MSstatsPTM: MSstatsPTM: A package for detecting differencially abundant...

In devonjkohler/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

A set of tools for detecting differentially abundant PTMs and proteins in shotgun mass spectrometry-based proteomic experiments. The package can handle a variety of acquisition types, including label free, DDA, DIA, and TMT. The package includes tools to convert raw data from different spectral processing tools, summarize feature intensities, and fit a linear mixed effects model. Additionally the package includes functionality to plot a variety of data visualizations.

functions

• MaxQtoMSstatsPTMFormat : Generates MSstatsPTM required input format for TMT MaxQuant outputs.

• ProgenesistoMSstatsPTMFormat : Generates MSstatsPTM required input format for non-TMT Proteoviz outputs.

• SpectronauttoMSstatsPTMFormat : Generates MSstatsPTM required input format for non-TMT Spectronaut outputs.

• dataSummarizationPTM : Summarizes PSM level quantification to peptide (modification) and protein level quantification. For use in non-TMT analysis

• dataSummarizationPTM_TMT : Summarizes PSM level quantification to peptide (modification) and protein level quantification. For use in TMT analysis.

• dataProcessPlotsPTM : Visualization for explanatory data analysis. Specifically gives ability to plot Profile and Quality Control plots.

• groupComparisonPTM : Tests for significant changes in PTM and protein abundance across conditions. Adjusts PTM fold change for changes in protein abundance.

• groupComparisonPlotsPTM : Visualization for model-based analysis and summarization

devonjkohler/MSstatsPTM documentation built on Dec. 19, 2021, 11:01 p.m.