reconstructChromPeakSpectra

[Slycopersicum]

Hi, I was trying to use this function for mse data.
I want to ask if there is some way to indicate the reconstruct of the ms2 for the ms1 peak saved in featuredata.
Or use the ms1 peaks common in all my samples.
Also other question is about if the reconstruct can be achive using findchrompeak( msLevel = 2L, add= TRUE),
instead of using the findChromPeaksIsolationWindow.

Thank you so much

[jorainer]

can you maybe provide some more information on your data? what is it? SWATH? DIA? note that at present this approach reconstructs only fragment spectra (from MS2 chrom peaks) separately for each file - there is no way (yet) to consider peaks present in all samples.

the advantage of findChromPeaksIsolationWindow is that MS2 chrom peaks are only identified in data (fragments) of ions generated/selected with the same isolation window. findChromPeaks(msLevel = 2) makes only sense, if the MS instrument fragmented all ions at the same time and no m/z isolation windows were used.