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


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Documentation for package ‘MSstatsTMT’ version 2.12.0

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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
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