MSstatsTMT {MSstatsTMT} | R Documentation

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

### Description

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.

- `OpenMStoMSstatsTMTFormat` : generates MSstatsTMT required input format for OpenMS 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.

[Package MSstatsTMT version 2.0.1 Index]