estimatePrecursorIntensity {xcms} | R Documentation

## Estimate precursor intensity for MS level 2 spectra

### 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 `bpparam()` 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

[Package xcms version 3.16.1 Index]