[en] The open spectral library MassBank (https://massbank.jp/) started in 2006 in Japan, as one of the first open source and open access cross-vendor mass spectral libraries. The first dedicated European MassBank server (https://massbank.eu/) was launched in 2011, adding spectra from compounds of environmental relevance to complement the original metabolomics focus. Recent developments boosted the FAIRness of MassBank data, and a redesigned web interface with modern architecture was launched in 2025. All records are under version control, and versioned releases are pushed to an independent data repository with digital object identifier assigned to each data release. Semantic metadata integrates the spectral data into the world of linked open data. The record format enables many downstream studies, and records are validated by an automated pipeline to ensure data quality upon submission and review existing records. The SPectraL hASH was added for spectral content-based access. MassBank is cross-integrated in several resources such as MassBank of North America, Global Natural Product Social Molecular Networking, PubChem, the US EPA CompTox Dashboard, NORMAN Database System, RforMassSpectrometry, and more. MassBank now boasts a total of 119 845 spectra of 18 529 compounds from 53 contributors from around the world.
Disciplines :
Chemistry
Author, co-author :
Neumann, Steffen ; Computational Plant Biochemistry, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany ; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
Meier, René; Computational Plant Biochemistry, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
Wenk, Michael; Computational Plant Biochemistry, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
ELAPAVALORE, Anjana ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Environmental Cheminformatics
Nishioka, Takaaki; The Mass Spectral Data Working Group of the Mass Spectrometry Society of Japan. Yamabuki-cho 332-6, Shinjuku-ku, Tokyo 162-0801, Japan
Schulze, Tobias; Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, Leipzig 04318, Germany
Stravs, Michael; Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland ; TOFWERK AG, Thun 3645, Switzerland
Tsugawa, Hiroshi ; Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo184-8588, Japan
Matsuda, Fumio; Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, The University of Osaka. 1-5, Yamadaoka, Suita, Osaka 565-0871, Japan
Stein Steven E., NIST/EPA/NIH Mass Spectral Library-PC Version, NIST Standard Reference Database. National Institute of Standards and Technology. 10.18434/T4H594.
Giera M, Aisporna A, Uritboonthai W et al. The hidden impact of in-source fragmentation in metabolic and chemical mass spectrometry data interpretation. Nat Metab. 2024;6:1647–8. 10.1038/s42255-024-01076-x.
Wang M, Carver JJ, Phelan VV et al. Sharing and community curation of mass spectrometry data with global natural products social molecular networking. Nat Biotechnol. 2016;34:828–37. 10.1038/nbt.3597.
Vinaixa M, Schymanski EL, Neumann S et al. Mass spectral databases for LC/MS- and GC/MS-based metabolomics: state of the field and future prospects. Trends Analyt Chem. 2016;78:23–35. 10.1016/j.trac.2015.09.005.
Horai H, Arita M, Kanaya S et al. MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom. 2010;45:703–14. 10.1002/jms.1777.
Huber C, Müller E, Schulze T et al. Improving the screening analysis of pesticide metabolites in human biomonitoring by combining high-throughput in vitro incubation and automated LC–HRMS data processing. Anal Chem. 2021;93:9149–57. 10.1021/acs.analchem.1c00972.
Moseley HNB, Rocca-Serra P, Salek RM et al. InChI isotopologue and isotopomer specifications. J Cheminform. 2024;16:54. 10.1186/s13321-024-00847-8.
Djoumbou Feunang Y, Eisner R, Knox C et al. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform. 2016;8:61. 10.1186/s13321-016-0174-y.
Stravs MA, Schymanski EL, Singer HP et al. Automatic recalibration and processing of tandem mass spectra using formula annotation: recalibration and processing of MS/MS spectra. J Mass Spectrom. 2013;48:89–99. 10.1002/jms.3131.
Tsugawa H, Kind T, Nakabayashi R et al. Hydrogen rearrangement rules: computational MS/MS fragmentation and structure elucidation using MS-FINDER software. Anal Chem. 2016;88:7946–58. 10.1021/acs.analchem.6b00770.
Stravs M, Schymanski EL, Neumann S et al. 2017. RMassBank. BioConductor. 10.18129/B9.BIOC.RMASSBANK.
Willighagen EL, Mayfield JW, Alvarsson J et al. The chemistry development kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform. 2017;9:33. 10.1186/s13321-017-0220-4.
Huber F, Verhoeven S, Meijer C et al. matchms—processing and similarity evaluation of mass spectrometry data. J Open Source Softw. 2020;5:2411.
Pavlov D, Rybalkin M, Karulin B. Bingo from SciTouch LLC: chemistry cartridge for Oracle database. J Cheminform. 2010;2:F1. 10.1186/1758-2946-2-S1-F1.
Zasso M, Patiny L, Sander T et al. openchemlib-js: library to manipulate chemical structures and reactions in JavaScript. Version v9.13.0. Zenodo. 10.5281/ZENODO.5139988. 28 October 2025.
