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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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msLevel=2L chromatograms (MRM or SRM) not working with MsExperiment interface #725

Closed jmorim closed 3 months ago

jmorim commented 3 months ago

Data is an mzML converted from an Agilent 6495 triple quad, run in dynamic MRM mode

data = readMsExperiment(file)
spectra(data)
#      msLevel     rtime scanIndex
#    <integer> <numeric> <integer>
#1           2    93.051         1
#2           2    93.304         2
#3           2    93.556         3
chromatogram(data) |> plot()

all chromatograms empty

chromatogram(data, msLevel=2L) |> plot()

all chromatograms empty

might be something obvious i'm missing but the readMsData interface worked.

jorainer commented 3 months ago

we did not (yet) update the code to import/handle MRM/SRM data. for chromatographic data we're still using/relying on the MSnbase package - until we proceed with the Chromatograms package - but that will still take some time.

I will close the issue, feel free to reopen if needed.