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mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.

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Title: mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.
Authors: Van Den Bossche T; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium.; CompOmics, VIB─UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium., Alexandrov T; Department of Pharmacology, University of California San Diego, La Jolla, California 92093, United States.; Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States., Bilbao A; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.; US Department of Energy Agile BioFoundry, Emeryville, California 94608, United States., Bittremieux W; University of Antwerp, 2020 Antwerpen, Belgium., Brigante FI; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic., Chambers MC; University of Washington, Seattle, Washington 98195, United States., Charkow J; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada., Deutsch E; Institute for Systems Biology, Seattle, Washington 98109, United States., Dowsey AW; Department of Population Health Sciences, Oakfield House, Oakfield Grove, University of Bristol, BS8 2BN Bristol, United Kingdom., El Abiead Y; University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, California 92093, United States., Gabriels R; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium.; CompOmics, VIB─UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium., Hecht H; RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic., Heuckeroth S; mzio GmbH, Altenwall 26, 28195 Bremen, Germany., Klein JA; Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States., Knierman M; Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 95051, United States., Martens L; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium.; CompOmics, VIB─UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.; BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, Strasbourg 67000, France.; Infrastructure Nationale de Protéomique ProFI-FR2048, Strasbourg 67087, France., Moritz RL; Institute for Systems Biology, Seattle, Washington 98109, United States., McCall LI; San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92115, United States., Neumann S; Leibniz Institute of Plant Biochemistry, Halle 06120, Germany.; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig 04103, Germany., Perez-Riverol Y; European Molecular Biology Laboratory─European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom., Röst HL; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada.; Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1A8, Canada., Price EJ; RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic., Shofstahl J; Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States., Tabb DL; European Research Institute for the Biology of Ageing, University Medical Center of Groningen, Groningen 9700 RB, Netherlands., Uszkoreit J; Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, Bochum D-44801, Germany.; Ruhr University Bochum, Medical Faculty, Core Unit Bioinformatics ─CUBiMed.RUB, Bochum D-44801, Germany., Vizcaíno JA; European Molecular Biology Laboratory─European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom., Wang M; Department of Computer Science, University of California Riverside, 900 University Ave. Riverside, California 92521, United States., Willems S; Research and Development, Bruker Belgium nv., Kontich 2550, Belgium., Winkelhardt D; Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, Bochum D-44801, Germany.; Ruhr University Bochum, Medical Faculty, Core Unit Bioinformatics ─CUBiMed.RUB, Bochum D-44801, Germany., Kohlbacher O; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen D-72074, Germany.; Institute for Bioinformatics and Medical Informatics, 72076 Tübingen, Germany.; Translational Bioinformatics, University Hospital Tübingen, 72074 Tübingen, Germany., Wein SP; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen D-72074, Germany.; OpenMS Inc., Erie, Pennsylvania 16502, United States.
Source: Journal of proteome research [J Proteome Res] 2025 Nov 07; Vol. 24 (11), pp. 5329-5335. Date of Electronic Publication: 2025 Oct 02.
