ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

Devreese, R.; Jachmann, C.; Van Puyvelde, B.; Anagho-Mattanovich, H. A.; Wolski, W. E.; Webel, H.; Anagho-Mattanovich, M.; Bittremieux, W.; Chaoui, K.; Chiva, C.; Claeys, T.; Castaneda Cortes, H. M.; Devos, S.; Dhaenens, M.; Doncheva, N. T.; Dorfer, V.; Eisenacher, M.; Gabriels, R.; Giai Gianetto, Q.; Hollenstein, D. M.; Jensen, L. J.; Kasalica, V.; Langella, O.; Lennartsson, C.; Lux, D.; Martens, L.; Matondo, M.; Mendes Maia, T.; Mouton-Barbosa, E.; Nameni, A.; Nielsen, M. L.; Olsen, J. V.; Palmblad, M.; Panse, C.; Perez-Riverol, Y.; Pominova, M.; Rykaer, M.; Sabido, E.; Schessner, J.; Schnei

doi:10.64898/2025.12.09.692895

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bioRxiv · 10.64898/2025.12.09.692895

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

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Abstract

Mass spectrometry (MS)-based proteomics is a well-established strategy for analyzing complex biological mixtures. Many MS instruments and data acquisition strategies are available, and the data they acquire differ substantially, thus requiring tailored analysis algorithms. Hence, many dedicated bioinformatics workflows are developed. These are in constant evolution, and the community lacks a centralized platform for comparing their performance. Here, we propose ProteoBench, a single platform that brings together software developers and software users to provide an ever-evolving comparison of state-of-the-art proteomics data processing tools. ProteoBench is an open-source resource that enables the community to evaluate data analysis workflows, develop benchmarking modules dedicated to specific comparisons, and discuss the best methods to compare software tools. The platform ensures that the benchmark evolves alongside advances in proteomics data analysis workflows. ProteoBench guides researchers towards the best-suited tool and parameters for their specific project and data according to their needs, and developers can test their newly developed tools or workflows privately, before adding them as public references. This community-driven effort will increase transparency and reproducibility between MS data analysis workflows, as well as facilitate the development and publication of software workflows in the field.

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Devreese, R., Jachmann, C., Van Puyvelde, B., Anagho-Mattanovich, H. A., Wolski, W. E., Webel, H., Anagho-Mattanovich, M., Bittremieux, W., Chaoui, K., Chiva, C., Claeys, T., Castaneda Cortes, H. M., Devos, S., Dhaenens, M., Doncheva, N. T., Dorfer, V., Eisenacher, M., Gabriels, R., Giai Gianetto, Q., Hollenstein, D. M., Jensen, L. J., Kasalica, V., Langella, O., Lennartsson, C., Lux, D., Martens, L., Matondo, M., Mendes Maia, T., Mouton-Barbosa, E., Nameni, A., Nielsen, M. L., Olsen, J. V., Palmblad, M., Panse, C., Perez-Riverol, Y., Pominova, M., Rykaer, M., Sabido, E., Schessner, J., Schnei. 2025-12-11. ProteoBench: the community-curated platform for comparing proteomics data analysis workflows. https://doi.org/10.64898/2025.12.09.692895

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