reconstructChromPeakSpectra: Data independent acquisition (DIA): reconstruct MS2 spectra

Description Usage Arguments Details Value Author(s) See Also

View source: R/functions-XCMSnExp.R

Description

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

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reconstructChromPeakSpectra(
  object,
  expandRt = 0,
  diffRt = 2,
  minCor = 0.8,
  intensity = "maxo",
  peakId = rownames(chromPeaks(object, msLevel = 1L)),
  BPPARAM = bpparam()
)

Arguments

object

XCMSnExp with identified chromatographic peaks.

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.

Details

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

The resulting MSpectra object provides also the peak IDs of the MS2 chromatographic peaks for each spectrum as well as their correlation value.

Value

MSpectra() with the reconstructed MS2 spectra for all MS1 peaks in object. Contains empty Spectrum2 objects 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. MSpectra metadata columns "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).

Author(s)

Johannes Rainer, Michael Witting

See Also

findChromPeaksIsolationWindow() for the function to perform MS2 peak detection in DIA isolation windows and for examples.


xcms documentation built on Nov. 8, 2020, 5:13 p.m.