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
exprsToRatios-methods   Calculate all ratio pairs
extractPrecSpectra-methods
                        Extracts precursor-specific spectra from an
                        'MSnExp' object
featureCV               Calculates coeffivient of variation for
                        features
fillUp                  Fills up a vector
formatRt                Format Retention Time
getVariableName         Return a variable name
iTRAQ4                  iTRAQ 4-plex set
impute-methods          Quantitative proteomics data imputation
itraqdata               Example 'MSnExp' data set
makeMTD                 Creates the mzTab metadata section
makePEP                 Creates the mzTab peptide section
makePRT                 Creates the mzTab protein section
nQuants                 Count the number of quantitfied features.
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.
readMzTabData           Read an 'mzTab' file
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
writeMzTabData          Writes an 'MSnSet' to an mzTab file
