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Updated: Aug 4, 2025
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
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MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with
Devon Kohler1, Mateusz Staniak2, Tsung-Heng Tsai1
1Khoury College of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States.
Journal of Proteome Research
|April 5, 2023
Summary
The updated MSstats v4.0 package enhances statistical analysis for mass spectrometry proteomics, improving usability and accuracy in detecting differentially abundant proteins. This version offers better performance and computational efficiency for complex proteomic experiments.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- The MSstats R-Bioconductor package is a key tool for statistical analysis in quantitative mass spectrometry-based proteomics.
- Increasing experimental complexity necessitates updates to robust statistical software for detecting differentially abundant proteins.
Purpose of the Study:
- To detail the substantial updates in the new MSstats v4.0 package.
- To highlight improvements in usability, versatility, accuracy, and computational resource utilization.
- To compare MSstats v4.0 with previous versions and competing software (MSqRob, DEqMS).
Main Methods:
- Substantial refactoring of MSstats code for improved memory usage and computation speed.
- Updating statistical models to a more robust workflow.
- Integration of new converters for seamless input from upstream data processing tools.
Main Results:
- MSstats v4.0 demonstrates improved usability, versatility, and accuracy in statistical methodology.
- New converters reduce manual user effort by directly integrating upstream processing tool outputs.
- Empirical comparisons show MSstats v4.0 outperforms previous versions and competing packages (MSqRob, DEqMS) in performance and usability.
Conclusions:
- MSstats v4.0 represents a significant advancement for statistical analysis in quantitative proteomics.
- The updated package offers enhanced performance, efficiency, and user-friendliness for analyzing complex proteomic datasets.
- MSstats v4.0 is recommended for researchers seeking robust and accurate differential protein abundance analysis.
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