MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

A set of tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.

functions

• PDtoMSstatsTMTFormat : generates MSstatsTMT required input format for Proteome discoverer output.

• MaxQtoMSstatsTMTFormat : generates MSstatsTMT required input format for MaxQuant output.

• SpectroMinetoMSstatsTMTFormat : generates MSstatsTMT required input format for SpectroMine output.

• proteinSummarization : summarizes PSM level quantification to protein level quantification.

• dataProcessPlotsTMT : visualizes for explanatory data analysis.

• groupComparisonTMT : tests for significant changes in protein abundance across conditions.