BMDMS-NP: A comprehensive ESI-MS/MS spectral library of natural compounds

The Bioinformatics & Molecular Design Research Center Mass Spectral Library – Natural Products (BMDMS-NP) is a library containing the mass spectra of natural compounds, especially plant specialized metabolites. At present, the library contains the electrospray ionization tandem mass spectrometry (ESI-MS/MS) spectra of 2739 plant metabolites that are commercially available. The contents of the library were made comprehensive by incorporating data generated under various experimental conditions for compounds with diverse molecular structures. The structural diversity of the BMDMS-NP data was evaluated using molecular fingerprints, and it was sufficiently exhaustive enough to represent the structures of the natural products commercially available. The MS/MS spectra of each metabolite were obtained with different types/brands of ion traps (tandem-in-time) or combinations of mass analyzers (tandem-in-space) at multiple collision energies. All spectra were measured repeatedly in each environment because variations can occur in spectra, even under the same conditions. Moreover, the probability, separability of searching, and transferability of this spectral library were evaluated against those of MS/MS libraries, namely: NIST17 and MoNA. [Display omitted] •The BMDMS-NP library contains ESI MS/MS spectra of plant specialized metabolites.•Metabolites in the library are as structurally diverse as phytochemicals in ZINC15.•For comprehensiveness, data were recorded under various experimental conditions.•Data blocks defined by environment conditions were applied to the library search.•The BMDMS-NP with command-line executable source codes and record data are publicly available.