MSstatsPTM              MSstatsPTM: A package for detecting
                        differencially abundant post translational
                        modifications (PTM) in shotgun mass
                        spectrometry-bsed proteomic experiments.
MaxQtoMSstatsPTMFormat
                        Convert output of TMT labeled MaxQuant
                        experiment into MSstatsPTM format
ProgenesistoMSstatsPTMFormat
                        Converts non-TMT Progenesis output into the
                        format needed for MSstatsPTM
SpectronauttoMSstatsPTMFormat
                        Converts raw PTM MS data from Spectronautt into
                        the format needed for MSstatsPTM.
annotSite               Annotate modification site
dataProcessPlotsPTM     Visualization for explanatory data analysis
dataSummarizationPTM    Process MS PTM and global protein data
dataSummarizationPTM_TMT
                        Process MS PTM and global protein data produced
                        via tandem mass tag labeling
groupComparisonPTM      Model PTM and/or protein data and make
                        adjustments if needed
groupComparisonPlotsPTM
                        Visualization for model-based analysis and
                        summarization
locateMod               Locate modified sites with a peptide
locatePTM               Annotate modified sites with associated
                        peptides
raw.input               Example of input PTM dataset for
                        LabelFree/DDA/DIA experiments.
raw.input.tmt           Example of input PTM dataset for TMT
                        experiments.
summary.data            Example of output from dataSummarizationPTM
                        function for non-TMT data
summary.data.tmt        Example of output from dataSummarizationPTM_TMT
                        function for TMT data
tidyFasta               Read and tidy a FASTA file
