .DAT-file that you want to export. This can be seen in Mascot Daemon or in the search log. The export_batch.pl script should be placed in the cgi folder of your Mascot Server. Execute the script from the command prompt or by double-clicking on it.

X!Tandem output xml files can be imported into Proteios. To perform batch searches the tandem_batch.pl script can be used. It should be placed in the thegpm-cgi folder on your GPM installation. As with the Mascot script you have to log on to the server to execute the script. It will save the settings used in a batch_settings folder with a prefix of your choice and date. The next time you execute the script the parameters used last time will be loaded.

Step by step instruction

Attached is a document which describes how to import data and generate reports from a 2D-gel based workflow, as it is done at SWEGENE in Lund.

Last modified 11 years ago Last modified on Oct 18, 2006, 2:01:39 PM

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