Description Usage Arguments Details Value Author(s) See Also
View source: R/functions-XCMSnExp.R
Reconstructs MS2 spectra for each MS1 chromatographic peak (if possible) for data independent acquisition (DIA) data (such as SWATH). See the LC-MS/MS analysis vignette for more details and examples.
1 2 3 4 5 6 7 8 9 | reconstructChromPeakSpectra(
object,
expandRt = 0,
diffRt = 2,
minCor = 0.8,
intensity = "maxo",
peakId = rownames(chromPeaks(object, msLevel = 1L)),
BPPARAM = bpparam()
)
|
object |
|
expandRt |
|
diffRt |
|
minCor |
|
intensity |
|
peakId |
optional |
BPPARAM |
parallel processing setup. See |
In detail, the function performs for each MS1 chromatographic peak:
Identify all MS2 chromatographic peaks from the isolation window
containing the m/z of the ion (i.e. the MS1 chromatographic peak) with
approximately the same retention time than the MS1 peak (accepted rt shift
can be specified with the diffRt
parameter).
Correlate the peak shapes of the candidate MS2 chromatographic peaks with
the peak shape of the MS1 peak retaining only MS2 chromatographic peaks
for which the correlation is > minCor
.
Reconstruct the MS2 spectrum using the m/z of all above selected MS2
chromatographic peaks and their intensity (either "maxo"
or "into"
).
Each MS2 chromatographic peak selected for an MS1 peak will thus represent
one mass peak in the reconstructed spectrum.
The resulting MSpectra
object provides also the peak IDs of the MS2
chromatographic peaks for each spectrum as well as their correlation value.
MSpectra()
with the reconstructed MS2 spectra for all MS1 peaks
in object
. Contains empty Spectrum2 objects for MS1 peaks for
which reconstruction was not possible (either no MS2 signal was recorded
or the correlation of the MS2 chromatographic peaks with the MS1
chromatographic peak was below threshold minCor
. MSpectra
metadata
columns "ms2_peak_id"
and "ms2_peak_cor"
(of type CharacterList()
and NumericList()
with length equal to the number of peaks per
reconstructed MS2 spectrum) providing the IDs and the correlation of the
MS2 chromatographic peaks from which the MS2 spectrum was reconstructed.
As retention time the median retention times of all MS2 chromatographic
peaks used for the spectrum reconstruction is reported. The MS1
chromatographic peak intensity is reported as the reconstructed
spectrum's precursorIntensity
value (see parameter intensity
above).
Johannes Rainer, Michael Witting
findChromPeaksIsolationWindow()
for the function to perform MS2
peak detection in DIA isolation windows and for examples.
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