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Volume 57 (2009)
- Issue 6 Pages 371-
- Issue 5 Pages 331-
- Issue 4 Pages 241-
- Issue 3 Pages 117-
- Issue 2 Pages 45-
- Issue 1 Pages 1-
Volume 57, Issue 3
Displaying 1-16 of 16 articles from this issue
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TECHNICAL REPORT
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Hideaki YAMADA, Kazuya ICHIKI, Yoshihiko NAKATA, Satoshi NINOMIYA, Tos ...2009 Volume 57 Issue 3 Pages 117-121
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSWe developed a processing technique for biological samples, that is, animal cells, for imaging mass spectrometry using gas cluster ion beams. Secondary ion mass spectrometry has been investigated for cellular imaging with high spatial resolution. Nanoscale processing techniques are needed for cellular level imaging, for example, for removing contamination from cell surfaces and exposing the insides of cells. In this study, we compared the mass spectrum of the unetched cell sample to that of the cell irradiated with an Ar cluster ion beam. The contamination was removed from the sample surface and the signals of intracellular components were detected. The results indicate that the cells were etched with low damage using the gas cluster ion beam. Finally, we compared the ion image of an unetched cell to that of an etched cell and demonstrated that the technique of cluster ion irradiation could be applied to the processing of samples for cellular level imaging mass spectrometry.View full abstractDownload PDF (687K)
REGULAR PAPER
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Hirofumi NAGAO, Shigeo HAYAKAWA, Mami HASHIMOTO, Kenichi IWAMOTO, Mich ...2009 Volume 57 Issue 3 Pages 123-132
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSA JEOL JMS-HX110 double-focusing mass spectrometer was combined with the collision cell and spherical electric sector of a HITACHI M80-B instrument to perform tandem mass spectrometry experiments. A quadrupole lens doublet was mounted between the mass spectrometer and the collision cell to improve ion transmission into the collision cell. The detection system was also improved to expand the mass range of product ions. These improvements provided reliable spectra of high-energy electron transfer dissociation (HE-ETD) of peptides using an alkali metal target. The present results demonstrated that HE-ETD by a single collision with an alkali metal target could determine the amino acid sequence and phosphorylation site of peptides.View full abstractDownload PDF (1801K)
REVIEWS
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Yuki SUGIURA, Mitsutoshi SETOU2009 Volume 57 Issue 3 Pages 133-143
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSMatrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS; also referred to as mass spectrometry imaging; MSI) enables the visualization of the distribution of a range of biomolecules that have varied structures in the cells and tissue sections. This emerging imaging technique was initially developed as a tool for protein imaging, but recently it is increasingly being used for the imaging of small organic molecules. IMS is an effective technique for the imaging of small metabolites, including endogenous metabolites such as lipids and exogenous drugs because of the following advantages: First, IMS does not require any specific labels or probes. Second, IMS is a non-targeted imaging method. Finally, the simultaneous imaging of many types of metabolite molecules is possible, and all these features are necessary for the assessment of metabolite localization. In this review, we discuss the capability of current IMS techniques for imaging small molecules, and introduce representative studies on imaging of endogenous and exogenous metabolites. In addition, the limitations and problems of the technique are also discussed, and reports of progress toward solving the problems with this technique are also introduced.View full abstractDownload PDF (2334K) -
Takeshi MASUDA, Yasushi ISHIHAMA2009 Volume 57 Issue 3 Pages 145-151
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSShotgun proteomics based on liquid chromatography/mass spectrometry has been widely used to provide a large-scale view of the proteome, including protein expression, localization, modification, and protein-protein interaction. However, it is still challenging tasks to carry out membrane protein-targeted proteome analysis due to the hydrophobic nature of proteins with transmembrane domains. Here, we review current sample preparation techniques such as enrichment, solubilization, and digestion for membrane proteomics and focus on phase-transfer surfactant-based approaches recently developed by our group. We also discuss future developments for membrane proteome focused shotgun proteomics.View full abstractDownload PDF (960K)
COMMENTARIES
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Takao SHIMIZU2009 Volume 57 Issue 3 Pages 153-155
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSLipids are playing at least 4 essential roles in the living systems. It is a major component of cellular membrane, highly efficient source of energy, modifying molecules of proteins (lipid modification) and bioactive compounds. Because of the difficulty in handling and insolubility in water, the research of lipids has been relatively slow in the field of molecular biology and cellular biology. We have studied for more than two decades on the roles of eicosanoids (bioactive lipids derived from carbon 20 polyunsaturated fatty acids); its biosynthesis and receptor/signal transduction by the use of cellular biology and knockout mouse studies. Recently, during the search of glycerophospholipid biosynthesis, we have discovered an enzyme involved in the surfactant production in the lung. Herein summarized are recent progresses of studies on lipid mediators, from prostaglandins to pulmonary surfactant lipids.View full abstractDownload PDF (1046K) -
Makoto TANAKA2009 Volume 57 Issue 3 Pages 157-166
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSCurrent drug discovery, clinical development, and approval process is long, expensive, and inefficient. Less than 1 in 10 promising drug candidates entering phase I clinical trials eventually receive regulatory approval. This is an alarming statistic for the pharmaceutical industry, and the traditional drug development paradigm is no longer sustainable in the face of high attrition risk and increasing development cost. The core problem is lack of innovation in developing effective new therapies for unmet medical needs. There is an urgent need to improve productivity in pharmaceutical research & development (R & D) by closing the gap between bench and bedside and making much earlier and more accurate go/no-go decisions. A paradigm shift that will reinvent the process of R & D is emerging in the pharmaceutical industry. It is time for pharmaceutical companies to introduce new innovative thinking into current drug development strategies.
