Atsushi Yamamoto

Winners of CASMI2013: Automated Tools and Challenge Data.

CASMI (Critical Assessment of Small Molecule Identification) is a contest in which participants identify the molecular formula and chemical structure of challenging molecules using blind mass spectra as the challenge data. Seven research teams participated in CASMI2013. The winner of CASMI2013 was the team of Andrew Newsome and Dejan Nikolic, the University of Illinois at Chicago, IL, USA. The team identified 15 among 16 challenge molecules by manually interpreting the challenge data and by searching in-house and public mass spectral databases, and chemical substance and literature databases. MAGMa was selected as the best automated tool of CASMI2013. In some challenges, most of the automated tools successfully identified the challenge molecules, independent of the compound class and magnitude of the molecular mass. In these challenge data, all of the isotope peaks and the product ions essential for the identification were observed within the expected mass accuracy. In the other challenges, most of the automated tools failed, or identified solution candidates together with many false-positive candidates. We then analyzed these challenge data based on the quality of the mass spectra, the dissociation mechanisms, and the compound class and elemental composition of the challenge molecules.

Two New Gangliosides, Acanthagangliosides I and J from the StarfishAcanthaster planci

A new ganglioside molecular species named AG-1 has obtained from the whole body of starfish Acanthaster planci (crown of thorns). The structure of this ganglioside have been elucidated by enzymatic hydrolysis with the endo-type glycosidase. Enzymatic hydrolysis gave an oligosaccharide and ceramides, quantitatively. The oligosaccharide moiety was determined mainly using 2D-NMR experiments as β-Fucf-(14)-α-Galp-(14)-α-NeuAc-(23)-β-Galp-(14)-Glcp. Meanwhile, the ceramide moiety was elucidated by NMR and GC-MS analysis as the mixture of (2S,2′S,3S,4R)-2-(2′-hydroxydocosanoyl)amino-1,3,4-trihydoxyhexadecane, and (2S,2′S,3S,4R)-2-(2′-hydroxytetracosanoyl)amino-1,3,4-trihydoxyhexadecane. Reversed-phase HPLC of AG-1 gave two kinds of gangliosides named acanthagangliosides I (1) and J (2). Their structures have been identified by negative FAB-MS.

Use of high-resolution mass spectrometry to identify precursors and biodegradation products of perfluorinated and polyfluorinated compounds in end-user products

Structural identification of perfluoroalkyl and polyfluoroalkyl substances found in end-user products and their biodegradation products was performed using ultra-high resolution mass spectrometry. Little attention has so far been paid to the environmental burden of perfluorooctane sulfonate and perfluorooctanoic acid from compounds with a molar mass of ~2,000. Analysis of end-user waterproofing and stain repellent products revealed the presence of numerous ions with molar masses ranging from 1,000 to 2,000 and complex mass spectra. Ultra-high resolution mass spectrometry determined the accurate mass of the observed ions, allowing the cleavage position and fragment structure to be determined. The precursor structures were determined based on reconstitution of the retrieved fragments. Products of fluorochemical manufacturers before voluntary regulation comprised compounds with plural perfluorooctyl chains. In the current product lines, compounds comprising perfluorobutyl chains were detected. Biodegradation tests using activated sludge revealed that biodegradation products consistent with those reported previously were generated even from complex end-user products. For example, the biodegradation test revealed the formation of N-ethyl perfluorooctane sulfonamido acetic acid and various fluorotelomer acids in the samples. The results of the present study suggest that the environmental burden of these compounds should be reevaluated.

Characterization of Mycolic Acids in Total Fatty Acid Methyl Ester Fractions from Mycobacterium Species by High Resolution MALDI-TOFMS.

Mycolic acids (MAs) are characteristic components of bacteria in the suborder Corynebacterineae, such as Mycobacterium. MAs are categorized into subclasses based on their functional bases (cyclopropane ring, methoxy, keto, and epoxy group). Since MAs have heterogeneity among bacterial species, analyzing of MAs are required in the chemotaxonomic field. However, their structural analysis is not easy because of their long carbon-chain lengths and several functional groups. In this study, total fatty acid (FA) methyl ester (ME) fraction of M. tuberculosis H37Rv was analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOFMS) with a spiral ion trajectory (MALDI spiral-TOFMS). The distributions of carbon-chain length and their relative peak intensities were confirmed with those obtained by analysis of each subclass fraction which was separated from total FA ME fraction using thin-layer chromatography (TLC). The observed major peaks were reliably assigned as MAs owing to the high mass accuracy (error<3 ppm). The types of MA subclasses, their distributions of carbon-chain lengths, their relative peak intensities, and the ratio of even- and odd-numbered carbon-chain MAs for the total FA ME fraction were consistent with those of MA subclass fractions. To visualize whole MAs, contour maps of relative peak intensities for whole MAs were created. The contour maps indicated the MA subclasses and their distributions of carbon-chains with relative peak intensities at a glance. Our proposed method allows simple characterization in a short time and thus enables the analysis of large numbers of samples, and it would contribute to the chemotaxonomy.

