Integrative analysis of multimodal mass spectrometry data in MZmine 3

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Bibliographic Details
Published in	Nature biotechnology Vol. 41; no. 4; pp. 447 - 449
Main Authors	Schmid, Robin, Heuckeroth, Steffen, Korf, Ansgar, Smirnov, Aleksandr, Myers, Owen, Dyrlund, Thomas S., Bushuiev, Roman, Murray, Kevin J., Hoffmann, Nils, Lu, Miaoshan, Sarvepalli, Abinesh, Zhang, Zheng, Fleischauer, Markus, Dührkop, Kai, Wesner, Mark, Hoogstra, Shawn J., Rudt, Edward, Mokshyna, Olena, Brungs, Corinna, Ponomarov, Kirill, Mutabdžija, Lana, Damiani, Tito, Pudney, Chris J., Earll, Mark, Helmer, Patrick O., Fallon, Timothy R., Schulze, Tobias, Rivas-Ubach, Albert, Bilbao, Aivett, Richter, Henning, Nothias, Louis-Félix, Wang, Mingxun, Orešič, Matej, Weng, Jing-Ke, Böcker, Sebastian, Jeibmann, Astrid, Hayen, Heiko, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, Pluskal, Tomáš
Format	Journal Article
Language	English
Published	New York Nature Publishing Group US 01.04.2023 Nature Publishing Group
Subjects	631/114/1314 631/61/320 Agriculture Bioinformatics Biomedical and Life Sciences Biomedical Engineering/Biotechnology Biomedicine Biotechnology Correspondence Life Sciences Mass spectrometry Mass Spectrometry - methods Mass spectroscopy Software
Online Access	Get full text
ISSN	1087-0156 1546-1696 1546-1696
DOI	10.1038/s41587-023-01690-2

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Bibliography:	SourceType-Scholarly Journals-1 ObjectType-Correspondence-1 content type line 14 content type line 23 L.-F.-N., A.R.-U., A.B., R.S., S.H., A.K., M.O., P.C.D., D.P., U.K., H.H., X.D., S.B. initiated and/or supervised projects related to MZmine development. R.S., D.P., L.-F.N., Mi.W. conceptualized and developed the FBMN and IIMN workflows in MZmine H.R. and A.J. planned and carried out animal study ZH235/17. K.D., M.F., R.S., S.H., S.B. assisted with the integration of SIRIUS and data exchange. A.R.-U., T.P. conceptualized the exact mass calibration module. M.L. developed support for the open data format ‘Aird’. Ma.W. developed the mass-voltammogram module. C.B., T.D., S.H., L.M., Ol.M., R.S., M.E. wrote the documentation for MZmine. S.H., R.S. developed parallel sample alignment. A.K. provided TDF-SDK for native .tdf import and supervised S.H. for its implementation. S.H., R.S., A.K. implemented imzML support and developed imaging feature detection. T.S.D implemented mzTab, MGF & MSP support and various peak information (FWHM, tailing factor, asymmetry factor, RT start and RT end). S.H., R.S., A.K., T.P. conceptualized the combined workflow for MALDI-IMS-MS imaging and LC-IMS-MS, developed the code, and tested the workflow. S.H. prepared sheep brain lipid extracts, prepared MALDI samples, acquired imaging data, analyzed imaging and chromatographic data. P.O.H., C.B. provided testing data and feedback for LC- and IMS-MS imaging workflows. Author contributions S.H., A.K. developed ion mobility feature detection. All authors edited and approved the final manuscript. S.H., R.S., P.C.D., T.P., A.K. wrote and edited the initial manuscript. R.S., Mi.W. developed parallel gap-filling. S.H. developed the ion mobility data support, native tdf support, ion mobility gap filling, added ion mobility visualization modules, recreated project load/save. R.S., S.H., D.P. conducted the performance tests. These authors contributed equally A.J. prepared thin sections and histologic tissue stainings of the sheep brain dataset and supplied the tissue samples for extraction. 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. E.R. acquired LC-IMS-MS2 lipid data. A.K., H.H. developed lipid annotation modules and workflows and made it IMS aware. R.S., S.H., A.K., T.P. A.S., Ow.M., T.S.D., R.B., K.J.M., N.H., M.L., A.S., Z.Z., M.F., K.D., Ma.W., Mi.W., S.J.H., Ol.M., K.P., C.J.P., T.R.F., T.S., and more have contributed open source code to MZmine. R.S., S.H., T.P. are coordinating the MZmine open source project. R.S., L.-F.N., D.P., A.S, Z.Z., Mi.W, P.C.D. contributed to the linking with GNPS to facilitate molecular networking in MZmine. R.S., C.B., A.K. worked on the mass spectral library creation and matching workflows. S.J.H. developed diagnostic fragmentation filtering. R.S., S.H. profiled and optimized MZmine’s memory consumption and processing throughput.
ISSN:	1087-0156 1546-1696 1546-1696
DOI:	10.1038/s41587-023-01690-2