MassBank: a public repository for sharing mass spectral data for life sciences

Abstract

MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry (EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MS(n) data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10,286 volatile natural and synthetic compounds, and 3045 ESI-MS(2) data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI-MS(2) data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass-to-charge ratio are optimized to the ESI-MS(2) data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS(2) data on an identical compound under different collision-induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21-23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data.

Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

“…This was the result of an interfering isobaric m/z 113 ion contaminant present in the analyzed samples. To overcome this, we chose to use uridine (UR), which produces protonated U by elimination of a ribose moiety [12,16]. For QIT, we were able to simply select [UR + H] + at m/z 245 in MS 2 in order to obtain [U + H] + at m/z 113 as a precursor in MS 3 .…”

“…All collision energy (CE) values are presented in figure captions. In order to carry out the dissociation of protonated uracil at m/z 113, protonated uridine (m/z 245), which is known to produce abundant protonated uracil as its primary MS 2 dissociation product [12,16], was infused and selected in MS 2 . Protonated uracil at m/z 113 was then selected as the MS 3 precursor and its dissociation product selected as precursors in MS 4 .…”

“…Such de novo identification aims to correlate observed spectral features in MS/MS to the structures of investigated species based on established reactivity for a class of compounds [4,[6][7][8][9]. The idea of using MS/MS as stand-alone identification tool is of increasing interest and is also being addressed using other more general approaches intended to generalize dissociation pathways [10], to automate data analysis [11], or to compile spectra in databases [12,13].…”

Flavonoids and Auxin Transport Inhibitors Rescue Symbiotic Nodulation in the Medicago truncatula Cytokinin Perception Mutant cre1

“…Flavonoid standards were obtained from Sigma-Aldrich (kaempferol, naringenin, quercetin, morin, and hesperetin), Indofine Chemical Company (isoliquiritigenin, liquiritigenin, formononetin, daidzein, and biochanin A), Fluka (apigenin), and ICN Biomedicals (genistein). For identification and relative quantification (peak area ratio of the endogenous analyte/internal standard) of flavonoid compounds where standards were not available to us (medicarpin and chrysoeriole), the mass spectra of flavonoid compounds detected in samples were compared with the mass bank database (Horai et al, 2010) and the literature (Guo et al, 2008;Li et al, 2013).…”

Screening of pharmaceuticals and illicit drugs in wastewater and surface waters of Spain and Italy by high resolution mass spectrometry using UHPLC-QTOF MS and LC-LTQ-Orbitrap MS

“…For most compounds evaluated SDLs were 0.02 or 0.1 µg/L (Diaz et al, 2013;Hernández et al, 2015). For compounds where no standards were available, the database included data regarding fragment ions and molecular formula from literature or online databases such as MassBank (Horai et al, 2010).…”