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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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number of peaks per spectrum #152

Closed ypriverol closed 3 months ago

ypriverol commented 3 months ago

Hi @alchemistmatt :

We are using msgf+ in combination with other search engines like comet and SAGE and I just saw that those search engines have a filter for the number of peaks in the spectrum, comet = 10, sage = 15. Im wondering if this could be possible to be implemented in msgf+ or if is already possible to filter based in number of peaks.

Regards Yasset

alchemistmatt commented 3 months ago

This option is supported, but only if you use a parameter file (using the -conf switch, as described at https://msgfplus.github.io/msgfplus/MSGFPlus.html)

Browse parameter files at: https://github.com/MSGFPlus/msgfplus/blob/master/docs/ParameterFiles/

Example parameter file with this option (though it's currently commented out using #): MSGFPlus_PartTryp_MetOx_20ppmParTol.txt

ypriverol commented 3 months ago

@alchemistmatt do you think would be possible to implement this in the command-line, I could try to do a PR?

FarmGeek4Life commented 3 months ago

The parameter is technically usable from the command line, with "-minNumPeaks n", but it's hidden from all of the help documentation.

https://github.com/MSGFPlus/msgfplus/blob/master/src/main/java/edu/ucsd/msjava/params/ParamManager.java See lines 112, 708, and 803

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ypriverol commented 3 months ago

Yes. Actually, I was checking the code now and in fact all the parameters can be used from the code ;) I was actually reading that line now. Thanks a lot.

I will test that line now:

-minNumPeaks 15

ypriverol commented 3 months ago

I will close the issue ;)

alchemistmatt commented 3 months ago

I updated the documentation to mention -minNumPeaks https://msgfplus.github.io/msgfplus/MSGFPlus.html