analyzeMsMs: Analyze MSMS spectra

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Analyzes MSMS spectra of a compound by fitting formulas to each subpeak.

Usage

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
)

Arguments

msmsPeaks	A 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).
mode	Specifies the processing mode, i.e. which molecule species the spectra contain. 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.)
detail	Whether detailed return information should be provided (defaults to FALSE). See below.
run	"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".
filterSettings	Settings for the filter parameters, by default loaded from the RMassBank settings set with e.g. 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).
spectraList	The list of MS/MS spectra present in each data block. As also defined in the settings file.
method	Selects which function to actually use for data evaluation. The default "formula" runs a full analysis via formula assignment to fragment peaks. The alternative setting "intensity" calls a "mock" implementation which circumvents formula assignment and filters peaks purely based on intensity cutoffs and the satellite filtering. (In this case, the ppm and dbe related settings in filterSettings are ignored.)

Details

The analysis function uses Rcdk. Note that in this step, satellite peaks are removed by a simple heuristic rule (refer to the documentation of filterPeakSatellites for details.)

Value

The processed RmbSpectraSet object. Added (or filled, respectively, since the slots are present before) data include

list("complete")	whether all spectra have useful value
list("empty")	whether there are no useful spectra
list("children")	The processed 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 All other entries are retained from the original RmbSpectrum2.

Functions

• analyzeMsMs.formula: Analyze the peaks using formula annotation

• analyzeMsMs.intensity: Analyze the peaks going only by intensity values

Author(s)

Michael Stravs

See Also

msmsWorkflow, filterLowaccResults, filterPeakSatellites, reanalyzeFailpeaks

Examples

	## Not run: analyzed <- analyzeMsMs(spec, "pH", TRUE)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.