I'm having trouble getting reproducible peak areas with findChromPeaks and MatchedFilterParam on centroided high-res MS data. While the peak height (maxo) is spot-on with the manual integration results from the instrument software (Thermo Freestyle), the peak areas are in may cases off by up to 50%.
It seems this is strongly dependent on the FWHM setting in the MatchedFilterParam object, but there is no setting that give consistent results over the range in peak widths.
Am I missing something or is this just how the algorithm models the peak (instead of measuring the area under the peak)?
PS: I tried CentWaveParam first, but this one was missing obvious peaks entirely (and had the same issue with peak areas)
Thanks a lot, -Y
Object of class: MatchedFilterParam
fwhm: 6 sigma: 2.547987 max: 50 snthresh: 100 steps: 1 mzdiff: 0.03 index: FALSE