getMultipleBPC: Extract multiple ion chromatograms from mass spectrometry...

In HiResTEC: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data

Extract multiple ion chromatograms from mass spectrometry data.

Description

getMultipleBPC will extract multiple BPCs from an 'xcmsRaw' or 'xcmsRawLike' object for a vector of mz within the limits given by rt, rt_dev and mz_dev.

Usage

getMultipleBPC(
  x,
  mz = NULL,
  mz_dev = 0.005,
  rt = NULL,
  rt_dev = 2,
  zeroVal = NA,
  smooth = 0,
  returnEIC = FALSE
)

Arguments

x	'xcmsRaw' or 'xcmsRawLike' object.
mz	Numeric vector of masses or NULL (default) to return the overall BPC.
mz_dev	Allowed mass deviations (can be a single numeric, a vector, a matrix with one row (lower bound, upper bound) or a matrix with length(mz) rows giving lower and upper bound for each mz).
rt	Target retention time or NULL (default) to use full time range.
rt_dev	Allowed time deviation (if rt is specified).
zeroVal	Set values <=0 to NA or keep as is with NULL.
smooth	Window size for moving average smoother, 0 = no smoothing.
returnEIC	Return EIC instead of BPC?

Details

While there are other functions to extract BPC information from raw data, this one is particularly useful to get all traces belonging to a isotopologue group. It will attach several derived values to the results object, i.e. describing the observed mass shift (deviation from expected value) which is helpful in QC for non-targeted tracer analyses. While the 'mz' and 'mz_dev' parameters can be vectorized, the 'rt' and 'rt_dev' values will be consistently used for all ion traces.

Value

A matrix with scan wise (rows) intensities for all requested masses (columns) as either EIC or BPC.

References

Uses C code modified from XCMS (see citation("xcms")).

Examples

raw <- HiResTEC::raw
# search for mz = 556.263 and its isotopic traces
mz <- 556.263 + c(0:3) * 1.0034
getMultipleBPC(x = raw[[1]], mz = mz, mz_dev = 0.04, rt = 1026)

HiResTEC documentation built on April 3, 2025, 9:35 p.m.