Statistical Characterization of Post-translational Modifications

---

Documentation for package ‘MSstatsPTM’ version 2.9.1

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

Help Pages

MSstatsPTM-package	MSstatsPTM: A package for detecting differentially abundant post-translational modifications (PTM) in mass spectrometry-based proteomic experiments.
annotSite	Annotate modification site
dataProcessPlotsPTM	Visualization for explanatory data analysis
dataSummarizationPTM	Data summarization function for label-free MS experiments targeting PTMs.
dataSummarizationPTM_TMT	Data summarization function for TMT labelled MS experiments targeting PTMs.
designSampleSizePTM	Planning future experimental designs of PTM experiments in sample size calculation
DIANNtoMSstatsPTMFormat	Convert the output of DIA-NN PSM file into MSstatsPTM format
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	Perform differential analysis on MS-based proteomics experiments targeting PTMs
locateMod	Locate modified sites with a peptide
locatePTM	Annotate modified sites with associated peptides
MaxQtoMSstatsPTMFormat	Convert output of label-free or TMT MaxQuant experiments 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
MetamorpheusToMSstatsPTMFormat	Import Metamorpheus files into PTM format
MSstatsPTM	MSstatsPTM: A package for detecting differentially abundant post-translational modifications (PTM) in mass spectrometry-based 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
pd_testing_output	Example output of Proteome Discoverer converter
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