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

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.

Novel free ceramides as components of the soldier defense gland of the Formosan subterranean termite (Coptotermes formosanus).

Of the lipid extracts of the defense secretion from the Formosan subterranean termite, Coptotermes formosanus Shiraki, on high-performance thin-layer chromatography analysis, no glycolipids or phospholipids were detected, but free fatty acids and three novel ceramides were found (termed TL-1, TL-2, and TL-3). Free fatty acids were confirmed to be lignoceric acid (C24:0) and hexacosanoic acid (C26:0), as described previously [Chen, J., G. Henderson, and R. A. Laine. 1999. Lignoceric acid and hexacosanoic acid: major components of soldier frontal gland secretions of the Formosan subterranean termite (Coptotermes formosanus). J. Chem. Ecol. 25: 817-824]. TL-1, TL-2, and TL-3 were characterized as ceramides differing in hydrophobicity based on results of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis, mild alkaline treatment, GC-MS analysis of fatty acid methylesters, and GC-MS analysis of sphingoid long-chain bases (LCBs) as trimethylsilyl derivatives. Fatty acids in TL-1 and TL-2 were C18:0, C20:0, and C22:0, and those in TL-3 were 2-hydroxy C18:0, C20:0, and C22:0. The most predominant LCB in TL-2 was a novel trihydroxy C(14)-sphingosine, 1,3,9-trihydroxy-2-amino-6-tetradecene. TL-3 contained C(18)-sphinganine and two kinds of novel sphingadienines, 1,3-dihydroxy-2-amino-7,10-hexadecadiene and 1,3-dihydroxy-2-amino-11,14-eicosadiene. Although examination of the biological activities of these novel ceramides was beyond the scope of these studies, because of the minuscule quantities available from termite secretions, it will be interesting in the future to synthesize these molecules for biological testing.

Determination of bisphenol-A in water by semi-micro column high-performance liquid chromatography using 2-methoxy-4-(2-phthalimidinyl)phenylsulfonyl chloride as a fluorescent labeling reagent.

A highly sensitive method for the determination of bisphenol-A in water with semi-micro column high-performance liquid chromatography using 2-methoxy-4-(2-phthalimidinyl)phenylsulfonyl chloride as a fluorescent labeling reagent has been developed. The labeling reaction was carried out at 70 degrees C for 20 min in borate buffer (pH 9.5). The derivative eluted at 11.6 min on a reversed-phase column with methanol-water (78:22, v/v) at a flow-rate of 0.2 ml/min. The fluorescence was monitored at 308 nm for excitation and 410 nm for emission. The detection limit (S/N = 3) was 10 fmol per injection. The labeling yield was about 95%.

Production of 1,2-didocosahexaenoyl phosphatidylcholine by bonito muscle lysophosphatidylcholine/transacylase.

1,2-Didocosahexaenoyl phosphatidylcholine (PC), which has highly unsaturated fatty acid at both sn-1 and sn-2 positions of glycerol, is a characteristic molecular species of bonito muscle. To examine the involvement of a de novo route in its synthesis, the molecular species of phosphatidic acid (PA) were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-olato dizinc(II) complex, a novel phosphate-capture molecule. However, 1,2-didocosahexaenoyl species could not be detected. Next, 1,2-didocosahexaenoyl PC synthesis by the cytosolic lysophosphatidylcholine (LPC)/transacylase was examined using endogenous LPC from bonito muscle, in which the 2-docosahexaenoyl species is abundant. The LPC/transacylase synthesized 1,2-didocosahexaenoyl PC as the most abundant molecular species. For further characterization, the LPC/transacylase was purified to homogeneity from the 100,000 x g supernatant of bonito muscle. The isolated LPC/transacylase is a labile glycoprotein with molecular mass of 52 kDa including a 5-kDa sugar moiety. The LPC/transacylase showed a PC synthesis (transacylase activity) below and above the critical micelle concentration of substrate LPC, and fatty acid release (lysophospholipase activity) was always smaller than the transacylase activity, even with a monomeric substrate. These results suggest that the LPC/transacylase is responsible for the synthesis of 1,2-didocosahexaenoyl PC.

Small complex-type N-linked glycans are attached to cell-wall bound exo-beta-glucanases of both mung bean and barley seedlings.

N-linked glycans of wall-bound exo-beta-glucanases from mung bean and barley seedlings, namely Mung-ExoI and Barley-ExoII, were characterized. The N-linked glycans of Mung-ExoI and Barley-ExoII were liberated by gas-phase hydrazinolysis followed by re-N-acetylation. Their structures were determined by two-dimensional sugar-mapping analysis and MALDI-TOF mass spectrometry. N-glycans from both glucanases were of paucimannosidic-type (small complex-type) structures, Manalpha1-6(+/-Manalpha1-3)(Xylbeta1-2)Manbeta1-4GlcNAcbeta1-4(+/-Fucalpha1-3) GlcNAc, which are known as typical vacuole-type N-glycans. The results suggest that N-glycans of cell-wall glucanase were produced by partial trimming of complex-type N-glycans by exoglycosidases during its transport from Golgi apparatus to cell walls or in the cell walls.