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MZmine specifications


Unique identifier OMICS_02385
Name MZmine
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.17
Stability Stable
Maintained Yes


No version available


  • person_outline Tomáš Pluskal

Publications for MZmine

MZmine citations


Metabolome Integrated Analysis of High Temperature Response in Pinus radiata

Front Plant Sci
PMCID: 5914196
PMID: 29719546
DOI: 10.3389/fpls.2018.00485

[…] is of each batch, and the resolution was also checked with the aid of lock masses (phthalates). Blanks were also analyzed during the sequence.LC-Orbitrap-MS raw data were processed and compared using MZmine software version 2.10 (). MS1 spectra were filtered establishing a noise threshold at 5.5E03 and minimum peak height at 6E03 with a minimum time peak of 0.15 min. Peaks were smoothed and deconv […]


Discovery of urinary biomarkers to discriminate between exogenous and semi endogenous thiouracil in cattle: A parallel like randomized design

PLoS One
PMCID: 5896977
PMID: 29649241
DOI: 10.1371/journal.pone.0195351

[…] M-derived fragmentation spectrum (allowed deviations for in silico fragment matching ≤ 60 ppm or 0.02 Da). Data interpretation was supported by XCalibur 3.0 (Thermo Fisher Scientific, San Jose, USA), MZmine [], CSI:FingerID [], MetFrag [], MAGMa, and MZCloud.For a first set of compounds (, ), a strong structural relationship was noted between the proposed tentative identities and TU, which of cour […]


A protocol for high‐throughput, untargeted forest community metabolomics using mass spectrometry molecular networks

Appl Plant Sci
PMCID: 5895185
PMID: 29732263
DOI: 10.1002/aps3.1033
call_split See protocol

[…] nces in LC retention time that typically distinguish structural isomers with identical molecular masses. Olivon et al. () describe a bioinformatics workflow that integrates the MS analytical software MZmine 2 (Pluskal et al., ) into the workflow for the assembly of raw MS/MS spectra into molecular networks with GNPS. In the short term, we recommend preprocessing MS/MS data using MZmine 2 prior to […]


Dynamics of Metabolite Induction in Fungal Co cultures by Metabolomics at Both Volatile and Non volatile Levels

Front Microbiol
PMCID: 5807337
PMID: 29459851
DOI: 10.3389/fmicb.2018.00072
call_split See protocol

[…] ThermoRAW data were converted to the open MS format (.mzXML) using ProteoWizard. Data treatment and the dereplication process were performed using MZmine 2.14.2. The Dictionary of Natural Products was used as the database for the dereplication. The data treatment steps were performed using MZmine 2.14.2. Features detected from blank samples were […]


The Arabidopsis thaliana Knockout Mutant for Phytochelatin Synthase1 (cad1 3) Is Defective in Callose Deposition, Bacterial Pathogen Defense and Auxin Content, But Shows an Increased Stem Lignification

Front Plant Sci
PMCID: 5786554
PMID: 29403524
DOI: 10.3389/fpls.2018.00019

[…] through a comparison of m/z and fragmentation pattern with the data available in the MassBank public database and in the literature. Chromatogram data extraction and alignment were carried out using MZmine software. The relative quantification (i.e., comparison between samples) was based on the area of each of the signals extracted from the chromatograms and expressed as arbitrary units (a.u.) in […]


Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

PMCID: 5875998
PMID: 29342073
DOI: 10.3390/metabo8010008

[…] drying gas temperature, 330 °C; and nebulizer gas (N2), 30 psig. The raw LC-MS data was converted to mzdata.xml format by using MassHunter Qualitative Analysis (Agilent Technologies) and analyzed by mzMine 2 []. LC-fractionation of the plant extract was performed by an Agilent HPLC system (1200 series) coupled to an Agilent fraction collector (1100 series). The LC column, elution gradient, flow r […]


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MZmine institution(s)
Turku Centre for BiotechnologyTurku, Finland; VTT Technical Research Centre of FinlandEspoo, Finland

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