A set of tools for detecting differentially abundant PTMs and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. The functions in this package should be used after PTM/protein summarization. They can be used to both plot the summarized results and model the summarized datasets.
dataProcessPlotsTMTPTM : Data visualization of PTM and
global protein levels. Can plot either Profile plots to identify the
potential sources of variation for each protein, or quality control
plots to evaluate the systematic bias between MS runs.
groupComparisonTMTPTM : Tests for significant changes
in PTM abundance adjusted for global protein abundance across conditions
based on a family of linear mixed-effects models in TMT experiment.
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