Fumito Matsuura

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.

Structures of asparagine-linked oligosaccharides from hen egg-yolk antibody (IgY). Occurrence of unusual glucosylated oligo-mannose type oligosaccharides in a mature glycoprotein

Asparagine-linked oligosaccharides present on hen egg-yolk immunoglobulin, termed IgY, were liberated from the protein by hydrazinolysis. AfterN-acetylation, the oligosaccharides were labelled with a UV-absorbing compound,p-aminobenzoic acid ethyl ester (ABEE). The ABEE-derivatized oligosaccharides were fractionated by anion exchange, normal phase and reversed phase HPLC, and their structures were determined by a combination of sugar composition analysis, methylation analysis, negative ion FAB-MS, 500 MHz1H-NMR and sequential exoglycosidase digestions. IgY contained monoglucosylated oligomannose type oligosaccharides with structures of Glcα1-3Man7–9-GlcNAc-GlcNAc, oligomannose type oligosaccharides with the size range of Man5–9GlcNAc-GlcNAc, and biantennary complex type oligosaccharides with core region structure of Manα1-6(±GlcNAcβ1-4)(Manα1-3)Manβ1-4GlcNAcβ1-4(±Fucα1-6)GlcNAc. The glucosylated oligosaccharides, Glc1Man8GlcNAc2 and Glc1Man7GlcNAc2, have not previously been reported in mature glycoproteins from any source.

Phospholipids from the free-living nematodeCaenorhabditis elegans

The phospholipid and the fatty chain compositions of diacyl, alkylacyl and alkenylacyl glycerophospholipids of the free-living nematode,Caenorhabditis elegans, were investigated. The phospholipids were comprised of 54.5% ethanolamine glycerophospholipid (EGP), 32.3% choline glycerophospholipid (CGP), 8.1% sphingomyelin and 5.1% others. The most abundant fatty acid in CGP was eicosapentaenoic acid (20∶5n−3). The fatty acids in CGP were more unsaturated than those in EGP. Alkenylacyl and alkylacyl subclasses accounted for 1.0 and 2.6%, respectively, of CGP and 14.0 and 19.6%, respectively, of EGP. At least 80% of the alkenyl and alkyl groups were 18∶0 chains and the remaining were odd numbered chains. The potential presence of platelet-activating factor (PAF) was examined by bioassay, but PAF-like activity was not detected in the extracts of this nematode.

Chromatographic separation of asparagine-linked oligosaccharides labeled with an ultravioletabsorbing compound,p-aminobenzoic acid ethyl ester

AbstractWe have expanded on the suitability ofp-aminobenzoic acid ethyl ester as an ultraviolet-absorbing reagent [Wanget al., (1984) Anal Biochem 141:366–81] for the analysis of asparagine-linked oligosaccharides derived from glycoproteins. The oligosaccharides released from glycoproteins by hydrazinolysis/N-reacetylation were derivatized withp-aminobenzoic acid ethyl ester and the derivatives were purified and separated into neutral and acidic oligosaccharides on a PRE-SEP C18 cartridge. The acidic oligosaccharides could be further separated into a few species by high-voltage paper electrophoresis. p-Aminobenzoic acid ethyl ester derivatives of neutral oligosaccharides were analyzed by gel permeation chromatography on Bio-Gel P-4 and HPLC on a silica-based amide column. The elution profile and the proportion of the oligosaccharides were in agreement with literature values. The overall yield of oligosaccharides from glycoproteins was approximately 70%. Fifty pmol of oligosaccharide were detectable on Bio-Gel P-4 and 4–5 pmol on HPLC.

Structures of asparagine linked oligosaccharides of immunoglobulins (IgY) isolated from egg-yolk of Japanese quail

