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

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

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

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 and TMT experiments, acquired with DDA, DIA, SRM or PRM acquisition methods. The package includes tools to convert raw data from different spectral processing tools, summarize feature intensities, and fit a linear mixed effects model. A major advantage of the package is to leverage a separate global profiling run and adjust the PTM fold change for changes in the unmodified protein, showing the unconvoluted PTM fold change. Finally, the package includes functionality to plot a variety of data visualizations.

functions

• FragPipetoMSstatsPTMFormat : Generates MSstatsPTM required input format for TMT FragePipe outputs.

• MaxQtoMSstatsPTMFormat : Generates MSstatsPTM required input format for label-free and TMT MaxQuant outputs.

• ProgenesistoMSstatsPTMFormat : Generates MSstatsPTM required input format for label-free Progenesis outputs.

• SpectronauttoMSstatsPTMFormat : Generates MSstatsPTM required input format for label-free Spectronaut outputs.

• SkylinetoMSstatsPTMFormat : Generates MSstatsPTM required input format for Skyline outputs.

• PStoMSstatsPTMFormat : Generates MSstatsPTM required input format for PEAKS outputs.

• PDtoMSstatsPTMFormat : Generates MSstatsPTM required input format for Proteome Discoverer outputs.

• dataSummarizationPTM : Summarizes PSM level quantification to peptide (modification) and protein level quantification. For use in label-free 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

Author(s)

Maintainer: Devon Kohler [e-mail]

Authors:

• Tsung-Heng Tsai [e-mail]

• Ting Huang [e-mail]

• Mateusz Staniak [e-mail]

• Meena Choi [e-mail]

• Olga Vitek [e-mail]

See Also

Useful links:

• Report bugs at https://github.com/Vitek-Lab/MSstatsPTM/issues

Vitek-Lab/MSstatsPTM documentation built on Dec. 19, 2024, 6:02 a.m.