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Identifying the Sequence and Distinguishing the Oxidized—Methionine from Phenylalanine Peptides by MALDI TOF/TOF Mass Spectrometry in an Antarctic Bacterium Pseudomonas Syringae (01/Oct/2009)
This short note highlights a procedure to distinguish the residues having similar masses, oxidized methionine and phenylalanine containing peptides using MALDI TOF/TOF. The isotope intensities give a preliminary recognition of peptides containing oxidized methionine. In the peptides with partial oxidation of methionine a mass difference of 16 Da can be...
Role of Magnetic Resonance in Understanding the Pathogenesis of Hepatic Encephalopathy (23/Jan/2009)
A. Huda1,2, R.K. Gupta3, N. Rajakumar2 and M.A. Thomas21Department of Physics, California State University, Fresno, CA 93740. 2Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095. 3Department of Radiology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, India.AbstractA spectrum of neuropsychiatric abnormalities caused...
Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS) in Breast Cancer (30/Oct/2008)
Uma Sharma, Rani Gupta Sah and Naranamangalam R. Jagannathan Department of NMR and MRI Facility, All India Institute of Medical Sciences, New Delhi—110029, India. Abstract Breast cancer is a major health problem in women and early detection is of prime importance. Breast magnetic resonance imaging (MRI) provides...
Coherence Transfer in Spatially Resolved NMR (16/Sep/2008)
Narayanan Chandrakumar Department of Chemistry, Indian Institute of Technology-Madras, Chennai—600036, Tamil Nadu, India. Abstract We present an overview of some applications of coherence transfer experiments in spatially resolved NMR, with examples from imaging and volume localized spectroscopy. While the major preoccupation of spatially resolved NMR experiments is...
Sophisticated Functions for a Simple Molecule: The Role of Glucosylceramides in Fungal Cells (10/Sep/2008)
Leonardo Nimrichter1, Marcio L. Rodrigues1, Eliana Barreto-Bergter1 and Luiz R. Travassos2 1Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-590, Brazil. 2Unidade de Oncologia Experimental and Disciplina de Biologia Celular, Universidade Federal de São Paulo; São Paulo, SP 04023-062, Brazil. Abstract It...
Junfeng Liu1, Weichuan Yu2, Baolin Wu3 and Hongyu Zhao4 1Department of Statistics, West Virginia University, Morgantown, WV 26506, U.S.A. 2Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Sai Kung Kowloon, Hong Kong. 3Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455,...
Determination of Key Intermediates in Cholesterol and Bile Acid Biosynthesis by Stable Isotope Dilution Mass Spectrometry (25/Mar/2008)
Tadashi Yoshida1, Akira Honda2, Hiroshi Miyazaki3 and Yasushi Matsuzaki2 1Raffles Japanese Clinic, Singapore, Singapore. 2Tokyo Medical University, Kasumigaura Hospital, Ibaraki, Japan. 3Pharmax Institute, Kanagawa, Japan. Abstract For more than a decade, we have developed stable isotope dilution mass spectrometry methods to quantify key intermediates in cholesterol and bile...
Michael J. Walsh1, Maneesh N. Singh1,2, Helen F. Stringfellow2, Hubert M. Pollock3, Azzedine Hammiche3, Olaug Grude3, Nigel J. Fullwood1, Mark A. Pitt2, Pierre L. Martin-Hirsch1,2 and Francis L. Martin1 1Biomedical Sciences Unit, Department of Biological Sciences, Lancaster University, Lancaster, U.K. 2Lancashire Teaching Hospitals NHS Trust, Preston, U.K. and 3Department...
Detecting the Site of Phosphorylation in Phosphopeptides Without Loss of Phosphate Group Using MALDI TOF Mass Spectrometry (26/Feb/2008)
Medicharla V. Jagannadham and Ramakrishnan Nagaraj Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India. Abstract Phosphopeptides with one and four phosphate groups were characterized by MALDI mass spectrometry. The molecular ion of monophosphopeptide could be detected both as positive and negative ions by MALDI...
