Re: Quantifying centroided MS data with centWave
Reply #1 –
XCMS quantification works with centroided data. The shape of the mass peak is not reconstructed.
The profStep parameter is not related to continuous data. It is used to create extracted ion chromatograms (mass traces, m/z slices or profiles). The quantification is based on these profiles during fillPeaks. In my experience you get better result if you change the defaults (profStep = 0.1) in xcmsSet by setting profparam in xcmsSet. For example:
xcmsSet(files=files,
...,
profparam = list(step=0.005)
)
As far as I have been able to figure it is perfectly safe to set profStep very low since slices are combined to fit the ppm parameter anyway. Smaller slices uses more memory though.