Enhanced usability in the MSstats family of statistical analysis software for quantitative mass spectrometry(MS)-based proteomics
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This work presented new usability and infrastructure enhancements to the MSstats family of tools for statistical analysis of quantitative MS-based proteomics. The updates included expanded data converters (e.g., for DIA-NN, FragPipe, MetaMorpheus), scalable workflows for large datasets via MSstatsBig, improved support for planning TMT-labeled experiments, and new interactive visualization features. These developments reduced the coding burden on users, helped prevent common analytical mistakes, and make advanced statistical workflows more accessible, enabling accurate and efficient detection of differentially abundant proteins across diverse experimental designs.