estimatePrecursorIntensity: Estimate precursor intensity for MS level 2 spectra

In xcms: LC-MS and GC-MS Data Analysis

Description

'estimatePrecursorIntensity' determines the precursor intensity for a MS 2 spectrum based on the intensity of the respective signal from the neighboring MS 1 spectra (i.e. based on the peak with the m/z matching the precursor m/z of the MS 2 spectrum). Based on parameter 'method' either the intensity of the peak from the previous MS 1 scan is used ('method = "previous"') or an interpolation between the intensity from the previous and subsequent MS1 scan is used ('method = "interpolation"', which considers also the retention times of the two MS1 scans and the retention time of the MS2 spectrum).

Usage

estimatePrecursorIntensity(
  x,
  ppm = 10,
  method = c("previous", "interpolation"),
  BPPARAM = bpparam()
)

Arguments

x	'OnDiskMSnExp' or 'XCMSnExp' object.
ppm	'numeric(1)' defining the maximal acceptable difference (in ppm) of the precursor m/z and the m/z of the corresponding peak in the MS 1 scan.
method	'character(1)' defining the method how the precursor intensity should be determined (see description above for details). Defaults to 'method = "previous"'.
BPPARAM	parallel processing setup. See [bppara()] for details.

Value

'numeric' with length equal to the number of spectra in 'x'. 'NA' is returned for MS 1 spectra or if no matching peak in a MS 1 scan can be found for an MS 2 spectrum

Author(s)

Johannes Rainer

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