chromPeakSpectra {xcms}

R Documentation

Extract spectra associated with chromatographic peaks

Description

Extract (MS1 or MS2) spectra from an XCMSnExp object for each identified chromatographic peak. The function returns by default spectra for chromatographic peaks of all MS levels, but parameter peaks allows to restrict the result to selected chromatographic peaks. For msLevel = 1L (only supported for return.type = "Spectra" or return.type = "List") MS1 spectra within the retention time boundaries (in the file in which the peak was detected) are returned. For msLevel = 2L MS2 spectra are returned for a chromatographic peak if their precursor m/z is within the retention time and m/z range of the chromatographic peak. Parameter method allows to define whether all or a single spectrum should be returned:

• method = "all": (default): return all spectra for each peak.

• method = "closest_rt": return the spectrum with the retention time closest to the peak's retention time (at apex).

• method = "closest_mz": return the spectrum with the precursor m/z closest to the peaks's m/z (at apex); only supported for msLevel = 2L.

• method = "signal": return the spectrum with the sum of intensities most similar to the peak's apex signal ("maxo"); only supported for msLevel = 2L.

• method = "largest_tic": return the spectrum with the largest total signal (sum of peaks intensities).

• method = "largest_bpi": return the spectrum with the largest peak intensity (maximal peak intensity).

Parameter return.type allows to specify the type of the result object. Please use return.type = "Spectra" or return.type = "List", return.type = "list" or the default return.type = "MSpectra" will be deprecated (also, they do not support extracting MS1 spectra).

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

Usage

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

Arguments

x	XCMSnExp object with identified chromatographic peaks.
msLevel	integer(1) defining whether MS1 or MS2 spectra should be returned. msLevel = 1 is currently only supported for return.type being "Spectra" or "List".
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 spectra to include in the result. Defaults to method = "all". See function description for details.
skipFilled	logical(1) whether spectra for filled-in peaks should be reported or not.
return.type	character(1) defining the result type. Defaults to return.type = "MSpectra" but return.type = "Spectra" or return.type = "List" are preferred. See below for more information.
peaks	character, logical or integer allowing to specify a subset of chromatographic peaks in chromPeaks for which spectra should be returned (providing either their ID, a logical vector same length than nrow(chromPeaks(x)) or their index in chromPeaks(x)). This parameter overrides skipFilled and is only supported for return.type being either "Spectra" or "List".

Value

parameter return.type allow to specify the type of the returned object:

• return.type = "MSpectra": a MSpectra 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()).

• return.type = "Spectra": a Spectra object (defined in the Spectra package). The result contains all spectra for all peaks. Metadata column "peak_id" provides the ID of the respective peak (i.e. its rowname in chromPeaks() and "peak_index" its index in the object's chromPeaks matrix.

• 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.

• return.type = "List": List of length equal to the number of chromatographic peaks is returned with elements being either NULL (no spectrum found) or a Spectra object.

Author(s)

Johannes Rainer

Examples

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

## Subset the object to reduce runtime of the example
dda <- filterRt(dda, c(200, 400))

## Perform MS1 peak detection
dda <- findChromPeaks(dda, CentWaveParam(peakwidth = c(5, 15), prefilter = c(5, 1000)))

## Load the required Spectra package and return all MS2 spectro for each
## chromatographic peaks as a Spectra object
ms2_sps <- chromPeakSpectra(dda, return.type = "Spectra")
ms2_sps

## columns peak_id or peak_index assign spectra to the chromatographic peaks
ms2_sps$peak_id
ms2_sps$peak_index
chromPeaks(dda)

## Alternatively, return the result as a List of Spectra objects. This list
## is parallel to chromPeaks hence the mapping between chromatographic peaks
## and MS2 spectra is easier.
ms2_sps <- chromPeakSpectra(dda, return.type = "List")
ms2_sps[[1L]]
length(ms2_sps)

## In addition to MS2 spectra we could also return the MS1 spectrum for each
## chromatographic peak which is closest to the peak's apex position.
ms1_sps <- chromPeakSpectra(dda, msLevel = 1L, method = "closest_rt",
    return.type = "Spectra")
ms1_sps

## Parameter peaks would allow to extract spectra for specific peaks only
chromPeakSpectra(dda, msLevel = 1L, method = "closest_rt", peaks = c(3, 5))

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