MSstatsTMT              MSstatsTMT: A package for protein significance
                        analysis in shotgun mass spectrometry-based
                        proteomic experiments with tandem mass tag
                        (TMT) labeling
MaxQtoMSstatsTMTFormat
                        Generate MSstatsTMT required input format from
                        MaxQuant output
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.
SpectroMinetoMSstatsTMTFormat
                        Import data from SpectroMine
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
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.
