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Volume 55 (2007)
- Issue 6 Pages 363-
- Issue 5 Pages 311-
- Issue 4 Pages 261-
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Volume 55, Issue 3
Displaying 1-18 of 18 articles from this issue
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REVIEW
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Shigeru SUZUKI2007 Volume 55 Issue 3 Pages 117-125
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSGas chromatography/mass spectrometry and liquid chromatography/mass spectrometry provide a useful technical platform for analyzing environmental chemicals. Many measurement methods have been developed on this platform based on the present day needs. Simultaneous determination methods of substances such as pesticides, volatile organic compounds, polycyclic aromatic hydrocarbons, and persistent organic pollutants have been developed corresponding to their increase in the environment. One of the recent topics is the elucidation of structures of unknown environmental chemicals by analyzing their exact masses.View full abstractDownload PDF (1454K)
INTEGRATED PAPERS
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Daiki ASAKAWA, Kunihiko MORI, Kenzo HIRAOKA2007 Volume 55 Issue 3 Pages 127-135
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSA new ionization method, electrospray droplet impact ionization (EDI), has been developed for matrix-free secondary-ion mass spectrometry (SIMS). The charged droplets formed by electrospraying 1 M acetic acid aqueous solution are sampled through an orifice with a diameter of 400 μm into the first vacuum chamber, transported into a quadrupole ion guide, and accelerated at 10 kV after exiting the ion guide. The droplets impact on a dry solid sample (no matrix used) deposited on a stainless steel substrate. The secondary ions formed by the impact are transported to a second quadrupole ion guide and are mass-analyzed by an orthogonal time-of-flight mass spectrometer. EDI/SIMS was found to be an easy to operate and versatile method for molecular-level surface analysis.View full abstractDownload PDF (1385K) -
Hiroaki SUZUKI, Tohru YAMAGAKI, Kazuo TACHIBANA2007 Volume 55 Issue 3 Pages 137-144
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSEfficient ionization of neutral oligosaccharides in negative-ion matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was achieved; harmine (7-methoxy-1-methyl-9H-pyrido[3,4-b]indole) was used as a matrix and ammonium chloride was added as a chloride source to generate chlorinated molecules of neutral oligosaccharide. Increasing the molar amount of ammonium chloride gradually increased the ionization efficiency, which was saturated by adding over 2 molar equivalents of ammonium chloride to the matrix. Ionization efficiency increased when the concentration of salt was high. The results of solid phase fluorescence spectra of mixed crystals indicated that harmine was protonated and formed the hydrochloride salt. Results of ultraviolet absorption spectra showed that harmine hydrochloride absorbed ultraviolet laser irradiation from a nitrogen laser (337 nm) more effectively than harmine, and that ionization efficiency of the chlorinated molecule increased. Harmine hydrochloride was the most effective matrix.View full abstractDownload PDF (1124K)
NOTE
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Mass Microscopy to Reveal Distinct Localization of Heme B (m/z 616) in Colon Cancer Liver MetastasisShuichi SHIMMA, Mitsutoshi SETOU2007 Volume 55 Issue 3 Pages 145-148
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSImaging mass spectrometry (imaging MS) of tissue sections has become one of the main subjects in surface analysis. However, it is not easy to identify the molecular species present in imaged signals. We successfully performed imaging MS and tandem mass spectrometry (MSn) on the tissue section using a matrix-assisted laser desorption/ionization quadrupole-ion-trap time-of-flight mass spectrometer. We called the method “mass microscopy,” which is a combination of high spatial resolution imaging MS and MSn. This paper describes mass microscopy of a human liver section with metastatic colon cancer. The imaging result of m/z 616 showed low ion intensity in a cancerous region. To identify the molecule that is responsible for the generation of m/z 616, we performed MS2 and MS3 on the liver section. Considering the m/z value and peak pattern in MS2 and MS3 data, it was found that m/z 616 was generated from heme B. Heme B consists of an iron atom and porphyrin, and is known as a prosthetic group in hemoglobin, which is a protein in erythrocytes. Our results indicate the difference between the blood rich organ liver and ischemic metastatic colon cancer.View full abstractDownload PDF (496K)
COMMENTARIES
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Yasuhide NAITO2007 Volume 55 Issue 3 Pages 149-156
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSIn the last decade, the field of mass spectrometry has changed radically, particularly mass spectrometry of biomolecules. The expansion in scope has led to growth in the number of terms and in the use of these terms by those not trained in mass spectrometry. As a result, compilations of terms and definitions, such as the forthcoming IUPAC compilation, should represent an extensive revision and expansion of their previous versions. Several arguments on terms concerning mass spectrometry have been raised by both domestic and international communities. This article summarizes the arguments and current status of the compilation to present the latest trends in mass spectrometry terminology.View full abstractDownload PDF (804K) -
Yasushi ISHIHAMA2007 Volume 55 Issue 3 Pages 157-164
