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

## Documentation for package ‘MSstatsTMTPTM’ version 1.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.