Structures of the Asn linked oligosaccharides of quail egg-yolk immunoglobulin (IgY) were determined in this study. Asn linked oligosaccharides were cleaved from IgY by hydrazinolysis and labelled withp-aminobenzoic acid ethyl ester (ABEE) afterN-acetylation. The ABEE labelled oligosaccharides were then fractionated by a combination of Concanavalin A-agarose column chromatography and anion exchange, normal phase and reversed phase HPLC before their structures were determined by sequential exoglycosidase digestion, methylation analysis, HPLC, and 500 MHz1H-NMR spectroscopy. Quail IgY contained only neutral oligosaccharides of the following categories: the glucosylated oligomannose type (0.6%, Glcα1-3Glcα1-3Man9GlcNAc2; 35.6%, Glcα1-3Man7–9GlcNAc2). oligomannose type (15.0%, with the structure Man5–9GlcNAc2) and biantennary complex type with core structures of-Manα1-3(-Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAc (9.9%),-Manα1-3(GlcNAcβ1-4)(-Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAc (25.1%) and-Manα1-3(GlcNAcβ1-4)(-Manα1-6)Manβ1-4GlcNAcβ1-4(Fucα1-6)GlcNAc (11.4%). Although never found in mammalian proteins, glucosylated oligosaccharides (Glc1Man7–9GlcNAc2) have been located previously in hen IgY.

Further characterization of allergenically active oligosaccharitols isolated from a sea squirt H-antigen.

Complete primary structures of five allergenically active oligosaccharitols (HPG-beta 2-N5a, -N6, -N7a, -N7b, and -N9) derived from a sea squirt H-antigen were studied. Structural characterization was carried out by a new method in which products of limited periodate oxidation, followed by derivatization with p-aminobenzoic acid ethyl ester, were analyzed by a combination of HPLC, fast atom-bombardment mass spectrometry, sequential glycosidase digestion, methylation analysis, and 500-MHz 1H NMR. Established structures of GalNAc beta 1-4 (GalNAc alpha 1-2Fuc alpha 1-3) GlcNAc beta 1-3GalNAc-ol, GalNAc beta 1-4GlcNAc beta 1-3 (GalNAc beta 1-4GlcNAc beta 1-6) GalNAc-ol, GalNAc beta 1-4GlcNAc beta 1-3[GalNAc beta 1-4 (Fuc alpha 1-3) GlcNAc beta 1-6] GalNAc-ol, GalNAc beta 1-4 (Fuc alpha 1-3) GlcNAc beta 1-3[GalNAc beta 1-4 (Fuc alpha 1-3) GlcNAc beta 1-6] GalNAc-ol, and GalNAc beta 1-4 (GalNAc alpha 1-2Fuc alpha 1-3)GlcNAc beta 1-3 [GalNAc beta 1-4 (GalNAc alpha 1-2Fuc alpha 1-3)GlcNAc beta 1-6]GalNAc-ol are represented by HPG-beta 2-N5a, -N6, -N7a, -N7b, and -N9, respectively. These structures have not been encountered previously. Oligosaccharide units GalNAc alpha 1-2Fuc alpha 1-, GalNAc beta 1-4GlcNAc beta 1-, and Fuc alpha 1-3GlcNAc beta 1- are considered to be the allergenically specific epitopes. Partial assignments of 500-MHz 1H NMR spectra of these novel O-linked oligosaccharitols were attempted.

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 C14-sphingosine, 1,3,9-trihydroxy-2-amino-6-tetradecene. TL-3 contained C18-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.

Glycerol-, inositol-, and reducing end hexose-containing oligosaccharides in human urine

Ten previously unreported oligosaccharides have been purified from the urines of human subjects using a combination of gel filtration, ion exchange, and thin-layer chromatographies. Their structures were determined by direct probe mass spectrometry, methylation analysis, and proton NMR spectroscopy of the permethylated oligosaccharide alditols.On the basis of composition, the oligosaccharides could be divided into three groups. Five oligosaccharides containing glycerol were characterized as glucosylα1-1′glycerol; glucosylβ1-1′glycerol; galactosylβ1-1′glycerol; glucosyl-1-1′(fucosyl-1-2′)glycerol and/or fucosyl-1-1′(glucosyl-1-2′)glycerol; and glucosyl-1-1′(galactosyl-1-2′)glycerol or galactosyl-1-1′(glucosyl-1-2′)glycerol. Four inositol-containing oligosaccharides were characterized as galactosylβ1 (fucosylα1)inositol,N-acetylgalactosaminylα1 (fucosylα1)inositol, fucosylα1-2galactosylβ1 (N-acetylgalactosaminylα1)inositol and fucosylα1-2galactosylβ1-4-N-acetylglucosaminylα1(N-acetylgalactosaminylα1)inositol. Finally, galactosylα1-3(fucosylα1-2)galactosylβ1-6galactosylα1-4(fucosylα1-3)glucose, an oligosaccharide with glucose at its reducing end, was tentatively identified. The significance and possible origins of the carbohydrate structures are discussed.