MSstatsTMTPTM           MSstatsTMTPTM: A package for detecting
                        differencially abundant post translational
                        modifications (PTM) in shotgun mass
                        spectrometry-bsed proteomic experiments with
                        tandem mass tag (TMT) labeling.
dataProcessPlotsTMTPTM
                        Visualization for explanatory data analysis -
                        TMT experiment
example.contrast.matrix
                        Example contrast matrix for input into the
                        groupComparisonTMTPTM function
groupComparisonTMTPTM   Model PTM and/or protein data and make
                        adjustments if needed
model.results.contrast
                        Ouput of groupComparisonTMTPTM for specific
                        comparisons of interest
model.results.pairwise
                        Ouput of groupComparisonTMTPTM for full
                        pairwise test
quant.msstats.protein   Example of output from proteinSummarizaiton
                        function for Protein data
quant.msstats.ptm       Example of output from proteinSummarizaiton
                        function for PTM data
raw.protein             Example of input Protein dataset for TMT
                        experiments.
raw.ptm                 Example of input PTM dataset for TMT
                        experiments.
