omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.

Segers, A.; Castiglione, C.; Vanderaa, C.; De Baere, E.; Martens, L.; Risso, D.; Clement, L.

doi:10.1101/2025.03.24.644996

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bioRxiv · 10.1101/2025.03.24.644996

omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.

Segers, A.·Castiglione, C.·Vanderaa, C.·De Baere, E.·Martens, L.·Risso, D.·Clement, L.

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Abstract

The unprecedented speed and sensitivity of mass spectrometry (MS) unlocked large-scale applications of proteomics and even enabled proteome profiling of single cells. However, this fast-evolving field is hindered by a lack of scalable dimensionality reduction tools that can compensate for substantial batch effects and missingness across MS runs. Therefore, we present omicsGMF, a fast, scalable, and interpretable matrix factorization method, tailored for bulk and single-cell proteomics data. Unlike current workflows that sequentially apply imputation, batch correction, and principal component analysis, omicsGMF integrates these steps into a unified framework, dramatically enhancing data processing and dimensionality reduction. Additionally, omicsGMF provides robust imputation of missing values, outperforming bespoke state-of-the-art imputation tools. We further demonstrate how this integrated approach increases statistical power to detect differentially abundant proteins in the downstream data analysis. Hence, omicsGMF is a highly scalable approach to dimensionality reduction in proteomics, that dramatically improves many important steps in proteomics data analysis.

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Segers, A., Castiglione, C., Vanderaa, C., De Baere, E., Martens, L., Risso, D., Clement, L.. 2025-03-28. omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.. https://doi.org/10.1101/2025.03.24.644996

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