MsBackend               Mass spectrometry data backends
MsBackendCached         Base MsBackend class providing data caching
                        mechanism
Spectra                 The Spectra class to manage and access MS data
chunkapply              Apply a function stepwise to chunks of data
combinePeaks            Aggregating and combining mass peaks data
combinePeaksData        Combine peaks with similar m/z across spectra
compareSpectra          Spectra similarity calculations
concatenateSpectra      Merging, aggregating and splitting Spectra
countIdentifications    Count the number of identifications per scan
deisotopeSpectra        Filter and subset Spectra objects
estimatePrecursorIntensity,Spectra-method
                        Estimate Precursor Intensities
estimatePrecursorMz     Estimating precursor m/z valus for DDA data
fillCoreSpectraVariables
                        Fill spectra data with columns for missing core
                        variables
filterFourierTransformArtefacts
                        Fast fourier transform artefact filter
filterPeaksRanges       Filter peaks based on spectra and peaks
                        variable ranges
fragmentGroupIndex      Mass fragmentation collections of each full
                        scan
joinPeaks               Join (map) peaks of two spectra
neutralLoss             Calculate Neutral Loss Spectra
plotMzDelta             MZ delta Quality Control
precursorPurity         Calculating Precursor Purity for MS2 spectra
processingChunkSize,Spectra-method
                        Parallel and chunk-wise processing of 'Spectra'
processingLog           Data manipulation and analysis methods
spectra-plotting        Plotting Spectra
spectraData             Accessing mass spectrometry data
spectraVariableMapping
                        Mapping between spectra variables and data file
                        fields
