DIANNtoMSstatsPTMFormat
                        Convert the output of DIA-NN PSM file into
                        MSstatsPTM format
FragPipetoMSstatsPTMFormat
                        Convert output of TMT labeled Fragpipe data
                        into MSstatsPTM format.
MSstatsPTM              MSstatsPTM: A package for detecting
                        differentially abundant post-translational
                        modifications (PTM) in mass spectrometry-based
                        proteomic experiments.
MSstatsPTMSiteLocator   Locate modification site number and amino acid
MaxQtoMSstatsPTMFormat
                        Convert output of label-free or TMT MaxQuant
                        experiments into MSstatsPTM format
MetamorpheusToMSstatsPTMFormat
                        Import Metamorpheus files into PTM format
PDtoMSstatsPTMFormat    Convert Proteome Discoverer output into
                        MSstatsPTM format
PStoMSstatsPTMFormat    Convert Peaks Studio output into MSstatsPTM
                        format
ProgenesistoMSstatsPTMFormat
                        Converts non-TMT Progenesis output into the
                        format needed for MSstatsPTM
SkylinetoMSstatsPTMFormat
                        Convert Skyline output into MSstatsPTM format
SpectronauttoMSstatsPTMFormat
                        Convert Spectronaut output into MSstatsPTM
                        format
annotSite               Annotate modification site
dataProcessPlotsPTM     Visualization for explanatory data analysis
dataSummarizationPTM    Data summarization function for label-free MS
                        experiments targeting PTMs.
dataSummarizationPTM_TMT
                        Data summarization function for TMT labelled MS
                        experiments targeting PTMs.
designSampleSizePTM     Planning future experimental designs of PTM
                        experiments in sample size calculation
fragpipe_annotation     Example annotation file for a TMT FragPipe
                        experiment.
fragpipe_annotation_protein
                        Example annotation file for a global profiling
                        run TMT FragPipe experiment.
fragpipe_input          Output of FragPipe TMT PTM experiment
fragpipe_input_protein
                        Output of FragPipe TMT global profiling
                        experiment
groupComparisonPTM      Perform differential analysis on MS-based
                        proteomics experiments targeting PTMs
groupComparisonPlotsPTM
                        Visualization for model-based analysis and
                        summarization
locateMod               Locate modified sites with a peptide
locatePTM               Annotate modified sites with associated
                        peptides
maxq_lf_annotation      Example annotation file for a label-free
                        MaxQuant experiment.
maxq_lf_evidence        Example MaxQuant evidence file from the output
                        of a label free experiment
maxq_tmt_annotation     Example annotation file for a TMT MaxQuant
                        experiment.
maxq_tmt_evidence       Example MaxQuant evidence file from the output
                        of a TMT experiment
pd_annotation           Example annotation file for a label-free
                        Proteome Discoverer experiment.
pd_psm_input            Example Proteome Discoverer evidence file from
                        the output of a label free experiment
pd_testing_output       Example output of Proteome Discoverer converter
raw.input               Example of input PTM dataset for
                        LabelFree/DDA/DIA experiments.
raw.input.tmt           Example of input PTM dataset for TMT
                        experiments.
spectronaut_annotation
                        Example annotation file for a label-free
                        Spectronaut experiment.
spectronaut_input       Example Spectronaut evidence file from the
                        output of a label free experiment
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
