Skip to content

Science

Peer-reviewed, not just marketed.

The methods inside mzmine are published in Nature Biotechnology, Nature Communications, Nature Methods and Analytical Chemistry. You can read them, check them, and cite them, which is not something most commercial analytical software can offer.

Open Innovation Academic program

Open source since 2005 · Independently validated · Freely citable

20+
Years of open development
7,000+
Peer-reviewed citations
20,000+
Active users worldwide

Key publications

The methods, in the literature.

2023
Integrative analysis of multimodal mass spectrometry data in MZmine 3 (opens in a new tab)
Schmid et al. · Nature Biotechnology 41, 447–449
The methods paper for the platform itself. Cite this one if you cite only one.
2026
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS (opens in a new tab)
Bushuiev et al. · Nature Biotechnology 44, 630–640
A foundation model for MS2 spectra, trained on millions of unannotated spectra.
2025
MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries (opens in a new tab)
Brungs, Schmid, Heuckeroth et al. · Nature Methods 22, 2028–2031
How the in-house libraries are built, and why an MSn library beats a flat MS2 one.
2025
Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine (opens in a new tab)
Rudt et al. · Analytical Chemistry 97, 7781–7788
Applied work from the mzio team, with Heuckeroth, Schmid, Pluskal and Korf as co-authors.
2023
On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging (opens in a new tab)
Heuckeroth et al. · Nature Communications 14, 7495
SIMSEF: systematic on-tissue MS2 acquisition.
2021
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment (opens in a new tab)
Schmid et al. · Nature Communications 12, 3832
Resolves adducts and in-source fragments into single molecular identities.
2020
Feature-based molecular networking in the GNPS analysis environment (opens in a new tab)
Nothias, Petras, Schmid et al. · Nature Methods 17, 905–908
The networking method the drug discovery and dereplication workflows rest on.
2020
Expanding the Kendrick Mass Plot Toolbox in MZmine 2 to Enable Rapid Polymer Characterization in Liquid Chromatography-Mass Spectrometry Data Sets (opens in a new tab)
Korf, Fouquet, Schmid et al. · Analytical Chemistry 92, 628–633
The Kendrick toolbox behind the PFAS and polymers workflow.
2019
Lipid Species Annotation at Double Bond Position Level with Custom Databases by Extension of the MZmine 2 Open-Source Software Package (opens in a new tab)
Korf, Jeck, Schmid et al. · Analytical Chemistry 91, 5098–5105
Custom lipid classes and double-bond-position annotation, the basis of the lipidomics rules.
2018
Three-dimensional Kendrick mass plots as a tool for graphical lipid identification (opens in a new tab)
Korf, Vosse, Schmid et al. · Rapid Communications in Mass Spectrometry 32, 981–991
The original Kendrick mass defect work these tools grew out of.

Who wrote them

The people who built it are the people who published it.

This is not a company that licensed someone else's algorithm. Most of the papers above have an mzio founder as first or senior author. The people who wrote the methods are the people who answer your support tickets.

Meet the team
CSO and co-founder

Robin Schmid

First author on MZmine 3 (Nature Biotechnology 2023) and on ion identity molecular networking (Nature Communications 2021).

CTO and co-founder

Steffen Heuckeroth

First author on on-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging (Nature Communications 2023).

CEO and co-founder

Ansgar Korf

Senior author on the trapped-ion-mobility lipid A profiling paper (Analytical Chemistry 2025).

Scientific adviser and co-founder

Tomáš Pluskal

Took mzmine on from Matej Orešič's lab in 2006 and led the MZmine 2 redesign (BMC Bioinformatics 2010).

Open innovation

Twenty years open, and staying that way.

mzmine has been developed in the open since 2005. The source is on GitHub, the methods are published in the peer-reviewed literature, and the Community plan is free for degree-awarding institutions.

Inspectable

Read the implementation of any algorithm you are about to publish with.

Extensible

Write a module and test it on its own, without touching the rest of the software.

Citable

A stable, peer-reviewed reference for your methods section.

Citing mzmine

Using mzmine in a paper?

Cite the MZmine 3 platform paper (Schmid et al., Nature Biotechnology, 2023) alongside the specific method paper for any specialised module you used: feature-based or ion identity molecular networking, SIMSEF, DreaMS, MSnLib, the Kendrick mass plot tools or the custom lipid classes. If you are unsure which applies, ask us and we will tell you rather than guess on your behalf.

Ask about citations

Get started

Free for academic research, permanently.

If you are at a degree-awarding institution, the Community plan is free. Register with your institutional email.

Join the academic program Compare plans