All functions

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

globalConverterPTM()

General converter function for MSstatsPTM.

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.

tidyFasta()

Read and tidy a FASTA file