Searching MGF-format files

[Viktor Granholm]

Hi group,

I have a question regarding searching spectra-files in the MGF-format, using Crux v1.39. 

I have set the --spectrum-parser option to pwiz, but I seem to get an empty output. Should Crux automatically detect that I'm using an MGF-file, or should I specify it somehow? In the standard-error, it says INFO: Reading in ms2 file CID_IT_Tryp.mgf

Which perhaps suggests that Crux thinks I'm using an ms2-file?

Thanks for any help, and tell me if more information is needed.

Viktor

[Kaipo Tamura]

Hi Viktor,

I believe that this is a bug. Both the pwiz and crux parser options
should automatically recognize MGF files by their extensions (the
"Reading in ms2 file" message appears regardless of the filetype).

I will have a look at the code and see if I can figure out what is going
on. Something to try in the meantime would be using the default spectrum
parser (i.e. "--spectrum-parser crux") and see if the output is still empty.

Thanks,
Kaipo

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[Kaipo Tamura]

Hi Viktor,

I attached a patch that should resolve the issue. If you would prefer a
binary or the patch does not work please let us know.

Thanks,
Kaipo

[Viktor Granholm]

Hi Kaipo,

thanks for the help. The patch seems to work just great.

Best,

Viktor

2013/1/10 Kaipo Tamura <kai...@uw.edu>

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[Viktor Granholm]

Hi again Kaipo,

it took me some time to realize it, but I've discovered a problem when running Crux v1.39 in the 'sequest-search'-mode and the pwiz_parser.patch on MGF-format files. I suppose the 'sequest-search' mode might be deprecated by now, but the problem might be seen elsewhere too. In the SQT-format output, the scan numbers (or spectrum numbers) are always 0, which makes downstream processing hard.

Is there a way to solve this, or would you like more information?

Thank you,

Viktor

2013/1/11 Viktor Granholm <viktor....@scilifelab.se>