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

Journal Article · Thu Oct 02 00:00:00 UTC 2025 · Journal of Proteome Research

DOI: https://doi.org/10.1021/acs.jproteome.5c00435 · OSTI ID:3025223

Van Den Bossche, Tim  ^[1]; Alexandrov, Theodore ^[2]; Bilbao, Aivett  ^[3]; Bittremieux, Wout  ^[4]; Brigante, Federico Ivan  ^[5]; Chambers, Matthew Chase ^[6]; Charkow, Joshua  ^[7]; Deutsch, Eric ^[8]; Dowsey, Andrew W.  ^[9]; El Abiead, Yasin  ^[2]; Gabriels, Ralf  ^[1]; Hecht, Helge  ^[10]; Heuckeroth, Steffen  ^[11]; Klein, Joshua A. ^[12]; Knierman, Michael ^[13]; Martens, Lennart  ^[14]; Moritz, Robert L.  ^[8]; McCall, Laura-Isobel  ^[15]; Neumann, Steffen  ^[16]; Perez-Riverol, Yasset  ^[17] ; Röst, Hannes L. ^[7]; Price, Elliott J. ^[10]; Shofstahl, Jim  ^[18]; Tabb, David L. ^[19]; Uszkoreit, Julian  ^[20]; Vizcaíno, Juan Antonio  ^[17]; Wang, Mingxun ^[21]; Willems, Sander ^[22]; Winkelhardt, Dirk  ^[20]; Kohlbacher, Oliver  ^[23]; Wein, Samuel P.  ^[24]

---

1. Ghent Univ. (Belgium); Flanders Institute for Biotechnology (VIB), Ghent (Belgium)
2. Univ. of California, San Diego, CA (United States)
3. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); USDOE Agile BioFoundry, Emeryville, CA (United States)
4. Univ. of Antwerp (Belgium)
5. Czech Academy of Sciences (CAS), Prague (Czech Republic)
6. Univ. of Washington, Seattle, WA (United States)
7. Univ. of Toronto, ON (Canada)
8. Institute for Systems Biology (ISB), Seattle, WA (United States)
9. Univ. of Bristol (United Kingdom)
10. Masaryk Univ., Brno (Czech Republic)
11. mzio GmbH, Bremen (Germany)
12. Boston Univ., MA (United States)
13. Agilent Technologies, Santa Clara, CA (United States)
14. Ghent Univ. (Belgium); Flanders Institute for Biotechnology (VIB), Ghent (Belgium); Univ. of Strasbourg (France); Centre National de la Recherche Scientifique (CNRS), Strasbourg (France). BioOrganic Mass Spectrometry Laboratory (LSMBO), Hubert Curien Multi-disciplinary Institute (IPHC); Proteomics French Infrastructure (ProFI), Strasbourg (France)
15. San Diego State Univ., CA (United States)
16. Leibniz Institute of Plant Biochemistry, Halle (Germany); German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig (Germany)
17. European Molecular Biology Laboratory─European Bioinformatics Institute (EMBL-EBI), Hinxton (United Kingdom)
18. Thermo Fisher Scientific, San Jose, CA (United States)
19. University Medical Center of Groningen (Netherlands)
20. Ruhr Univ., Bochum (Germany)
21. Univ. of California, Riverside, CA (United States)
22. Bruker Belgium nv., Kontich (Belgium)
23. Univ. of Tubingen (Germany)
24. Univ. of Tubingen (Germany); OpenMS Inc., Erie, PA (United States)

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: Chan Zuckerberg Initiative; National Institutes of Health (NIH); National Science Foundation (NSF); USDOE
• Grant/Contract Number: AC05-76RL01830
• OSTI ID: 3025223
• Report Number(s): PNNL-SA-216747
• Journal Information: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 11 Vol. 24; ISSN 1535-3893; ISSN 1535-3907
• Publisher: American Chemical Society (ACS)Copyright Statement
• Country of Publication: United States
• Language: English