Wohlgemuth G, Mehta SS, Mejia RF et al. SPLASH, a hashed identifier for mass spectra. Nat Biotechnol. 2016;34:1099–101. 10.1038/nbt.3689.
Heller S, McNaught A, Stein S et al. InChI—the worldwide chemical structure identifier standard. J Cheminform. 2013;5:7. 10.1186/1758-2946-5-7.
Yamamoto A, Tokai N, Kakehashi R et al. Fragmentation considerations using amidoamine oxide homologs. Mass Spectrom. 2024;13:A0158. 10.5702/massspectrometry.A0158.
Sumner LW, Amberg A, Barrett D et al. Proposed minimum reporting standards for chemical analysis: chemical analysis working group (CAWG) metabolomics standards initiative (MSI). Metabolomics. 2007;3:211–21. 10.1007/s11306-007-0082-2.
Schymanski EL, Jeon J, Gulde R et al. Identifying small molecules via high resolution mass spectrometry: communicating confidence. Environ Sci Technol. 2014;48:2097–8. 10.1021/es5002105.
Elapavalore A, Kondić T, Singh RR et al. Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures. Environ Sci: Process Impacts. 2023;25:1788–801. 10.1039/D3EM00181D.
Kim S, Chen J, Cheng T et al. PubChem 2025 update. Nucleic Acids Res. 2025;53:D1516–25. 10.1093/nar/gkae1059.
Williams AJ, Grulke CM, Edwards J et al. The CompTox chemistry dashboard: a community data resource for environmental chemistry. J Cheminform. 2017;9:61. 10.1186/s13321-017-0247-6.
Dulio V, Koschorreck J, van Bavel B et al. The NORMAN Association and the European partnership for chemicals risk assessment (PARC): let’s cooperate!. Environ Sci Eur. 2020;32:100. 10.1186/s12302-020-00375-w.
Mohammed Taha H, Aalizadeh R, Alygizakis N et al. The NORMAN suspect list exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry. Environ Sci Eur. 2022;34:104. 10.1186/s12302-022-00680-6.
Vrandečić D, Krötzsch M. Wikidata: a free collaborative knowledgebase. Commun ACM. 2014;57:78–85.
Tsugawa H, Cajka T, Kind T et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods. 2015;12:523–6. 10.1038/nmeth.3393.
Tsugawa H, Ikeda K, Takahashi M et al. A lipidome atlas in MS-DIAL 4. Nat. Biotechnol. 2020;38:1159–63. 10.1038/s41587-020-0531-2.
Schmid R, Heuckeroth S, Korf A et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat Biotechnol. 2023;41:447–9. 10.1038/s41587-023-01690-2.
Pluskal T, Castillo S, Villar-Briones A et al. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics. 2010;11:395. 10.1186/1471-2105-11-395.
Helmus R, ter Laak TL, van Wezel AP et al. patRoon: open source software platform for environmental mass spectrometry based non-target screening. J Cheminform. 2021;13:1. 10.1186/s13321-020-00477-w.
Helmus R, van de Velde B, Brunner AM et al. patRoon 2.0: improved non-target analysis workflows including automated transformation product screening. JOSS. 2022;7:4029. 10.21105/joss.04029.
Ruttkies C, Schymanski EL, Wolf S et al. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform. 2016;8:3. 10.1186/s13321-016-0115-9.
Rainer J, Vicini A, Salzer L et al. A Modular and expandable ecosystem for metabolomics data annotation in R. Metabolites. 2022;12:173. 10.3390/metabo12020173.
Wilkinson MD, Dumontier M, Aalbersberg IJ et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018. 10.1038/sdata.2016.18.
Bach E, Schymanski EL, Rousu J. Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data. Nat Mach Intell. 2022;4:1224–37. 10.1038/s42256-022-00577-2.
Dablanc A, Hennechart S, Perez A et al. FragHub: a mass spectral library data integration workflow. Anal Chem. 2024;96:12489–96. 10.1021/acs.analchem.4c02219.
Stanstrup J, Neumann S, Vrhovšek U. PredRet: prediction of retention time by direct mapping between multiple chromatographic systems. Anal Chem. 2015;87:9421–8. 10.1021/acs.analchem.5b02287.
MassBank consortium and its contributors MassBank/MassBank-data. version 2025.05.1. Zenodo. 10.5281/ZENODO.15341877. 5 Ma. 2025.
Neumann S, Schymanski EL, Meier R et al. MassBank3: the spectral reference library’s next generation software product. v2025.10.4. Zenodo. 10.5281/ZENODO.16923315. 29 October 2025.
MassBank Consortium MassBank-similarity-api. Version v1.8-matchms-0.31.0. Zenodo. 10.5281/ZENODO.17143724. 29 October 2025.
MassBank Consortium MassBank-export-api. Version v1.18. Zenodo. 10.5281/ZENODO.17143361. 29 October 2025.
MassBank Consortium MassBank-charts. Version massbank-similarity-api-0.1.1. Zenodo. 10.5281/ZENODO.17143930. 29 October 2025.