Translational research in the pharmaceutical industry is intended to facilitate the transition of new ideas in basic science to patient cure through improvement of R & D productivity. Exploratory clinical trials, targeted medicine, and biomarkers are major tools for translational research. Simple introduction of new technologies and sciences into the current system/organization is not sufficient. We must change the current paradigm (business model) and, more importantly, our way of thinking (mindset). In this article, the potential roles of translational research in pharmaceutical R & D are discussed, focusing on early drug development (from discovery to proof of concept).View full abstractDownload PDF (2201K) -
Tomoyuki OE2009 Volume 57 Issue 3 Pages 167-172
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSBiological macromolecules, such as deoxyribonucleic acid (DNA) and proteins, are exposed to higher chemical stresses during some physiological events such as increased oxidative stress from degenerative aging diseases and higher glucose stress in diabetes mellitus. Therefore, the resulting chemical modifications can provide significant information about biological events. Chemically modified DNA and abundant proteins have been analyzed by mass spectrometry, mainly for use as dosimeters of chemical exposure. However, quantitative analyses of bioactive peptides and proteins in specific diseases have relied almost exclusively on the use of immunoassay-based procedures with no concern for possible minute chemical modifications. Therefore, important information could be overlooked, or considerable misunderstandings could be created, if the modifications are not distinguished and if they alter protein functions such as phosphorylation. I believe that chemical modifications on biological macromolecules could play important roles, not only as diagnostic and therapeutic markers, but also as triggers that initiate some diseases. In this article, I first introduce my previous research on biomarkers such as DNA adducts and chemically modified proteins. I then present a novel “omics” strategy for biomarker discovery using minute chemical modifications on biological macromolecules.View full abstractDownload PDF (1001K) -
Junichi KAMIIE2009 Volume 57 Issue 3 Pages 173-176
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSWe have developed a high-throughput strategy for focused absolute quantitative proteomics using multi-channel selected-reaction-monitoring mass-spectrometric analysis with in silico peptide selection criteria, and confirmed its quantitative accuracy and reproducibility. The method was applied to examine simultaneously the expression levels of 34 drug transporter proteins, which have been reported to be functionally expressed in the relevant tissues, in mouse tissues. The developed method will provide an inclusive assay platform for all transporter proteins expressed both in animal/human tissues and would contribute progress of drug discovery and development.View full abstractDownload PDF (666K) -
Nobuharu GOTO2009 Volume 57 Issue 3 Pages 177-182
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSLow success rates of research and development (R&D) are a serious issue in pharmaceutical industries. This is attributed to the dramatic decline (from 88% in 1994, <55% in 1998, 40% in 2000, to nearly 30% in 2005) in phase II stage of drug development, also known as the proof of concept (POC) stage, partly because of the lack of predictive animal models and no previous human knowledge on drug candidates with novel targets and/or mechanisms. New technologies, such as global omics (genomics, transcriptomics, proteomics, and metabolomics), systems biology, and in vivo imaging tools (magnetic resonance imaging: MRI, positron emission tomography: PET, single photon emission computed tomography: SPECT, computed tomography: CT), are being developed and used for advancing molecular understanding of human diseases. Application of these biomarkers would increase confidence in drug candidates, enhance cost-effective decision making in exploratory development, and increase the success rate of the POC stage. In this study, our principle and examples of biomarkers research as well as general information on biomarkers including the definition and factors that affect the R&D paradigm are described.View full abstractDownload PDF (2019K) -
Akiyoshi HIRAYAMA, Kenjiro KAMI, Masahiro SUGIMOTO, Masaru TOMITA, Hir ...2009 Volume 57 Issue 3 Pages 183-186
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSCapillary electrophoresis-mass spectrometry based metabolomics exhibits unlimited potentials to elucidate global metabolic profiles of various types of samples including clinical tissues. In addition, non-targeted metabolome analysis by this method holds the promise of discovering novel biomarker candidates. In this commentary, we introduce our strategies for studying cancer-specific metabolism by analyzing metabolome of surgically excised tumor tissues.View full abstractDownload PDF (578K) -
—Development and Applications—Yoshihiro KITA, Takao SHIMIZU2009 Volume 57 Issue 3 Pages 187-194
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSLipid mediators, including eicosanoids and the platelet activating factor (PAF), are produced from common precursor phospholipids in mammalian tissues and cells. They play diverse roles in a variety of pathological and physiological contexts. For comprehensive lipid mediator profiling purposes, we have developed a liquid chromatography/mass spectrometry (LC-MS) multiplex quantitation method that covers eicosanoids and PAF. In this article, we describe the development of the LC-MS system, the sample pretreatment procedure optimized for this system, and application of lipid mediator profiling in macrophages and animal disease models. Also, we briefly introduce our perspective on label-free differential phospholipid analysis using ultra performance liquid chromatography/mass spectrometry (UPLC-MS).View full abstractDownload PDF (1479K) -
