Protein identification using Mascot research engine

[sabikh]

Hi:
I would like to use Mascot research engine for protein identification for MS/MS files obtained by LCQ thermofinnigan system. I do not have Sequest. I know that first I have to convert these files to ASC ones, but do not know how. Any help will be very appreciated.
Thanks

[Kostas Petritis]

Sabikh,

1) You need to have the lcq_dta.exe program located at C:\Xcalibur\system\programs\
Newer versions of Xcalibur that ship with the LTQ have renamed this program to extract_msn.exe

2) You need to have the Microsoft .NET framework installed. Download from:
http://www.microsoft.com/downloads/
or more specifically
http://www.microsoft.com/downloads/deta ... laylang=en

3a) You need to be able to convert the .raw files to .mgf files and you do need to write a small script to do that (or someone must give it to you) then edit the Runme.bat file to include the path to the .Raw file

3b) To convert several .Raw files, simply call the Step1_ConvertRawToMGF.bat file numerous times in the Runme.bat file

4) Once you've edited Runme.bat, save it, then double click to run.