# Handling and Managing Peptide Spectrum Matches

## Documentation for package ‘PSMatch’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

PSMatch-package | PSMatch: Handling and Managing Peptide Spectrum Matches
addFragments | labels MS2 Fragments
adjacencyMatrix | Convert to/from an adjacency matrix.
adjacencyMatrix,ConnectedComponents | Connected components
adjacencyMatrix-method | Connected components
adjacencyMatrix-method | A class for peptide-spectrum matches
calculateFragments | Calculate ions produced by fragmentation with variable modifications
calculateFragments-method | Calculate ions produced by fragmentation with variable modifications
ccMatrix | Connected components
ConnectedComponents | Connected components
connectedComponents | Connected components
ConnectedComponents-class | Connected components
defaultNeutralLoss | Calculate ions produced by fragmentation with variable modifications
describePeptides | Describe protein and peptide compositions
describeProteins | Describe protein and peptide compositions
dims,ConnectedComponents | Connected components
dims-method | Connected components
filterPsmDecoy | Filter out unreliable PSMs.
filterPsmFdr | Filter out unreliable PSMs.
filterPsmRank | Filter out unreliable PSMs.
filterPSMs | Filter out unreliable PSMs.
filterPsmShared | Filter out unreliable PSMs.
getAminoAcids | Amino acids
getAtomicMass | Atomic mass.
labelFragments | labels MS2 Fragments
length,ConnectedComponents | Connected components
length-method | Connected components
makeAdjacencyMatrix | Convert to/from an adjacency matrix.
makePeptideProteinVector | Convert to/from an adjacency matrix.
modificationPositions | Calculate ions produced by fragmentation with variable modifications
ncols,ConnectedComponents | Connected components
ncols-method | Connected components
nrows,ConnectedComponents | Connected components
nrows-method | Connected components
plotAdjacencyMatrix | Convert to/from an adjacency matrix.
plotSpectraPTM | Function to plot MS/MS spectra with PTMs
prioritiseConnectedComponents | Connected components
prioritizeConnectedComponents | Connected components
PSM | A class for peptide-spectrum matches
PSM,character | A class for peptide-spectrum matches
PSM,data.frame | A class for peptide-spectrum matches
PSM,PSM | A class for peptide-spectrum matches
PSM-class | A class for peptide-spectrum matches
PSMatch | PSMatch: Handling and Managing Peptide Spectrum Matches
psmVariables | A class for peptide-spectrum matches
readPSMs | A class for peptide-spectrum matches
reduced | A class for peptide-spectrum matches
reduced<- | A class for peptide-spectrum matches
reducePSMs | A class for peptide-spectrum matches
show,ConnectedComponents | Connected components
[,ConnectedComponents,integer,ANY,ANY | Connected components
[,ConnectedComponents,logical,ANY,ANY | Connected components
[,ConnectedComponents,numeric,ANY,ANY | Connected components
[-method | Connected components