MIAPE-class             The "MIAPE" Class for Storing Proteomics
                        Experiment Information
MSnExp-class            The 'MSnExp' Class for MS Data And Meta-Data
MSnProcess-class        The "MSnProcess" Class
MSnSet-class            The "MSnSet" Class for MS Proteomics Expression
                        Data and Meta-Data
MSnbase-package         MSnbase: Base Functions and Classes for
                        MS-based Proteomics
NAnnotatedDataFrame-class
                        Class Containing Measured Variables and Their
                        Meta-Data Description for Multiplexed
                        Experiments.
ReporterIons-class      The "ReporterIons" Class
Spectrum-class          The "Spectrum" Class
Spectrum1-class         The "Spectrum1" Class for MS1 Spectra
Spectrum2-class         The "Spectrum2" Class for MSMS Spectra
TMT6                    TMT 6-plex set
clean-methods           Cleans 'MSnExp' or 'Spectrum' instances
combineFeatures         Combines features in an 'MSnSet' object
extractPrecSpectra-methods
                        Extracts precursor-specific spectra from an
                        'MSnExp' object
extractSpectra-methods
                        Extracts a set of spectra from an 'MSnExp'
                        object
fillUp                  Fills up a vector
formatRt                Format Retention Time
iTRAQ4                  iTRAQ 4-plex set
itraqdata               Example 'MSnExp' data set
normalise-methods       Normalisation of 'MSnExp', 'MSnSet' and
                        'Spectrum' objects
pSet-class              Class to Contain Raw Mass-Spectrometry Assays
                        and Experimental Metadata
plot-methods            Plotting 'Spectrum' object(s)
plot2d-methods          The 'plot2d' method for 'MSnExp' quality
                        assessment
plotDensity-methods     The 'plotDensity' method for 'MSnExp' quality
                        assessment
plotMzDelta-methods     The delta m/z plot for 'MSnExp' quality
                        assessment
plotNA-methods          Exploring missing data in 'MSnSet' instances
precSelection           Number of precursor selection events
purityCorrect-methods   Performs reporter ions purity correction
quantify-methods        Quantifies 'MSnExp' and 'Spectrum' objects
readIspyData            Reads an ispy2 result spread sheet and creates
                        a fully featured 'MSnSet' instance.
readMSData              Imports mass-spectrometry raw data files as
                        'MSnExp' instances.
readMSnSet              Read 'MSnSet'
readMgfData             Import mgf files as 'MSnExp' instances.
removePeaks-methods     Removes low intensity peaks
removeReporters-methods
                        Removes reporter ion tag peaks
trimMz-methods          Trims 'MSnExp' or 'Spectrum' instances
writeMgfData-methods    Write an experiment or spectrum to an mgf file
