Statistical Characterization of Post-translational Modifications

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Documentation for package ‘MSstatsPTM’ version 2.0.3

Help Pages

annotSite Annotate modification site
dataProcessPlotsPTM Visualization for explanatory data analysis
dataSummarizationPTM Process MS PTM and global protein data
dataSummarizationPTM_TMT Process MS PTM and global protein data produced via tandem mass tag labeling
designSampleSizePTM Planning future experimental designs of PTM experiments in sample size calculation
groupComparisonPlotsPTM Visualization for model-based analysis and summarization
groupComparisonPTM Model PTM and/or protein data and make adjustments if needed
locateMod Locate modified sites with a peptide
locatePTM Annotate modified sites with associated peptides
MaxQtoMSstatsPTMFormat Convert output of TMT labeled MaxQuant experiment into MSstatsPTM format
MSstatsPTM MSstatsPTM: A package for detecting differencially abundant post translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic experiments.
MSstatsPTMSiteLocator Locate modification site number and amino acid
PDtoMSstatsPTMFormat Convert Proteome Discoverer output into MSstatsPTM format
PhilosophertoMSstatsPTMFormat Convert output of TMT labaled Fragpipe (Philosopher) data into MSstatsPTM format.
ProgenesistoMSstatsPTMFormat Converts non-TMT Progenesis output into the format needed for MSstatsPTM
PStoMSstatsPTMFormat Convert Peaks Studio output into MSstatsPTM format
raw.input Example of input PTM dataset for LabelFree/DDA/DIA experiments.
raw.input.tmt Example of input PTM dataset for TMT experiments.
SkylinetoMSstatsPTMFormat Convert Skyline output into MSstatsPTM format
SpectronauttoMSstatsPTMFormat Convert Spectronaut output into MSstatsPTM format
summary.data Example of output from dataSummarizationPTM function for non-TMT data
summary.data.tmt Example of output from dataSummarizationPTM_TMT function for TMT data
tidyFasta Read and tidy a FASTA file