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Data availability
Datasets are available on MassIVE8 with the following accession IDs: MSV000088054, human cohort study, LC–MS, neg; MSV000087728, diverse plant extracts, LC–MS2, top-3 DDA, pos; MSV000090079, dissolved organic matter, LC–MS2, top-5 DDA, pos; MSV000090328, sheep brain, LC–TIMS-MS, PASEF, pos; MSV000090327, piper plant extracts, LC–TIMS-MS, PASEF, pos. IMS resolved ion identity molecular networking results are available through GNPS: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=7a06fa3dfadd4158bcb4ee300b574747
Code availability
The latest release of MZmine can be downloaded from https://www.mzmine.org. The complete source code is available at https://github.com/mzmine/mzmine3/ under the MIT license. The MZmine documentation is hosted on GitHub and available at https://www.mzmine.org/documentation.
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Acknowledgements
We thank Christopher Jensen and Gauthier Boaglio for their contributions to the MZmine codebase. We thank Jianbo Zhang and Zachary Russ for their donations to MZmine development. The MZmine 3 logo was designed by the Bioinformatics & Research Computing group at the Whitehead Institute for Biomedical Research. T.P. is supported by Czech Science Foundation (GA CR) grant 21-11563M and by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 891397. Support for P.C.D. was from US NIH U19 AG063744, P50HD106463, 1U24DK133658 and BBSRC-NSF award 2152526. T.S. acknowledges funding by Deutsche Forschungsgemeinschaft (441958208). M. Wang acknowledges the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337, a DOE Office of Science User Facility) and is supported by the Office of Science of the US Department of Energy operated under subcontract No. 7601660. E.R. and H.H. thank Wen Jiang (HILICON AB) for providing the iHILIC Fusion(+) column for HILIC measurements. M.F., K.D. and S.B. are supported by Deutsche Forschungsgemeinschaft (BO 1910/20). L.-F.N. is supported by the Swiss National Science Foundation (project 189921). D.P. was supported through the Deutsche Forschungsgemeinschaft (German Research Foundation) through the CMFI Cluster of Excellence (EXC-2124 — 390838134 project-ID 1-03.006_0) and the Collaborative Research Center CellMap (TRR 261 - 398967434). J.-K.W. acknowledges the US National Science Foundation (MCB-1818132), the US Department of Agriculture, and the Chan Zuckerberg Initiative. MZmine developers have received support from the European COST Action CA19105 — Pan-European Network in Lipidomics and EpiLipidomics (EpiLipidNET). We acknowledge the support of the Google Summer of Code (GSoC) program, which has funded the development of several MZmine modules through student projects. We thank Adam Tenderholt for introducing MZmine to the GSoC program.
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Authors and Affiliations
Contributions
R.S., S.H., T.P. are coordinating the MZmine open source project. S.H., R.S., P.C.D., T.P., A.K. wrote and edited the initial manuscript. S.H., R.S., A.K., T.P. conceived the combined workflow for MALDI–IMS–MS imaging and LC–IMS–MS, developed the code and tested the workflow. R.S., S.H., A.K., T.P. A. Smirnov, O. Myers, T.S.D., R.B., K.J.M., N.H., M.L., A. Sarvepalli, Z.Z., M.F., K.D., M. Wesner., M. Wang, S.J.H., O. Mokshyna, K.P., C.J.P., T.R.F., T.S. and more have contributed open source code to MZmine. C.B., T.D., S.H., L.M., O. Mokshyna, R.S., M.E. wrote the documentation for MZmine. L.-F.-N., A.R.-U., A.B., R.S., S.H., A.K., M.O., P.C.D., D.P., U.K., J.-K.W., H.H., X.D., S.B. initiated and/or supervised projects related to MZmine development. T.S., A.K., S.H., R.S., T.P., A.R.-U., A.B., N.H., D.P. were involved in the supervision of students for the Google Summer of Code program. R.S., L.-F.N., D.P., A. Sarvepalli, Z.Z., M. Wang, P.C.D. contributed to the linking with GNPS to facilitate molecular networking in MZmine. R.S., D.P., L.-F.N., M. Wang conceived and developed the FBMN and IIMN workflows in MZmine. S.H., R.S., A.K. implemented imzML support and developed imaging feature detection. S.H. developed the ion mobility data support, native .tdf support, ion mobility gap filling; added ion mobility visualization modules; recreated project load/save. A.K. provided TDF-SDK for native .tdf import and supervised S.H. for its implementation. S.H., A.K. developed ion mobility feature detection. A.K., H.H. developed lipid annotation modules and workflows and made it IMS aware. R.S., M. Wang developed parallel gap-filling. S.H., R.S. developed parallel sample alignment. T.S.D. implemented mzTab, MGF and MSP support and various peak information (FWHM, tailing factor, asymmetry factor, RT start and RT end). R.S., C.B., A.K. worked on the mass spectral library creation and matching workflows. K.D., M.F., R.S., S.H., S.B. assisted with the integration of SIRIUS and data exchange. A.R.-U., T.P. conceived the exact mass calibration module. M.L. developed support for the open data format ‘Aird’. S.J.H. developed diagnostic fragmentation filtering. M. Wesner developed the mass-voltammogram module. R.S., S.H. profiled and optimized MZmine’s memory consumption and processing throughput. S.H. prepared sheep brain lipid extracts, prepared MALDI samples, acquired imaging data, analyzed imaging and chromatographic data. H.R. and A.J. planned and carried out animal study ZH235/17. A.J. prepared thin sections and histologic tissue staining of the sheep brain dataset and supplied the tissue samples for extraction. P.O.H., C.B. provided testing data and feedback for LC–MS and IMS–MS imaging workflows. E.R. acquired LC–IMS–MS2 lipid data. R.S., S.H., D.P. conducted the performance tests. All authors edited and approved the final manuscript.
Corresponding author
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Competing interests
A.K. is employed at Bruker Daltonics GmbH & Co. KG. S.B., K.D. and M.F. are co-founders of Bright Giant. P.C.D. is a scientific advisor for Cybele and is a scientific advisor and a co-founder of Enveda, Arome and Ometa with prior approval by the University of California San Diego. M. Wang is a co-founder of Ometa Labs LLC. J.-K.W. is a member of the Scientific Advisory Board and a shareholder of DoubleRainbow Biosciences, Galixir and Inari Agriculture, which develop biotechnologies related to natural products, drug discovery and agriculture.
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Nature Biotechnology thanks Xiaotao Shen and Zheng-Jiang Zhu for their contribution to the peer review of this work.
Supplementary information
Supplementary Information
Supplementary Figs. 1–6, Supplementary Notes 1–3, Supplementary References
Supplementary Code
A ZIP archive with batch files for data processing using MZmine 3 and MZmine 2
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Schmid, R., Heuckeroth, S., Korf, A. et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat Biotechnol 41, 447–449 (2023). https://doi.org/10.1038/s41587-023-01690-2
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DOI: https://doi.org/10.1038/s41587-023-01690-2
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