buildIonTree            Build ion tree
createDB                Create a SQLite database
distMS2                 Distance metric for MS2 spectral similarity
                        measurement
formatSpec              Format mass spec matrix data into a string
                        format, or vice versa
getMSnRaw               Get MSn raw data
getMetaInfo             Get metadata information from data file in
                        mzXML
hasMS2                  Check which samples have MS2 spectra generated
iontree-class           Class "iontree"
iontree-package         MSn-iontree: Ion tree management and analysis
metaDataImport          Data entry of meta information
mzImport                Data entry of iontree into mz table
plot-methods            Plot iontree
plotSpectrum            Plot a spectrum
rs2iontree              Convert a data frame into iontree
saveMSnRaw              Retrieve MS2 and MS3 data and save as R binary
                        in the current folder
searchMS2               Search MS2 spectrum from sqlite database
show-methods            Show methods for class iontree
topIons                 Retain spectrum with the most intense ions
