Data independent acquisition (DIA): reconstruct MS2 spectra

Reconstructs MS2 spectra for each MS1 chromatographic peak (if possible) for data independent acquisition (DIA) data (such as SWATH). See the LC-MS/MS analysis vignette for more details and examples.

Usage

reconstructChromPeakSpectra(object, ...)

# S4 method for class 'XcmsExperiment'
reconstructChromPeakSpectra(
  object,
  expandRt = 0,
  diffRt = 2,
  minCor = 0.8,
  intensity = "maxo",
  peakId = rownames(chromPeaks(object, msLevel = 1L)),
  BPPARAM = bpparam()
)

# S4 method for class 'XCMSnExp'
reconstructChromPeakSpectra(
  object,
  expandRt = 0,
  diffRt = 2,
  minCor = 0.8,
  intensity = "maxo",
  peakId = rownames(chromPeaks(object, msLevel = 1L)),
  BPPARAM = bpparam(),
  return.type = c("Spectra", "MSpectra")
)

Arguments

object: XCMSnExp with identified chromatographic peaks.
...: ignored.
expandRt: numeric(1) allowing to expand the retention time range for extracted ion chromatograms by a constant value (for the peak shape correlation). Defaults to expandRt = 0 hence correlates only the signal included in the identified chromatographic peaks.
diffRt: numeric(1) defining the maximal allowed difference between the retention time of the chromatographic peak (apex) and the retention times of MS2 chromatographic peaks (apex) to consider them as representing candidate fragments of the original ion.
minCor: numeric(1) defining the minimal required correlation coefficient for MS2 chromatographic peaks to be considered for MS2 spectrum reconstruction.
intensity: character(1) defining the column in the chromPeaks matrix that should be used for the intensities of the reconstructed spectra's peaks. The same value from the MS1 chromatographic peaks will be used as precursorIntensity of the resulting spectra.
peakId: optional character vector with peak IDs (i.e. rownames of chromPeaks) of MS1 peaks for which MS2 spectra should be reconstructed. By default they are reconstructed for all MS1 chromatographic peaks.
BPPARAM: parallel processing setup. See bpparam() for more information.
return.type: character(1) defining the type of the returned object. Only return.type = "Spectra" is supported, return.type = "MSpectra" is deprecated.

Value

Spectra() object (defined in the Spectra package) with the reconstructed MS2 spectra for all MS1 peaks in object. Contains empty spectra (i.e. without m/z and intensity values) for MS1 peaks for which reconstruction was not possible (either no MS2 signal was recorded or the correlation of the MS2 chromatographic peaks with the MS1 chromatographic peak was below threshold minCor. Spectra variables "ms2_peak_id" and "ms2_peak_cor" (of type CharacterList() and NumericList() with length equal to the number of peaks per reconstructed MS2 spectrum) providing the IDs and the correlation of the MS2 chromatographic peaks from which the MS2 spectrum was reconstructed. As retention time the median retention times of all MS2 chromatographic peaks used for the spectrum reconstruction is reported. The MS1 chromatographic peak intensity is reported as the reconstructed spectrum's precursorIntensity value (see parameter intensity above).

Details

In detail, the function performs for each MS1 chromatographic peak:

Identify all MS2 chromatographic peaks from the isolation window containing the m/z of the ion (i.e. the MS1 chromatographic peak) with approximately the same retention time than the MS1 peak (accepted rt shift can be specified with the diffRt parameter).
Correlate the peak shapes of the candidate MS2 chromatographic peaks with the peak shape of the MS1 peak retaining only MS2 chromatographic peaks for which the correlation is > minCor.
Reconstruct the MS2 spectrum using the m/z of all above selected MS2 chromatographic peaks and their intensity (either "maxo" or "into"). Each MS2 chromatographic peak selected for an MS1 peak will thus represent one mass peak in the reconstructed spectrum.

The resulting Spectra() object provides also the peak IDs of the MS2 chromatographic peaks for each spectrum as well as their correlation value with spectra variables ms2_peak_id and ms2_peak_cor.

Author