Solid state phase behaviors of dodecyldimethylamine oxide: protonation and counterion effects

Abstract Solid phase behaviors of dodecyldimethylamine oxide (C12DAO) studied by differential scanning calorimetry and X-ray scattering have shown clearly the effects of protonation. Besides the protonated (cationic) (C12DAO HCl) and the nonionic (C12DAO) species, 1:1 composition or hemihydrochloride (C12DAO 1/2 HCl) was shown to be a stable complex. The phase behavior of C12DAOHCl was similar to that of dodecylammonium chloride rather than dodecyltrimethylammonium chloride (C12TACl), although similar crystal structure was suggested for C12DAOCl and C12TABr. Solid phase behaviors changed dramatically by changing the counterion from Cl− to NO3− or SO42− for both the cationic and 1:1 species.

Sensitive Detection of Aromatic Hydrophobic Compounds in Water and Perfluorooctane Sulfonate in Human Serum by Surface-Assisted Laser Desorption/Ionization Mass Spectrometry (SALDI-MS) with Amine Functionalized Graphene-Coated Cobalt Nanoparticles

In this article, we describe the application of surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) with the use of amine functionalized graphene-coated cobalt nanoparticles (CoC-NH2 nanoparticles) to analyse aromatic hydrophobic compounds that are known environmental contaminants, including polycyclic aromatic hydrocarbons (PAHs) and pentachlorophenol (PCP). Our results demonstrated that SALDI-MS can detect PCP, anthracene, and pyrene in water. In particular, the CoC-NH2 nanoparticles proved to be an efficient means of capturing PCP in water because of the high adsorption capacity of the nanoparticles for PCP, which resulted in a detectability of 100 ppt. Furthermore, the CoC-NH2 nanoparticles also functioned as an adsorbent for solid-phase extraction of perfluorooctane sulfonate (PFOS) from human serum, displaying good performance with a detectability of 10 ppb by SALDI-MS.

In-situ measurement in through-plane direction in PEMFC

Water management is a large issue for putting PEMFC to practical use. Appropriate water management enables us to suppress the drying in PEM (Polymer Electrolyte Membrane) and the flooding in GDL (Gas Diffusion Layer), which degrade the performance of PEMFC. Against the background of importance for the water management, we challenged to develop the measurement method to grasp the water behavior in PEMFC. Especially, we focused on through-plane direction measurement, because the through-plane direction in cell has major role for the transport of mass, heat and electric charge in the cell. We developed the three methods to measure the water in cell directly or indirectly: cross sectional cell: micro NMR-sensor array: micro thermocouple array. These three methods successively captured the distribution of the liquid water in GDL, the water content in PEM and the temperature in cell. The data obtained help us to give the possible mechanism of how the water in cell impacted the cell voltage.Copyright

Relaxed conditions of exchange on mechanism for exchanging parts of executed program

We proposed a control method for exchanging parts of an executing program. By applying this exchange method to a shared library that is linked dynamically, the contents of library functions that constitute the program can be changed without stopping processes that are providing services. In other words, maintenance tasks can be dynamically performed without suspending the services that are being provided. However, the program parts that are exchanged according to the proposed exchange method must satisfy strict exchange conditions, making it difficult to create program parts that are to be exchanged. Therefore, in this paper, we describe an exchange method in which the exchange conditions have been relaxed. Also, we point out a problem in which relaxing the exchange conditions causes the exchanging time to be significantly increased when exchanging parts for a program that is mainly a CPU-bound program compared with a program that is mainly an I/O-bound program. Then, to deal with this problem, we propose methods of devising process scheduling mechanisms to shorten the exchanging time. Specifically, we show a mechanism that temporarily suspends exchangeable processes early and a mechanism that preferentially executes unexchangeable processes. In addition, we implement and evaluate both of these mechanisms and show the effectiveness of each mechanism.