The platform
One analytical platform for every modality you run.
mzmine takes raw files from any major vendor and returns an aligned, annotated feature table: LC-MS, GC-MS, ion mobility and MS imaging, in one interface, on your own hardware.
Vendor and open formats · On your own hardware · 30-day trial
Modalities
Every acquisition type, one feature table.
LC-MS, GC-MS, ion mobility, direct infusion and MS imaging, processed by the same engine and aligned into a single result you can interrogate as a whole. Multimodal studies stop being separate projects.
LC-MS
DDA and DIA, from single injections to cohort-scale batches. Advanced spectra merging gives you control over how fragmentation evidence is pooled.
GC-MS
GC/EI and GC/CI profiling with fast spectral deconvolution, feature alignment and an interactive deconvolution result viewer.
Ion mobility
The mobility dimension is treated as data, not metadata. It is carried through detection, alignment and annotation rather than reduced to a number in a column.
MS imaging
Every pixel keeps its raw spectrum, with co-localisation and molecular networking in the same environment as your LC-MS work. On-tissue MS2 acquisition is available on timsTOF fleX instruments.
The workflow
Raw file to annotated result.
Every step ships with a default a reviewer will accept, and every parameter stays open to an expert who wants to change it.
Import
Native readers for every major vendor. No conversion step, no intermediate format, no loss.
Mass detection
Centroiding and noise handling tuned to the acquisition, not to a generic default.
Feature resolving
Chromatogram building and deconvolution that survives co-elution and tailing peaks.
Alignment
One feature table across the entire study, not a chain of pairwise comparisons.
Ion identity networking
Adducts, in-source fragments and isotopologues collapse into single molecular identities.
Annotation
Millions of reference spectra searched in seconds, with prediction tools where the library ends.
The interface
Inspect any result back to the raw scan.
The dashboard is not a report viewer. Every number in the feature table is a live link to the evidence underneath it: the chromatographic shape, the MS1 envelope, the MS2 that produced the annotation.
mzwizard
Answer a few questions about your instrument and study design, and it builds the whole batch for you.
Compound dashboard
Annotation agreement, adduct support, RT stability and in-source fragmentation, scored per feature.
Library management
Build, version and share in-house spectral libraries so the whole department searches the same reference set.
Throughput
One file in under a second.
That is the number everything else scales from, and it holds on real data, not a synthetic benchmark. Batch processing is the default mode here, not an advanced feature you have to go and find.
Built for batches
Hundreds of files as one reproducible job a technician can launch.
Auditable by design
The batch file is the method. Save it, version it, hand it to a reviewer.
Scales with the hardware
Desktop, workstation or your own compute cluster.
In production
Running at cohort and screening scale.
“As part of the R&D scent team at IFF, working with complex and diverse natural product extracts, efficient data processing, deconvolution, annotation, chemometrics, and interactive visualization are crucial for high-throughput understanding. mzmine Pro has provided us with not only a powerful and efficient GC-MS workflow to investigate volatile compounds but also a highly advanced LC-MS workflow, perfectly aligned with our aspirations. These tools are essential for enhancing our work, fostering innovation, and deepening our understanding of complex natural matrices.”
“My lab develops and applies bioanalytical tools to determine the role of small molecules in complex ecosystems. Mass Spectrometry is our tool of choice to profile large environmental studies, often exceeding 1000 samples per study. With mzmine, we can analyze the vast amount of data in less than an hour, giving us time to focus on the actual biology. Our current processing record of ultra-complex dissolved organic matter samples is more than 8000 samples in 45 min.”
“As part of our drug discovery workflow, we analyze hundreds of complex fungal samples every week. mzmine PRO provides the necessary processing power and innovative compound discovery tools, such as library generation, interactive molecular networking, and database search to swiftly accelerate our daily routine. Data processing is no longer a bottleneck.”
Plans
Free for academic research, licensed for commercial use
The Community plan is the full analytical platform, free for students, teachers and university researchers. Commercial plans add commercial licensing and support; PRO adds IT integration and the detector coverage regulated labs need.
Get started
See mzmine running on your own data.
Send us a few representative files. We will build the workflow and show you the result before you commit to anything.