chromPeakSpectra {xcms} | R Documentation |
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("MSpectra", "list") )
x |
XCMSnExp object with identified chromatographic peaks. |
msLevel |
|
expandRt |
|
expandMz |
|
ppm |
|
method |
|
skipFilled |
|
return.type |
|
Which object is returned depends on the value of return.type
:
For 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()
).
If return.type = "list"
: list
of list
s 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") ## 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))) ms2_sps <- chromPeakSpectra(dda) ms2_sps ## Metadata column `peak_id` contains the ID of the chromatographic peak ## of the MS2 spectrum