Hi,

I did use it for some test data and it works quite well. I recommend to use different search engines for analysis. There is a good tool available to combine searches from Mascot, OMSSA and X!Tandem called "Peptideshaker". This tool also estimates FDRs by using a target and decoy approach. For searching OMSSA and X!Tandem you use the "SearchGUI".

Have a look here:

http://code.google.com/p/peptide-shaker/

https://code.google.com/p/searchgui/

The searchGUI automatically creates a reverse_concatenated DB which you should also use for your Mascot search.

Cheers, Stephan

You can use this link http://pubchem.ncbi.nlm.nih.gov/omssa/win32.htm

Hi,

I did use it for some test data and it works quite well. I recommend to use different search engines for analysis. There is a good tool available to combine searches from Mascot, OMSSA and X!Tandem called "Peptideshaker". This tool also estimates FDRs by using a target and decoy approach. For searching OMSSA and X!Tandem you use the "SearchGUI".

Have a look here:

http://code.google.com/p/peptide-shaker/

https://code.google.com/p/searchgui/

The searchGUI automatically creates a reverse_concatenated DB which you should also use for your Mascot search.

Cheers, Stephan

I'll add my vote to Stephan's suggestion, SearchGUI and PeptideShaker are brilliant.

Thanks all

Thanks Stephan. I have downloaded peptide shaker/search GUI. i'll analyze my samples with this algorithm and will ask you if I'll find any problem.