Re: Tandem MS/MS .d files and Proteowizard
Reply #7 –
The diffreport contained picked peaks. I don't see how the number of mass spectra should relate to that.
I would at least set:
method = 'centWave'
profparam= list(step=0.005)
and prefilter to c(3,X) where X is something appropriate for your system (it should correspond to the lowest intensity you want to be considered for a peak). Also set peakwidth to something appropriate. See ?findPeaks.centWave. You can perhaps lower the ppm from the default of 25 Da but I doubt it will have a big effect. You should always set it well above your machines theoretical accuracy as this is always far on the optimistic side compared to real world experiments.
Often if peaks are missing, however, it is a problem in your "group" step. Be aware that minsamp and minfrac are counted in each sample class separately. mzwid in "group" can probably be lowered significantly from the default of 0.25. 0.05 or even lower might be appropriate for you. You need to play with the settings here too.
Also if you didn't you need to use fillPeaks.
I still don't think using msn2xcmsRaw is right for you. If your files contain an MS1 trace you need to use that in my opinion. If you really only have a data dependent MS2 trace I don't see how you could sensibly compare samples using that.