Common Peak Approach Using Mass Spectrometry Data Sets for Predicting the Effects of Anticancer Drugs on Breast Cancer (14/Dec/2007)
Masaru Ushijima1, Satoshi Miyata1, Shinto Eguchi4, Masanori Kawakita5, Masataka Yoshimoto6, Takuji Iwase3, Futoshi Akiyama2, Goi Sakamoto2, Koichi Nagasaki1, Yoshio Miki1,2, Tetsuo Noda1,2, Yutaka Hoshikawa1,2 and Masaaki Matsuura1,2 1Genome Center, Japanese Foundation for Cancer Research, Tokyo, Japan. 2Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan....
S.J. Shahtaheri1, M. Khadem1, F. Golbabaei1 and A. Rahimi-Froushani2 1Department of Occupational Health, Tehran University of Medical Sciences, Iran. 2Department of Epidemiology and Biostatistics, Tehran University of Medical Sciences, Iran.Abstract: Chromium is an important constituent widely used in different industrial processes for production...
Comparison of Computational Algorithms for the Classification of Liver Cancer using SELDI Mass Spectrometry: A Case Study (11/Dec/2007)
Changyu Shen1, Timothy E Breen1,5, Lacey E Dobrolecki2, C. Max Schmidt3,4,5,6,7, George W. Sledge2,5 , Kathy D. Miller2,5 and Robert J Hickey2,5 1Division of Biostatistics, Department of Medicine, Indiana University School of Medicine, 410 West 10th st., 2Division of Hematology/Oncology, Department of Medicine, Indiana University School of...
Ming Lu1,2, Kym F. Faull3, Julian P. Whitelegge3, Jianbo He1,2, Dejun Shen1,2, Romaine E. Saxton4 and Helena R. Chang1,2,4 1Gonda/UCLA Breast Cancer Research Laboratory; 2Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California; 3The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the...
Yukie Sasakura1, Makoto Nogami1, Noriko Kobayashi2 and Katsuhiro Kanda1 1Bio-Medical Center, R&D Division, Nanotechnology Product Business Group, Hitachi High-Technologies Corporation, Hitachinaka, Ibaraki, 312-8504, Japan. 2Naka Application Center, Nanotechnology Product Business Group, Hitachi High-Technologies Corporation, Hitachinaka, Ibaraki, 312-0057, Japan.Abstract: A protein digestion system using immobilized enzymes for protein identification and glycochain...
Parametric Power Spectral Density Analysis of Noise from Instrumentation in MALDI TOF Mass Spectrometry (17/Sep/2007)
Hyunjin Shin1, Miray Mutlu2, John M. Koomen3 and Mia K. Markey4 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, U.S.A. 2Department of Electrical and Electronics Engineering, Bilkent University, Bilkent Ankara, Turkey. 3H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A. 4The University of Texas Department...
Comparison of Supervised Classification Methods for Protein Profiling in Cancer Diagnosis (19/Jul/2007)
Nadège Dossat1,2, Alain Mangé2,3,5, Jérôme Solassol2,3,5, William Jacot2,4, Ludovic Lhermitte2,3,5, Thierry Maudelonde2,3,5, Jean-Pierre Daurès1,2,6 and Nicolas Molinari1,2,6 1IURC, Department of Biostatistic, Epidemiology and Clinical Research, Montpellier, France. 2University of Montpellier I, Montpellier, France. 3CHU Montpellier, Hôpital Arnaud de Villeneuve, Department of Cellular Biology, Montpellier, France. 4CHU Montpellier, Hôpital Arnaud de...
Xutao Deng1, Huimin Geng2 and Hesham H. Ali1 1College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, U.S.A. 2Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, U.S.A.Abstract: Many studies showed inconsistent cancer biomarkers due to bioinformatics artifacts. In this paper...
Kate W. Jordan1, Wenlei He1, Elkan F. Halpern2, Chin-Lee Wu1 and Leo L. Cheng1,2 Departments of 1Pathology and 2Radiology Massachusetts General Hospital, Harvard Medical School Boston, Massachusetts.Abstract: Accurate interpretation and correlation of tissue spectroscopy with pathological conditions requires disease specific tissue metabolite databases; however, specimens for research are often kept...
