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
extractPrecSpectra-methods
                        Extracts precursor-specific spectra from an
                        'MSnExp' object
extractSpectra-methods
                        Extracts a set of spectra from an 'MSnExp'
                        object
formatRt                Format Retention Time
iTRAQ4                  iTRAQ 4-plex set
pSet-class              Class to Contain Raw Mass-Spectrometry Assays
                        and Experimental Metadata
plot-methods            Plotting 'Spectrum' object(s)
plot2d-methods          Graphical overview of the 'MSnExp' object
quantify-methods        Quantifies 'MSnExp' and 'Spectrum' objects
readIspyData            Reads an ispy2 result spread sheet and creates
                        a fully featured 'MSnSet' instance.
readMzXMLData           Import mzXML files as 'MSnExp' instances.
removePeaks-methods     Removes low intensity peaks
trimMz-methods          Trims 'MSnExp' or 'Spectrum' instances
