filter fragmentation method from output

[Srdfr]

Hi, 

Is there a way you can filter out the MS fragmentation method from your output?

We would like to use the same parameter file for different Mass specs (and their fragmentation methods) as a quality control approach.

activation_method = ALL is used in the search.

Thank you!

Sara

[Jimmy Eng]

Sara,

Currently Comet does not report the fragmentation method in any of its output.  The value set for the "activation_method" parameter is passed to the MSToolkit file parsing library to filter which spectra get returned to Comet for analysis.  We pass the requested fragmentation methods to MSToolkit for filtering but I don't believe there's currently a mechanism to return the actual fragmentation method strings to Comet.  I can ask the MSTookit developer to add/support this little bit of functionality.  If we go this route, in what Comet output formats would you like to see the fragmentation method reported ... an extra column in the text output file?  pepXML?

Alternatively, a less graceful but quicker and cleaner (not having to touch Comet code) option is to get you a separate tool that simply dumps the scan number and fragmentation method for any input file.  You would merge this output with the search result output for your filtering.  If this route is a feasible workaround, let me know what OS you use (Windows? Linux?) and I'll throw together that tool for you.

Jimmy

[Srdfr]

Dear Jimmy,

Thank you so much for your reply.

The second option sounds indeed like a quicker and cleaner solution. Would it be possible to give me both the Windows and Unix workaround? I'm mainly testing on windows and afterwords we will implement on our unix server system.

Thank you so much, I really appreciate the support.

Best,

Sara

[Jimmy Eng]

I'll send you another email offline with a link to a little tool using Thermo's .NET library that you can also run under Linux/Unix using Mono.

[Srdfr]

Thank you!