chromPeakSpectra: Extract (MS2) spectra associated with chromatographic peaks
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Value Author(s) Examples

Extract (MS2) spectra from an XCMSnExp object that represent ions within the rt and m/z range of each chromatographic peak (in the same file /sample in which the peak was detected). All MS2 spectra are returned for chromatographic peak i for which the precursor m/z is >= chromPeaks(x)[i, "mzmin"] and <= chromPeaks(x)[i, "mzmax"] and the retention time is >= chromPeaks(x)[i, "rtmin"] and <= chromPeaks(x)[i, "rtmax"].

See also the LC-MS/MS data analysis vignette for more details and examples.

chromPeakSpectra(
  x,
  msLevel = 2L,
  expandRt = 0,
  expandMz = 0,
  ppm = 0,
  method = c("all", "closest_rt", "closest_mz", "signal"),
  skipFilled = FALSE,
  return.type = c("Spectra", "list")
)

`x`	XCMSnExp object with identified chromatographic peaks.
`msLevel`	`integer(1)` defining whether MS1 or MS2 spectra should be returned. Currently only `msLevel = 2` is supported.
`expandRt`	`numeric(1)` to expand the retention time range of each peak by a constant value on each side.
`expandMz`	`numeric(1)` to expand the m/z range of each peak by a constant value on each side.
`ppm`	`numeric(1)` to expand the m/z range of each peak (on each side) by a value dependent on the peak's m/z.
`method`	`character(1)` specifying which MS2 spectra should be included. Defaults to `"all"` in which all MS2 spectra within the rt and m/z range of a chromatographic peak are returned. `"closest_rt"` returns the one MS2 spectrum with the retention time closest to the chromatographic peak's apex rt. `"closest_mz"` returns the MS2 spectrum with the precursor m/z closest to the chromatographic peak's m/z. `"signal"` returns the MS2 spectrum which total signal is closest to the chromatographic peak's maximal signal (`"maxo"`).
`skipFilled`	`logical(1)` whether no spectra for filled-in peaks should be reported.
`return.type`	`character(1)` defining whether the result should be a Spectra object or a simple `list`. See below for more information.

Which object is returned depends on the value of return.type:

For return.type = "Spectra": a Spectra object with elements being Spectrum objects. The result objects contains all spectra for all peaks. Metadata column "peak_id" provides the ID of the respective peak (i.e. its rowname in chromPeaks()).
If return.type = "list": list of lists that are either of length 0 or contain Spectrum2 object(s) within the m/z-rt range. The length of the list matches the number of peaks.

Johannes Rainer

## Read a file with DDA LC-MS/MS data
fl <- system.file("TripleTOF-SWATH/PestMix1_DDA.mzML", package = "msdata")
dda <- readMSData(fl, mode = "onDisk")

## Perform MS1 peak detection
dda <- findChromPeaks(dda, CentWaveParam(peakwidth = c(5, 15)))
ms2_sps <- chromPeakSpectra(dda)
ms2_sps

## Metadata column `peak_id` contains the ID of the chromatographic peak
## of the MS2 spectrum