Reference

All functions
PTMods PTMods-package	Managing amino acid modifications for mass spectrometry in R.
addFixedModifications()	Add fixed modifications
addModifications()	Add fixed and variable modifications to peptide sequences
addVariableModifications()	Add variable modifications
aminoacids	Amminoacids data set.
combineModifications()	Combines consecutive modifications on amino acids in peptide sequences.
convertAnnotation()	Convert sequences from one annotation style to another
elements	Elements data set.
getCanonicalSequence()	Get canonical sequence from any peptidoform
getModificationsCounts()	Extract modification counts from one or more peptide sequences
modifications	Modifications data set.