Publication Type: Journal Article; Review
Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE
Database: MEDLINE Ultimate
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  Data: <searchLink fieldCode="AU" term="%22Van+Den+Bossche+T%22">Van Den Bossche T</searchLink>; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium.; CompOmics, VIB─UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Alexandrov+T%22">Alexandrov T</searchLink>; Department of Pharmacology, University of California San Diego, La Jolla, California 92093, United States.; Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States.<br /><searchLink fieldCode="AU" term="%22Bilbao+A%22">Bilbao A</searchLink>; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.; US Department of Energy Agile BioFoundry, Emeryville, California 94608, United States.<br /><searchLink fieldCode="AU" term="%22Bittremieux+W%22">Bittremieux W</searchLink>; University of Antwerp, 2020 Antwerpen, Belgium.<br /><searchLink fieldCode="AU" term="%22Brigante+FI%22">Brigante FI</searchLink>; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic.<br /><searchLink fieldCode="AU" term="%22Chambers+MC%22">Chambers MC</searchLink>; University of Washington, Seattle, Washington 98195, United States.<br /><searchLink fieldCode="AU" term="%22Charkow+J%22">Charkow J</searchLink>; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada.<br /><searchLink fieldCode="AU" term="%22Deutsch+E%22">Deutsch E</searchLink>; Institute for Systems Biology, Seattle, Washington 98109, United States.<br /><searchLink fieldCode="AU" term="%22Dowsey+AW%22">Dowsey AW</searchLink>; Department of Population Health Sciences, Oakfield House, Oakfield Grove, University of Bristol, BS8 2BN Bristol, United Kingdom.<br /><searchLink fieldCode="AU" term="%22El+Abiead+Y%22">El Abiead Y</searchLink>; University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, California 92093, United States.<br /><searchLink fieldCode="AU" term="%22Gabriels+R%22">Gabriels R</searchLink>; 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CompOmics, VIB─UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.; BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, Strasbourg 67000, France.; Infrastructure Nationale de Protéomique ProFI-FR2048, Strasbourg 67087, France.<br /><searchLink fieldCode="AU" term="%22Moritz+RL%22">Moritz RL</searchLink>; Institute for Systems Biology, Seattle, Washington 98109, United States.<br /><searchLink fieldCode="AU" term="%22McCall+LI%22">McCall LI</searchLink>; San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92115, United States.<br /><searchLink fieldCode="AU" term="%22Neumann+S%22">Neumann S</searchLink>; Leibniz Institute of Plant Biochemistry, Halle 06120, Germany.; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig 04103, Germany.<br /><searchLink fieldCode="AU" term="%22Perez-Riverol+Y%22">Perez-Riverol Y</searchLink>; European Molecular Biology Laboratory─European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Röst+HL%22">Röst HL</searchLink>; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada.; Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1A8, Canada.<br /><searchLink fieldCode="AU" term="%22Price+EJ%22">Price EJ</searchLink>; RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic.<br /><searchLink fieldCode="AU" term="%22Shofstahl+J%22">Shofstahl J</searchLink>; Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States.<br /><searchLink fieldCode="AU" term="%22Tabb+DL%22">Tabb DL</searchLink>; European Research Institute for the Biology of Ageing, University Medical Center of Groningen, Groningen 9700 RB, Netherlands.<br /><searchLink fieldCode="AU" term="%22Uszkoreit+J%22">Uszkoreit J</searchLink>; Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, Bochum D-44801, Germany.; Ruhr University Bochum, Medical Faculty, Core Unit Bioinformatics ─CUBiMed.RUB, Bochum D-44801, Germany.<br /><searchLink fieldCode="AU" term="%22Vizcaíno+JA%22">Vizcaíno JA</searchLink>; European Molecular Biology Laboratory─European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Wang+M%22">Wang M</searchLink>; Department of Computer Science, University of California Riverside, 900 University Ave. Riverside, California 92521, United States.<br /><searchLink fieldCode="AU" term="%22Willems+S%22">Willems S</searchLink>; Research and Development, Bruker Belgium nv., Kontich 2550, Belgium.<br /><searchLink fieldCode="AU" term="%22Winkelhardt+D%22">Winkelhardt D</searchLink>; Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, Bochum D-44801, Germany.; Ruhr University Bochum, Medical Faculty, Core Unit Bioinformatics ─CUBiMed.RUB, Bochum D-44801, Germany.<br /><searchLink fieldCode="AU" term="%22Kohlbacher+O%22">Kohlbacher O</searchLink>; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen D-72074, Germany.; Institute for Bioinformatics and Medical Informatics, 72076 Tübingen, Germany.; Translational Bioinformatics, University Hospital Tübingen, 72074 Tübingen, Germany.<br /><searchLink fieldCode="AU" term="%22Wein+SP%22">Wein SP</searchLink>; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen D-72074, Germany.; OpenMS Inc., Erie, Pennsylvania 16502, United States.
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  Data: <searchLink fieldCode="JN" term="%22101128775%22">Journal of proteome research</searchLink> [J Proteome Res] 2025 Nov 07; Vol. 24 (11), pp. 5329-5335. <i>Date of Electronic Publication: </i>2025 Oct 02.
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