analyzeMsMs(msmsPeaks, mode = "pH", detail = FALSE, run = "preliminary", filterSettings = getOption("RMassBank")$filterSettings, spectraList = getOption("RMassBank")$spectraList, method = "formula")
analyzeMsMs.formula(msmsPeaks, mode = "pH", detail = FALSE, run = "preliminary", filterSettings = getOption("RMassBank")$filterSettings)
analyzeMsMs.intensity(msmsPeaks, mode = "pH", detail = FALSE, run = "preliminary", filterSettings = getOption("RMassBank")$filterSettings)RmbSpectraSet object.
Corresponds to a parent spectrum and children MSMS spectra of one compound (plus some metadata).
The objects are typically generated with findMsMsHR, and populate the @spectrum slot
in a msmsWorkspace (refer to the corresponding
documentation for the precise format specifications).pH (positive H) specifies [M+H]+,
pNa specifies [M+Na]+, pM specifies [M]+,
mH and mNa specify [M-H]- and [M-Na]-,
respectively. (I apologize for the naming of pH which has
absolutely nothing to do with chemical pH values.)FALSE). See below."preliminary" or "recalibrated". In the
preliminary run, mass tolerance is set to 10 ppm (above m/z 120) and
15 ppm (below m/z 120), the default intensity cutoff is $10^4$ for positive
mode (no default cutoff in negative mode), and the column "mz" from
the spectra is used as data source. In the recalibrated run, the
mass tolerance is set to 5 ppm over the whole mass range, the default cutoff
is 0 and the column "mzRecal" is used as source for the m/z values.
Defaults to "preliminary".loadRmbSettings. Must contain:
ppmHighMass, allowed ppm deviation before recalibration
for high mass range
ppmLowMass, allowed ppm deviation before recalibration
for low mass range
massRangeDivision, division point between high and low mass
range (before recalibration)
ppmFine, allowed ppm deviation overall after recalibration
prelimCut, intensity cutoff for peaks in preliminary run
prelimCutRatio, relative intensity cutoff for peaks in
preliminary run, e.g. 0.01 = 1
fineCut, intensity cutoff for peaks in second run
fineCutRatio, relative intensity cutoff for peaks in
second run
specOkLimit, minimum intensity of base peak for spectrum
to be accepted for processing
dbeMinLimit, minimum double bond equivalent for accepted
molecular subformula.
satelliteMzLimit, for satellite peak filtering
(filterPeakSatellites: mass window to use for satellite
removal
satelliteIntLimit, the relative intensity below which to
discard "satellites". (refer to filterPeakSatellites).
RmbSpectraSet object.
Added (or filled, respectively, since the slots are present before) data include
RmbSpectrum2 objects (in a RmbSpectrum2List).
ok if the spectrum was successfully processed with at least one resulting peak
mz, intensity: note that mz/int pairs can be duplicated when multiple matches
are found for one mz value, therefore the two slots are not necessarily unchanged from before
rawOK (logical) whether the m/z peak passes satellite/low removal
low, satellite if TRUE, the peak failed cutoff (low) or was removed as satellite
formula, mzCalc, dppm, dbe Formula, calculated mass, ppm deviation and dbe assigned to a peak
formulaCount, dppmBest Number of formulae matched for this m/z value and ppm deviation of the best match
info Spectrum identifying information (collision energy, resolution, collision mode) from
the spectraList
RmbSpectrum2.
analyzeMsMs.formula: Analyze the peaks using formula annotation analyzeMsMs.intensity: Analyze the peaks going only by intensity values
filterPeakSatellites for details.)
msmsWorkflow, filterLowaccResults,
filterPeakSatellites, reanalyzeFailpeaks
## Not run: analyzed <- analyzeMsMs(spec, "pH", TRUE)
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