Toshihide NISHIMURA2009 Volume 57 Issue 3 Pages 195-200
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSThe results of recent worldwide activities undertaken to discover biomarkers of diseases suggest that huge numbers of promising biomarkers will soon be identified because of advances in quantitative proteomic platforms such as multiple-reaction monitoring mass spectrometry. These newly identified biomarkers will aid in the understanding of biology and other life sciences. The science of reductionism has aided in the understanding of the physical sciences; however, it is questionable whether reductionism is useful in understanding life sciences. The science of complexity has recently attracted the attention of scientists and has proven successful in areas such as economics, sociology, and so on. The author has therefore attempted to discuss the potential usefulness of the science of complexity in understanding life sciences and life itself.View full abstractDownload PDF (1555K) -
Yasushi KABURAGI, Ryo YAMASHITA, Eri TAKAHASHI, Kazuki YASUDA, Mitsuhi ...2009 Volume 57 Issue 3 Pages 201-206
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSThe prevalence of diabetes is rapidly increasing worldwide, thus leading to an increasing risk of diabetic microangiopathy, caused by prolonged hyperglycemia, as well as an increase in atherosclerotic diseases (macroangiopathy), of which diabetes is one of the risk factors. Complex gene-environment interactions make it difficult to investigate the molecular basis of diabetic etiology from clinical samples obtained from diabetic patients with wide-ranging backgrounds. In contrast, risk factors for diabetic complications such as micro- and macroangiopathies are common among patients with a variety of diabetic pathogeneses, thus enabling the proteomic search for biomarkers of diabetic complications from clinical samples feasible. In an attempt to identify diabetic biomarkers, we analyzed sera from more than 100 diabetic patients and approximately 40 control subjects, using cleavable isotope-coded affinity tag, followed by tandem mass spectrometry for protein sequencing and identification. These proteins, which were differentially expressed in the sera from diabetic patients, may be potential biomarkers of various pathological conditions related to diabetes. In another study, we developed a 2-dimensional gel-based method that enabled the analysis of approximately 2,000 protein spots by combining ultrafiltration, immunoaffinity depletion of major urinary proteins, and 2-dimensional difference gel electrophoresis. Using this experimental system, we analyzed urine samples collected from diabetic patients with or without microalbuminuria and healthy controls to search for early diagnostic markers of diabetic nephropathy. We identified 33 unique proteins (24 upregulated and 9 downregulated) that were differentially expressed in diabetic patients with microalbuminuria as compared to those in the healthy controls. Proteomic analyses of clinical samples from diabetic patients, animal models of diabetes, and cultured cells may help to elucidate the molecular mechanisms responsible for the development of various forms of diabetes and to identify diagnostic biomarkers of diabetic complications.View full abstractDownload PDF (1418K) -
Akira OKAMOTO, Keiko YAMADA, Michio OHTA2009 Volume 57 Issue 3 Pages 207-212
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSThe identification of proteins on immunoblotting membranes has been one of the great challenges in molecular biology. We have refined the on-membrane digestion strategy to apply that method to immunoblotting. This strategy involved three key points: (1) Use polyvinylpyrrolidone (average molecular weight 40,000, PVP-40) as a blocking agent; (2) use a polyvinylidine difluoride (PVDF) membrane rather than a nylon membrane in the immunoblotting procedure; and (3) perform on-membrane digestion using an aqueous reaction system, eliminating the organic solvent. Liquid chromatography-electrospray ionization-mass spectrometry/mass spectrometry (LC-ESI-MS/MS) was used for protein identification, because several proteins were detected from a single band or spot on the immunoblotting membrane. The contaminated proteins were derived from the anti-serum or the background of individual organisms. This method should differentiate between target proteins and contaminants, based on the information on the organism, organ, or protein location. We expect this strategy to shed light on all molecular biological studies, especially in infectious and autoimmune disease research.View full abstractDownload PDF (849K) -
Takemichi NAKAMURA2009 Volume 57 Issue 3 Pages 213-233
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSCharacterization of diverse organic molecules often requires manual interpretation of various types of mass spectra. Although specialized approach may be necessary for solving each specific problem, fundamentals of gas-phase chemistry of organic ions provide a common framework for understanding fragmentations observed in electron ionization mass spectrometry and tandem mass spectrometry coupled with soft ionization methods. This brief tutorial for practitioners in the mass spectrometry and related fields introduces the essence of spectral interpretation and structural characterization including the ion chemistry framework and some related topics.View full abstractDownload PDF (2352K)
Letter to the Editor
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Takeshi KASAMA2009 Volume 57 Issue 3 Pages 235-239
Published: June 01, 2009
Released on J-STAGE: June 15, 2009
JOURNAL FREE ACCESSDownload PDF (2528K)
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