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 in which they were detected is added to chromPeakData() data frame.

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).

Usage

findChromPeaksIsolationWindow(object, ...)

# S4 method for class 'MsExperiment'
findChromPeaksIsolationWindow(
  object,
  param,
  msLevel = 2L,
  isolationWindow = isolationWindowTargetMz(spectra(object)),
  chunkSize = 2L,
  ...,
  BPPARAM = bpparam()
)

# S4 method for class 'OnDiskMSnExp'
findChromPeaksIsolationWindow(
  object,
  param,
  msLevel = 2L,
  isolationWindow = isolationWindowTargetMz(object),
  ...
)

Arguments

object

MsExperiment, XcmsExperiment, OnDiskMSnExp or XCMSnExp object with the DIA data.

...

currently not used.

param

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

msLevel

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

isolationWindow

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.

chunkSize

if object is an MsExperiment or XcmsExperiment: integer(1) defining the number of files (samples) that should be loaded into memory and processed at a time. See findChromPeaks() for more information.

BPPARAM

if object is an MsExperiment or XcmsExperiment: parallel processing setup. See BiocParallel::bpparam() for more information.

Value

An XcmsExperiment or 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().

See also

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

Author

Johannes Rainer, Michael Witting