ConnectedComponents     Connected components
PSM                     A class for peptide-spectrum matches
PSMatch                 PSMatch: Handling and Managing Peptide Spectrum
                        Matches
adjacencyMatrix         Convert to/from an adjacency matrix.
calculateFragments      Calculate ions produced by fragmentation with
                        variable modifications
describeProteins        Describe protein and peptide compositions
filterPSMs              Filter out unreliable PSMs.
getAminoAcids           Amino acids
getAtomicMass           Atomic mass.
labelFragments          labels MS2 Fragments
plotSpectraPTM          Function to plot MS/MS spectra with PTMs