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSCurrent proteomics technologies based on miniaturized on-line liquid chromatography (LC) coupled with mass spectrometry (MS) allow us to analyze protein expression profiling with a high throughput. Compared to genome sequencing and microarray-based transcriptomics, however, proteomics is still under development to achieve coverage of the entire proteome. In this commentary, the optimization of proteomic nanoLC/MS systems is described. In addition, future development of the analytical systems to achieve the coverage of the entire proteome is discussed.View full abstractDownload PDF (1446K) -
Shun-ichiro IEMURA, Tohru NATSUME2007 Volume 55 Issue 3 Pages 165-171
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSFunctional proteomics aims to determine the cellular functions of genes directly at the protein level, and includes the comprehensive analysis of protein-protein interactions by affinity-based isolation of protein complexes. Mass spectrometry (MS) is a powerful method for the identification of proteins. To enhance the sensitivity and resolution of the MS/MS analysis, we developed a novel direct nanoflow liquid chromatography/MS/MS system. Furthermore, to enhance the sensitivity of the whole analysis system, we optimized the conditions of sample preparation. In this review, we describe the pull-down procedures.View full abstractDownload PDF (1165K) -
Takaya SATOH2007 Volume 55 Issue 3 Pages 173-181
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSProtein identification by peptide mass fingerprinting was performed with a high performance matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The analytic capability was evaluated using two mixtures consisting of three and five tryptic digests with internal and external calibration methods. In both methods, the high mass resolving power contributed to a precise selection of monoisotopic peaks from mass spectra. In the former method, the high mass accuracy facilitated unambiguous protein identification from protein database searches. In the latter method, the high mass accuracy allowed the discrimination of the matched peptides of positive proteins from those of false-positive proteins through the difference in their mass error distributions. The mass error distribution of the matched peptides of positive proteins consisted of about 10 ppm systematic error with a random error of several ppm, whereas that of the matched peptides of false-positive proteins was random within the selected range of the peptide tolerance window.View full abstractDownload PDF (1043K) -
Hiroshi MORIWAKI2007 Volume 55 Issue 3 Pages 183-191
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSLiquid chromatography/mass spectrometry (LC/MS) has become an invaluable technique for trace analysis of pollutants in the environment. Persistent organic pollutants (POPs), some of which are toxic, are monitored extensively in various environments. LC/MS for the analysis of POPs has the potential to contribute to the simplification of analytical methods. This article presents a review of the LC/MS methods for the determination of POPs.View full abstractDownload PDF (928K) -
Takeshi BAMBA, Eiichiro FUKUSAKI2007 Volume 55 Issue 3 Pages 193-199
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSIn this paper, we describe the usefulness of supercritical fluid chromatography (SFC) in the analysis of hydrophobic metabolites. The use of SFC in the analysis of plant polyprenols markedly improved the chromatographic resolution of polyprenol homologs and their geometric isomers, compared with conventional high-performance liquid chromatography. Individual homologs from 10 to 100 mers were separated under optimized SFC conditions. Then, we established an analytical system for fingerprinting and profiling of diverse lipids using supercritical fluid chromatography/mass spectrometry (SFC/MS). When a cyanopropylated silica gel packed column was used for the separation, 14 lipids were successfully detected, and the analysis time was less than 15 min. The use of an octadecylsilylated column resulted in separation, depending on the differences in the unsaturation of the fatty acid side chains and isomer separation.View full abstractDownload PDF (879K) -
Kenji HIROSE, Kiyoshi MARUNO, Hiroyasu YAMAMOTO2007 Volume 55 Issue 3 Pages 201-208
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSUltraPerformance liquid chromatography(R) (UPLC(R)), a novel liquid chromatographic technique, has become popular in recent years. By using sub-2 μm particles for the separation column, several times higher resolution, speed, and sensitivity of analysis can be obtained, compared with conventional high-performance liquid chromatography. This revolutionary technique is especially useful with mass spectrometry (MS). As a result of rapid development of the mass spectrometer in recent years, UPLC(R)/MS has been recognized as a new category of analytical technique and has been applied in various fields of science, such as biology, pharmaceuticals, the chemical industry, food safety, and environmental analysis. This commentary discusses the theory of UPLC(R) and the necessary instrumental performances of liquid chromatogram and mass spectrometer.View full abstractDownload PDF (1238K) -
Kanae TERAMOTO, Hiroaki SATO, Liwei SUN, Masaki TORIMURA, Hiroaki TAO2007 Volume 55 Issue 3 Pages 209-216
