Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Documentation for package ‘MSstatsTMTPTM’ version 1.0.2

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
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.
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.