# Statistical Characterization of Post-translational Modifications

## Documentation for package ‘MSstatsPTM’ version 1.4.0

- 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
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.
ProgenesistoMSstatsPTMFormat | Converts non-TMT Progenesis output into the format needed for MSstatsPTM
raw.input | Example of input PTM dataset for LabelFree/DDA/DIA experiments.
raw.input.tmt | Example of input PTM dataset for TMT experiments.
SpectronauttoMSstatsPTMFormat | Converts raw PTM MS data from Spectronautt into the format needed for MSstatsPTM.
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