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSMatrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is beginning to play an important role in rapid identification and classification of industrially useful or pathogenic bacteria. Instead of conventional mass spectral fingerprint approaches, MALDI-MS identification of bacteria using ca. 50 ribosomal subunit proteins as biomarkers has been proposed. In this bioinformatics-based method, the masses of ribosomal subunit proteins in bacterial lysates observed by MALDI-MS are compared with the calculated masses predicted from the amino acid sequences registered on protein databases such as Swiss-Prot. Therefore, taxonomic identification of bacteria at species level would be ideally performed. Considering the possible mismatch between the actual and calculated masses of the biomarkers, we further developed a highly reliable method applicable to bacterial classification at strain level by detailed characterization of expressed ribosomal subunit proteins of several bacteria. With our developed method using a verified mass list of expressed ribosomal proteins of genome-sequenced strains as a reference, bacterial samples isolated from soil could be successfully classified at strain level. As an application, detection of cross-contamination of culture collections was also described.View full abstractDownload PDF (1151K) -
Tatsuya YAMAMOTO, Kunihiko GEKKO2007 Volume 55 Issue 3 Pages 217-219
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSThe 70S ribosome of Escherichia coli, which plays a central role in peptide synthesis in cells, is a super-macro complex (2.7 MDa) comprising three RNA molecules and more than 50 proteins. We succeeded in measuring the hydrogen/deuterium exchange of 55 ribosomal proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The results revealed the structural flexibility and solvent accessibility of individual proteins, and provided useful information on the structure-flexibility-function relationships of 70S ribosome.View full abstractDownload PDF (807K) -
Hajime MIZUNO, Shunsuke IZUMI, Shiro KOMINAMI, Toshifumi HIRATA2007 Volume 55 Issue 3 Pages 221-225
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSMany static protein structures have been determined by X-ray crystallography and nuclear magnetic resonance (NMR). Protein dynamics has also been studied. The structure and dynamics of proteins provide critical information about their functional mechanisms. Recently, mass spectrometry has become an essential method to analyze protein topological structures and protein dynamics. We performed topological analysis of membrane proteins using mass spectrometry coupled with chemical cross-linking. The combination of chemical cross-linking and mass spectrometry is a powerful method for analyzing the topological organization of protein structures, protein complexes, and the interface between interacting subunits. In this paper, we introduce our strategies for studying the membrane-protein and protein-protein interaction sites of P450 17α with its redox partners, NADPH-cytochrome P450 reductase and cytochrome b5.View full abstractDownload PDF (927K) -
Mina HASEGAWA, Shigeo TAKENAKA, Shingo TSUYAMA2007 Volume 55 Issue 3 Pages 227-230
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSAnalysis of metabolome has become an emerging discipline under system biology. The goal of metabolomics is to identify and quantify all of the metabolites in a cell, tissue or organism. Here we summarize recent progress in metabolomics and its application.View full abstractDownload PDF (613K) -
Naoe YAMANE2007 Volume 55 Issue 3 Pages 231-240
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSThe quadrupole mass spectrometer is used for quantitative determination of drug concentrations in biological matrices because it has high selectivity. Though the use of high-performance liquid chromatography/tandem mass spectrometry makes it possible to conduct highly-sensitive determinations at the picogram level, sample pretreatment is essential for the removal of endogenous substances from matrices and to facilitate ionization of the drug substance. Appropriate sample pretreatment ensures avoidance of a decline in sensitivity and improves reproducibility. This commentary provides a discussion on the development of appropriate sample treatment, including cautionary points related to sample treatment procedures, and an explanation of methods for treating a variety of matrices, such as protein precipitation, liquid-liquid extraction, and solid-phase extraction.View full abstractDownload PDF (1617K)
Letter to the Editor
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Ryuichi ARAKAWA2007 Volume 55 Issue 3 Pages 241-243
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSDownload PDF (1455K)
Letter from the Editor-in-Chief
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Ken-ichi YOSHINO2007 Volume 55 Issue 3 Pages 245-260
Published: 2007
Released on J-STAGE: June 15, 2007
JOURNAL FREE ACCESSThe term “restriction enzyme” is derived from the phenomenon of host-controlled restriction and modification in viral infection of bacteria, not from the ability of enzymes to recognize the specific target nucleotide sequence in the DNA and break the DNA chain. That is, the term “restriction enzyme” is not derived from the fact that the cleavage site is restricted. Bacteria initially resist infections by new bacteriophages, and this “restriction” of viral growth stems from endonucleases within the cells that destroy foreign DNA molecules from bacteriophages. Restriction enzymes are a kind of nuclease that catalyze hydrolysis of DNA strands and were discovered during investigations of the phenomenon of host-controlled restriction and modification of bacteriophages. They are not peptidases (proteases). However, it is a common mistake to use the term “restriction enzyme” for amino acid residue-specific endopeptidase such as trypsin.View full abstractDownload PDF (2142K)
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