Hi,
this is a follow on of issue #723. @jorainer suggested to assign msLevel 1 to the first scan event, and 2 to the second. That way one MsExperiment object can be processed with findChromPeaks(object,msLevel=1L,...) and findChromPeaks(object,msLevel=2L,...) to obtain all chromPeaks in one object. That works fine. What is not working is extracting chromatograms with chromatogram(object,msLevel=2L).
Data from an Orbitrap Elite were converted with msconvert to mzML and read in and then split by the two scan events (they occur in the order below):
msexp <- readMsExperiment(spectraFiles = files[timeord], backend = MsBackendMzR(),sampleData = pd[timeord,])
mse1 <- filterSpectra(msexp, filter = filterFilterString, value = "FTMS + c ESI sid=10.00 SIM ms [300.00-800.00]")
mse2 <- filterSpectra(msexp, filter = filterFilterString, value = "FTMS + c ESI sid=10.00 SIM ms [600.00-1200.00]")
From here I obtained the expected chromatograms with
then chromatogram(msexp,mz=(394.75,394.77))|>plot() produces a chromatogram while chromatogram(msexp,mz=c(663.70,663.72),msLevel=2L)|>plot() comes up empty. In chromPeaks all possible peaks in the range from m/z 300 to 1200 are listed. Any ideas how I can draw the chromatograms for the second scan event? Or how to better deal with multiple scan events per file?
Hi, this is a follow on of issue #723. @jorainer suggested to assign
msLevel1 to the first scan event, and 2 to the second. That way oneMsExperimentobject can be processed withfindChromPeaks(object,msLevel=1L,...)andfindChromPeaks(object,msLevel=2L,...)to obtain allchromPeaksin one object. That works fine. What is not working is extracting chromatograms withchromatogram(object,msLevel=2L).Data from an Orbitrap Elite were converted with
msconvertto mzML and read in and then split by the two scan events (they occur in the order below):From here I obtained the expected chromatograms with
If I change the
msLevelinmsexpfor the second scan event to 2 withthen
chromatogram(msexp,mz=(394.75,394.77))|>plot()produces a chromatogram whilechromatogram(msexp,mz=c(663.70,663.72),msLevel=2L)|>plot()comes up empty. InchromPeaksall possible peaks in the range from m/z 300 to 1200 are listed. Any ideas how I can draw the chromatograms for the second scan event? Or how to better deal with multiple scan events per file?The versions of the relevant packages: