# Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

## Documentation for package ‘MSstatsTMT’ version 2.20.0

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

## Help Pages

MSstatsTMT-package | MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
annotation.mine | Example of annotation file for raw.mine, which is the output of SpectroMine.
annotation.mq | Example of annotation file for evidence, which is the output of MaxQuant.
annotation.pd | Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer
dataProcessPlotsTMT | Visualization for explanatory data analysis - TMT experiment
designSampleSizeTMT | Planning future experimental designs of Tandem Mass Tag (TMT) experiments acquired with Data-Dependent Acquisition (DDA or shotgun)
evidence | Example of output from MaxQuant for TMT-10plex experiments.
groupComparisonTMT | Finding differentially abundant proteins across conditions in TMT experiment
input.pd | Example of output from PDtoMSstatsTMTFormat function
MaxQtoMSstatsTMTFormat | Generate MSstatsTMT required input format from MaxQuant output
MSstatsTMT | MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
OpenMStoMSstatsTMTFormat | Generate MSstatsTMT required input format for OpenMS output
PDtoMSstatsTMTFormat | Convert Proteome Discoverer output to MSstatsTMT format.
PhilosophertoMSstatsTMTFormat | Convert Philosopher (Fragpipe) output to MSstatsTMT format.
proteinGroups | Example of proteinGroups file from MaxQuant for TMT-10plex experiments.
proteinSummarization | Summarizing peptide level quantification to protein level quantification
raw.mine | Example of output from SpectroMine for TMT-6plex experiments.
raw.om | Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.
raw.pd | Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.
SpectroMinetoMSstatsTMTFormat | Import data from SpectroMine