Statistical Characterization of Post-translational Modifications

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Documentation for package ‘MSstatsPTM’ version 2.11.3

• 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
dataProcessPTM	Data processing and summarization of peptide-level quantification to PTM and protein level quantification
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
ProteinProspectortoMSstatsPTMFormat	Generate MSstatsPTM required input format from Protein Prospector output
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