findChromPeaksIsolationWindow: Data independent acquisition (DIA): peak detection in...

View source: R/functions-XCMSnExp.R

findChromPeaksIsolationWindowR Documentation

Data independent acquisition (DIA): peak detection in isolation windows


The findChromPeaksIsolationWindow function allows to perform a chromatographic peak detection in MS level > 1 spectra of certain isolation windows (e.g. SWATH pockets). The function performs a peak detection, separately for all spectra belonging to the same isolation window and adds them to the chromPeaks() matrix of the result object, information about the isolation window they were detected in is added to chromPeakData(). Note that peak detection with this method does not remove previously identified chromatographic peaks (e.g. on MS1 level using the findChromPeaks() function but adds newly identified peaks to the existing chromPeaks() matrix.

Isolation windows can be defined with the isolationWindow parameter, that by default uses the definition of isolationWindowTargetMz(), i.e. chromatographic peak detection is performed for all spectra with the same isolation window target m/z (seprarately for each file). The parameter param allows to define and configure the peak detection algorithm (see findChromPeaks() for more information).


  msLevel = 2L,
  isolationWindow = isolationWindowTargetMz(object),



OnDiskMSnExp or XCMSnExp object with the DIA data.


Peak detection parameter object, such as a CentWaveParam object defining and configuring the chromographic peak detection algorithm. See also findChromPeaks() for more details.


integer(1) specifying the MS level in which the peak detection should be performed. By default msLevel = 2L.


factor or similar defining the isolation windows in which the peak detection should be performed with length equal to the number of spectra in object.


currently not used.


An XCMSnExp object with the chromatographic peaks identified in spectra of each isolation window from each file added to the chromPeaks matrix. Isolation window definition for each identified peak are stored as additional columns in chromPeakData().


Johannes Rainer, Michael Witting

See Also

reconstructChromPeakSpectra() for the function to reconstruct MS2 spectra for each MS1 chromatographic peak.

sneumann/xcms documentation built on March 18, 2023, 6:24 p.m.