# Statistical Characterization of Post-translational Modifications

## Documentation for package ‘MSstatsPTM’ version 2.0.3

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

## 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