# Statistical Characterization of Post-translational Modifications

## Documentation for package ‘MSstatsPTM’ version 2.2.0

- 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
designSampleSizePTM | Planning future experimental designs of PTM experiments in sample size calculation
FragPipetoMSstatsPTMFormat | Convert output of TMT labeled Fragpipe data into MSstatsPTM format.
fragpipe_annotation | Example annotation file for a TMT FragPipe experiment.
fragpipe_annotation_protein | Example annotation file for a global profiling run TMT FragPipe experiment.
fragpipe_input | Output of FragPipe TMT PTM experiment
fragpipe_input_protein | Output of FragPipe TMT global profiling experiment
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
maxq_lf_annotation | Example annotation file for a label-free MaxQuant experiment.
maxq_lf_evidence | Example MaxQuant evidence file from the output of a label free experiment
maxq_tmt_annotation | Example annotation file for a TMT MaxQuant experiment.
maxq_tmt_evidence | Example MaxQuant evidence file from the output of a TMT experiment
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
pd_annotation | Example annotation file for a label-free Proteome Discoverer experiment.
pd_psm_input | Example Proteome Discoverer evidence file from the output of a label free experiment
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
spectronaut_annotation | Example annotation file for a label-free Spectronaut experiment.
spectronaut_input | Example Spectronaut evidence file from the output of a label free experiment
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