Citations

Please cite the following papers depending on how you use mzmine.

Latest mzmine paper:

Schmid R, Heuckeroth S, Korf A et al. Nat Biotechnol. 2023;41: 447–449. https://www.nature.com/articles/s41587-023-01690-2

Latest mzmine protocol:

Heuckeroth S, Damiani T, Smirnov A, Mokshyna O, Brungs C, Korf A, Smith JD, Stincone P, Dreolin N, Nothias LF, Hyötyläinen T, Orešič M, Karst U, Dorrestein PC, Petras D, Du X, van der Hooft JJJ, Schmid R, Pluskal T. Nat Protoc. 2024 Sep;19(9):2597-2641. doi: 10.1038/s41596-024-00996-y. https://www.nature.com/articles/s41596-024-00996-y

Lipid annotation tools:

Korf A, Jeck V, Schmid R et al. 2019; Analytical chemistry, 91(8), 5098-5105 https://pubs.acs.org/doi/abs/10.1021/acs.analchem.8b05493

Rudt, E, Froning, M, Heuckeroth S et al. 2025; Anal. Chem., 97, 14, 7781–7788 https://doi.org/10.1021/acs.analchem.4c05989

4D Feature plot (Kendrick):

Korf A, Fouquet T, Schmid, R et al. S. 2019; Analytical chemistry, 92(1), 628-633. https://doi.org/10.1021/acs.analchem.9b03863

SIMSEF On-tissue dataset-dependent MALDI-TIMS-MS2 acquisition:

Heuckeroth S, Behrens A, Wolf C et al. 2023; Nature Communications, 14(1), 7495 https://doi.org/10.1038/s41467-023-43298-9

Spectral library generation:

Brungs C, Schmid R, Heuckeroth S et al. 2025; chemRxiv https://chemrxiv.org/engage/chemrxiv/article-details/67e12c85fa469535b95db52c

Feature-based Molecular Networking:

Nothias L-F, Petras D, Schmid R et al. Nat Methods. 2020;17: 905–908. https://www.nature.com/articles/s41592-020-0933-6

Ion Identity Molecular Networking:

Schmid R, Petras D, Nothias L-F et al. Nat Commun. 2021;12: 3832. https://www.nature.com/articles/s41467-021-23953-9

Networking with DreaMS

Bushuiev R, Bushuiev A, Samusevich R, Brungs C, Sivic J, Pluskal T chemRxiv 10.26434/chemrxiv-2023-kss3r-v2 https://doi.org/10.26434/chemrxiv-2023-kss3r-v2

Networking with MS2Deepscore:

de Jonge N, Joas D, Truong LJ, van der Hooft JJJ, Huber F bioRxiv 2024.03.25.586580 https://doi.org/10.1101/2024.03.25.586580