Mass spectrometry data platform
Accelerate scientific discoveries.
mzmine processes LC-MS, GC-MS, ion mobility, direct infusion, and MS imaging data in one platform: thousands of samples in minutes, securely inside your own environment.
No cloud upload required · 30-day trial · Vendor and open file formats
Why mzmine
One platform instead of five disconnected tools.
Most labs stitch together vendor software, scripts and spreadsheets to cover their data analysis needs. mzmine replaces that chain with a single platform, covering every modality, from raw file to scientific insights.
Every modality, one feature table
LC-MS, GC-MS, ion mobility, direct infusion and MS imaging in a single interface. One alignment, one result, no export-reimport loops between vendor tools.
From raw data to molecular structure
Calibration, feature finding, deconvolution, alignment, ion identity networking and annotation are built in. Results arrive with structures attached, not just m/z values.
Unprecedented speed and throughput
Batch-process hundreds of files in the time a single run used to take. Semi-automated, reproducible pipelines that a technician can launch and a reviewer can audit.
Applications
Built for the questions your lab actually asks.
The same engine, tuned to various analytical domains, each with its own best-practice workflow to extract the most from your data.
Metabolomics
Untargeted profiling at cohort scale, with molecular networking and library matching that survives thousands of samples.
Explore
Lipidomics
Rule-based lipid annotation following LSI guidelines, including retention time analysis and a dedicated dashboard for QC.
Explore
MS Imaging
On-tissue MS2 with SIMSEF, ion image co-registration and MALDI-TIMS workflows for spatial molecular maps.
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PFAS & Polymers
Homologous-series detection, Kendrick mass defect analysis and suspect screening in one workflow.
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Drug Discovery
Natural-product dereplication, library generation and interactive molecular networking across hundreds of extracts a week.
Explore
Impurity Analysis
Extractables & leachables at scale, with UV and MS traces correlated and aligned across hundreds of files and multiple acquisition modes.
ExploreThe platform
Best-practice workflows, not a blank canvas.
The mzio team has funneled 20 years of mass spectrometry data processing experience into mzmine. Every module ships with default settings, so a new user gets a publication-grade result on day one, and an expert can still customise every parameter.
mzwizard
Guided setup that builds a complete batch from your instrument and study design.
Interactive dashboards
Inspect any feature back to the raw scan, without leaving the result table.
Library management
Build, version and share in-house spectral libraries across the whole lab.
Vendor and open formats
Native readers for all major vendors and open formats with no conversion step.
Data sovereignty
Your data never leaves your environment.
mzmine runs on your hardware, behind your firewall. No upload, no vendor cloud, no third-party processing agreement to negotiate, which is exactly why central analytics departments in regulated industries can adopt it.
On-premise by default
Desktop, workstation or your own compute cluster. Air-gapped installations supported.
IP and compliance safe
Proprietary structures and unpublished results stay inside your internal environment.
Non-disruptive updates
Stable release channel so a validated workflow keeps producing the same answer.
Customers
What central analytics teams actually report back.
“As a central analytics department, we analyze a wide variety of highly complex samples. mzmine PRO has become an important part of our analytical toolbox because it allows us to keep all data fully within our internal environment, ensuring the highest levels of data security, IP protection, and regulatory compliance. With ongoing improvements and a non disruptive update approach, mzmine PRO provides a stable platform that meets our current research needs.”
“Merck KGaA in Darmstadt is home to a Central Analytics department working with highly complex LC-UV-HRMS data. Much of this work revolves around Extractables and Leachables studies, where large numbers of samples need to be processed quickly, consistently, and with a link between UV and MS information. That combination used to be a real bottleneck. mzmine PRO gave us a way out. Today we run semi-automated standardized workflows across more than 200 files and multiple acquisition modes, with UV and MS features correlated and aligned in a fraction of the time it used to take. The open vendor format, integrated library management system and interactive dashboard have made mzmine PRO an indispensable part of our analytical toolbox.”
“At Novonesis, a global leader in biotechnology, we have been leveraging mzmine PRO for semi-automated processing of both high- and low-resolution mass spectrometry data across a wide range of research applications. The platform’s speed, flexibility, and intuitive interface have significantly enhanced our analytical workflows. Our collaboration with the mzio development team has been exceptionally agile, with rapid turnaround from concept to implementation, enabling us to accelerate innovation and streamline critical processes.”
Plans
Free for science. Scaled for industry.
mzmine stays open and free for academic research. Commercial plans add support, integration and the features regulated labs need.
Download now and register for our academic program
- Academic program only
- GitHub Forum support
- Unlimited updates
- Contribute to our open-source code base
- Commercial use
Unlock the potential of mzmine for your lab
- 30-day trial
- Unlimited updates
- Commercial use
- Email support
- IT integration
- Early feature access
Accelerate your lab's discoveries
- Everything in CORE
- Email support
- Onboarding session
- IT integration
- MRM support
- Early feature access
Maximize your lab's performance
- Everything in PLUS
- Video call support
- IT integration
- MRM support
- UV, ELSD, other detectors
- Early feature access
Science
Peer-reviewed, not just marketed.
mzmine is developed in the open with the scientific community. The methods behind it are published, cited and independently validated, and the source code is on GitHub for anyone to inspect, extend or contribute to.
Get started
Ready to accelerate your lab’s discoveries?
Tell us about your instruments and sample load. We will show you the workflow on your own data, and give you a quote for the plan that fits.
