Libra works fine with ".mzML" files that contain only MS2 spectra (use: msconvert data.RAW --filter "msLevel 2"). Have used this mostly with Sequest output.
David Simpson On Feb 9, 2:47 pm, Luis Mendoza <[email protected]> wrote: > Hello, > Libra does require the mzXML file to be present (at the location > specified by the base_name attribute of the msms_run_summary tag in > the input pepXML file), since the reporter ion peaks need to be > extracted from the spectra. I am not sure if a file with only MS2 > scans will work -- I suppose it should, as long as the scan numbers > correspond to the ones in the pepXML identifications. Let us know if > that works! > > Cheers, > --Luis > > > > > > > > On Thu, Feb 9, 2012 at 6:21 AM, Gautam Saxena <[email protected]> wrote: > > Does Libra require the mzXML file to be present in order for it to > > run? (That is, if we used only mgf files to run the search via say > > OMSSA and if we did NOT have the correspoding mzXML files, then LIBRA > > will crash right? That said, does Libra require MS1 data in the mzXML > > file -- my guess is no.) > > > If Libra does require mzXML files (though not the MS1 data in the > > mzXML file), I'm assuming that I can still use a search engine that > > does not support mzXML (eg OMSSA) and still use Libra so long as I > > have a mzXML file that corresponds to the same name as the mgf file > > that OMSSA used? > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