Bias, Randomization, and Ovarian Proteomic Data: A Reply to "Producers and Consumers" (26/Feb/2007)
Keith A. Baggerly, Kevin R. Coombes, and Jeffrey S. Morris Department of Biostatistics, U.T. M.D. Anderson Cancer Center, Houston, Texas, USAAbstract: Proteomic patterns derived from mass spectrometry have recently been put forth as potential biomarkers for the early diagnosis of cancer. This approach has generated much excitement, particularly as initial...
Conventional gene expression profiling relies on using fluorescent detection of hybridized probes. Physical characteristics of fluorophores impose limitations on achieving a highly multiplex gene analysis of single cells. Our work demonstrates the feasibility of using metal-tagged in situ hybridization for mRNA detection by inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS...
Impact of Freeze-thaw Cycles and Storage Time on Plasma Samples Used in Mass Spectrometry Based Biomarker Discovery Projects (22/Feb/2007)
Breeana L Mitchella,b, Yutaka Yasuie, Christopher I Lia,c, Annette L. Fitzpatrickc, Paul D Lampea,b,d Public Health Sciencesa, Fred Hutchinson Cancer Research Center, Molecular and Cellular Biology Programb, Departments of Epidemiologyc, and Pathobiologyd, University of Washington, Department of Public Health Sciencese University of AlbertaAbstract: Mass spectrometry approaches to biomarker discovery in...
The Need for Review and Understanding of SELDI/MALDI Mass Spectroscopy Data Prior to Analysis (19/Feb/2007)
William E. Grizzle,a O. John Semmes,b William Bigbee,c Liu Zhu,a Gunjan Malik,b Denise K Oelschlager,a Barkha Manne,a Upender Mannea University of Alabama at Birmingham, Birmingham, AL;a Eastern Virginia Medical School, Norfolk, VA,b University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.cAbstract: Multiple studies have reported that surface enhanced laser desorption/ionization time...
Understanding the characteristics of mass spectrometry data through the use of simulation (18/Feb/2007)
Kevin R. Coombes1, John M. Koomen2, Keith A. Baggerly1, Jeffrey S. Morris1, and Ryuji Kobayashi2 Departments of 1Biostatistics and Applied Mathematics and 2Molecular Pathology, University of Texas M.D. Anderson Cancer Center, Houston TX 77030 USAAbstract:Background: Mass spectrometry is actively being used to discover disease-related proteomic patterns in complex mixtures of...
Ovarian Cancer Classification based on Mass Spectrometry Analysis of Sera (17/Feb/2007)
Baolin Wu1,6, Tom Abbott2, David Fishman5, Walter McMurray2, Gil Mor3, Kathryn Stone2, David Ward4, Kenneth Williams2, Hongyu Zhao1,4 1Department of Epidemiology and Public Health, 2W.M. Keck Biotechnology Resource Laboratory, 3Department of Obstetrics and Gynecology, 4Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. 5Department of OB/GYN, New...
Leukemia Associated Antigens: Their Dual Role as Biomarkers and Immunotherapeutic Targets for Acute Myeloid Leukemia (14/Feb/2007)
Barbara-Ann Guinn1, Azim Mohamedali1, Ken I. Mills2, Barbara Czepulkowski1, Michael Schmitt3 and Jochen Greiner31Department of Haematological Medicine, King’s College London School of Medicine, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU, 2Department of Haematology, University Hospital of Wales, Heath Park, Cardiff, CF4 4XN, U.K. 3Third Clinic for Internal Medicine,...
Deukwoo Kwon1, Mahlet G. Tadesse2, Naijun Sha3, Ruth M. Pfeiffer1 and Marina Vannucci41Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, U.S.A.2Department of Biostatistics & Epidemiology, University of Pennsylvania, Philadelphia, PA, U.S.A. 3Department of Mathematical Sciences, University of Texas at El Paso, TX, U.S.A. 4Department of Statistics, Texas...