MSstatsPTM: A package for detecting differencially abundant post translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic experiments.

Source: R/MSstatsPTM.R

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.

  • 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