findChromPeaksIsolationWindow {xcms} | R Documentation

## Data independent acquisition (DIA): peak detection in isolation windows

### Description

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 they were detected in is added to `chromPeakData()`. 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,
      param,
      msLevel = 2L,
      isolationWindow = isolationWindowTargetMz(object),
      ...
    )

### Arguments

`object` | `OnDiskMSnExp` or `XCMSnExp` object with the DIA data.
`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`.
`...` | currently not used.

### Value

An `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()`.

### Author(s)

Johannes Rainer, Michael Witting

### See Also

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

[Package xcms version 3.10.2 Index]