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.