MZmine protocols

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MZmine statistics

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Citations per year

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Popular tool citations

chevron_left Data normalization Metabolite identification Peak alignment Peak detection Noise filtering Spectral deconvolution Peak detection Metabolite quantification Spectral visualization Chromatogram alignment chevron_right
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Associated diseases

Associated diseases

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


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  • person_outline Tomáš Pluskal <>

Publications for MZmine

MZmine in pipelines

PMCID: 4846091
PMID: 27116459
DOI: 10.1371/journal.pone.0154043

[…] biological samples were collected at the od600 of 0.8±0.1. lc-ms data was converted into mzml format using ms convert software []. data preprocessing and statistical analysis were performed with mzmine 2.10 and metaboanalyst 3.0 [,]. for structure identification with metfusion, the ms/ms peak list was used as input into metfusion and then the molecule structures and scores were returned […]

PMCID: 4466249
PMID: 26067663
DOI: 10.1371/journal.pone.0129591

[…] set to 350°c and gas flow to 10 l/min, mass range acquisition 50–1700 da at 4 scans per second. after deconvolution, raw data were aligned and adducts [m+h+] searched against metlin, nist ms, and mzmine software. metabolite intensities were identified as the peak height for the largest precursor ion (not normalized)., one way analysis of variance (anova) [] was performed for biomass, n and p […]

PMCID: 4180160
PMID: 25279237
DOI: 10.5213/inj.2014.18.3.106

[…] the biological samples taken from the ic patients and normal (control) subjects., several statistical tools are currently used to analyze nmr and ms-based metabolomics datasets, which include xcms, mzmine, metalign, mathdamp, and lcmstats. for nmr data analysis, the significantly altered nmr peaks can be identified by using a probabilistic approach called bayesian quantification (bquant) [], […]

PMCID: 4252003
PMID: 25420746
DOI: 10.1186/s12859-014-0376-0

[…] spectral data. to test our algorithm, practical applications of ab3d for lc-ms data sets were evaluated using 3 datasets. comparisons were then carried out between widely used software tools such as mzmine 2, msight, superhirn, openms and our algorithm ab3d, using the same lc-ms datasets. all quantitative results were confirmed manually, and we found that ab3d could properly identify […]

PMCID: 4252003
PMID: 25420746
DOI: 10.1186/s12859-014-0376-0

[…] and four technical replicates of prepared samples were conducted for each bsa peptide concentration and all acquired raw ms1 and ms/ms data were input into all the peak detection algorithms (ab3d, mzmine 2, msight, superhirn and openms) to produce peak lists for each peptide spectrum. peaks identified as peptides of bsa or four standard proteins by either mascot [] or x! tandem [] […]

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MZmine in publications

PMCID: 5938395
PMID: 29765386
DOI: 10.3389/fpls.2018.00572

[…] for polar lipids. lc-ms data were recorded and processed with esquire control v5.2 and data analysis v3.2 (bruker corp.), respectively. the latter was used to convert.d raw data into net.cdf files. mzmine v2 was used for the detection, deconvolution and alignment of the m/z features to create the data matrices used for multivariate statistical analysis. quality controls were prepared by mixing […]

PMCID: 5914196
PMID: 29719546
DOI: 10.3389/fpls.2018.00485

[…] 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 […]

PMCID: 5910844
PMID: 29618609
DOI: 10.1073/pnas.1719407115

[…] separated by reversed-phase hplc on a dionex ultimate 3000 hplc (thermo fisher) and quantified with a thermo velos pro dual-pressure linear ion trap mass spectrometer., data were analyzed in mzmine2 () and r ( targeted peak integration was performed on baseline-corrected data. quantification was achieved by external calibration, accounting for the istd response, […]

PMCID: 5882858
PMID: 29615722
DOI: 10.1038/s41598-018-23847-9

[…] analysis of results, all chromatograms were pre-processed. this pre-processing includes: baseline correction, peak detection, chromatogram deconvolution and alignment, performed using the program mzmine. the parameters used to accomplish these were: rt range 2.8–34.0 min; m/z range 50–250; ms data noise level 1.0 × 104; m/z tolerance 0.5; chromatogram baseline level 1.0 × 103; peak duration […]

PMCID: 5882915
PMID: 29615816
DOI: 10.1038/s41598-018-23863-9

[…] with a column temperature of 25 °c. 4 µl was injected for negative ions and 2 µl for positive ions., raw data files were converted to mzxml file format using ms convert software (proteowizaed 3.0). mzmine 2 was used to identify features, deisotope, align features and perform gap filling to fill in any features that may have been missed in the first alignment algorithm. all adducts and complexes […]

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

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