Bibliography
- Schadt Eric E, Friend Stephen H, Shaywitz David A. A network view of disease and compound screening. Nat Rev Drug Discov 2009;8(4):286-95
- Ganter B, Giroux Craig N. Emerging applications of network and pathway analysis in drug discovery and development. Curr Opin Drug Discov Devel 2008;11(1):86-94
- Weckwerth W. Metabolomics in systems biology. Ann Rev Plant Biol 2003;54:669-89
- Wishart DS, Knox C, Guo AC, HMDB: a knowledge-base for the human metabolome. Nucleic Acids Res 2009;37(Database):D603-10
- Dettmer K, Aronov Pavel A, Hammock Bruce D. Mass spectrometry-based metabolomics. Mass Spectrom Rev 2007;26(1):51-78
- Lenz EM, Bright J, Knight R, Cyclosporin A-induced changes in endogenous metabolites in rat urine: a metabonomic investigation using high field 1H NMR spectroscopy, HPLC-TOF/MS and chemometrics. J Pharm Biomed Anal 2004;35(3):599-608
- Williams RE, Major H, Lock EA, D-Serine-induced nephrotoxicity: a HPLC-TOF/MS-based metabonomics approach. Toxicology 2005;207(2):179-90
- Issaq Haleem J, Abbott E, Veenstra Timothy D. Utility of separation science in metabolomic studies. J Sep Sci 2008;31(11):1936-47
- Want EJ, O'Maille G, Smith CA, Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal Chem 2006;78(3):743-52
- Le Belle JE, Harris NG, Williams SR, Bhakoo KK. A comparison of cell and tissue extraction techniques using high-resolution 1H-NMR spectroscopy. NMR Biomed 2002;15(1):37-44
- Canelas AB, ten Pierick A, Ras C, Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics. Anal Chem 2009;81(17):7379-89
- Tiziani S, Emwas A-H, Lodi A, Optimized metabolite extraction from blood serum for 1H nuclear magnetic resonance spectroscopy. Anal Biochem 2008;377(1):16-23
- Michopoulos F, Lai L, Gika H, UPLC-MS-based analysis of human metabonomics plasma for solvent precipitation using solvent precipitation or solid phase extraction. J Proteome Res 2009;8(4):2114-21
- Wenk MR. The emerging field of lipidomics. Nat Rev Drug Discov 2005;4(7):594-610
- Watson AD. Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res 2006;47(10):2101-11
- Steinberg D. Thematic review series: the pathogenesis of atherosclerosis. An interpretive history of the cholesterol controversy: part II: the early evidence linking hypercholesterolemia to coronary disease in humans. J Lipid Res 2005;46(2):179-90
- Hu C, van der Heijden R, Wang M, Analytical strategies in lipidomics and applications in disease biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009;877(26):2836-46
- Fernandis AZ, Wenk MR. Lipid-based biomarkers for cancer. J Chromatogr B Analyt Technol Biomed Life Sci 2009;877(26):2830-5
- Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37(8):911-7
- Alvarez JG, Touchstone JC. Separation of acidic and neutral lipids by aminopropyl-bonded silica gel column chromatography. J Chromatogr B Biomed Sci Appl 1992;577(1):142-5
- Ogiso H, Suzuki T, Taguchi R. Development of a reverse-phase liquid chromatography electrospray ionization mass spectrometry method for lipidomics, improving detection of phosphatidic acid and phosphatidylserine. Anal Biochem 2008;375(1):124-31
- Johanson RA, Berry GT. Brain phosphoinositide extraction, fractionation, and analysis by MALDI-TOF MS. Methods Mol Biol 2009;579:189-200
- Christie WW. Literature Survey-Solid Phase Extraction and Lipids. 2009; Available from: http://lipidlibrary.aocs.org/lit_surv/general/lit_spe.htm [Last accessed 12 September 2009]
- Brown MJ, Pleasure DE, Asbury AK. Microdissection of peripheral nerve: collagen and lipid distribution with morphological correlation. J Neurol Sci 1976;29(2-4):361-9
- Shimma S, Sugiura Y, Hayasaka T, MALDI-based imaging mass spectrometry revealed abnormal distribution of phospholipids in colon cancer liver metastasis. J Chromatogr B Analyt Technol Biomed Life Sci 2007;855(1):98-103
- Roy S, Touboul D, Brunelle A, Imaging mass spectrometry: a new tool for the analysis of skin biopsy. Application in Fabry's disease. Ann Pharm Fr 2006;64(5):328-34
- Griffiths William J, Wang Y. Mass spectrometry: from proteomics to metabolomics and lipidomics. Chem Soc Rev 2009;38(7):1882-96
- Griffiths WJ, Wang Y. Mass spectrometry: from proteomics to metabolomics and lipidomics. Chem Soc Rev 2009;38(7):1882-96
- Kanani H, Chrysanthopoulos Panagiotis K, Klapa Maria I. Standardizing GC-MS metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2008;871(2):191-201
- Soga T, Ohashi Y, Ueno Y, Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2003;2(5):488-94
- Wishart DS, Lewis MJ, Morrissey JA, The human cerebrospinal fluid metabolome. J Chromatogr B Analyt Technol Biomed Life Sci 2008;871(2):164-73
- Yu K, Sheng G, Sheng J, A metabonomic investigation on the biochemical perturbation in liver failure patients caused by hepatitis B virus. J Proteome Res 2007;6(7):2413-9
- Myint Khin T, Aoshima K, Tanaka S, Quantitative profiling of polar cationic metabolites in human cerebrospinal fluid by reversed-phase nanoliquid chromatography/mass spectrometry. Anal Chem 2009;81(3):1121-9
- Myint Khin T, Uehara T, Aoshima K, Oda Y. Polar anionic metabolome analysis by nano-LC/MS with a metal chelating agent. Anal Chem 2009;81(18):7766-72
- Nordstrom A, O'Maille G, Qin C, Siuzdak G. Nonlinear data alignment for UPLC-MS and HPLC-MS based metabolomics: quantitative analysis of endogenous and exogenous metabolites in human serum. Anal Chem 2006;78(10):3289-95
- Wilson ID, Nicholson JK, Castro-Perez J, High resolution “Ultra Performance” liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J Proteome Res 2005;4(2):591-8
- Evans AM, De Haven CD, Barrett T, Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. Anal Chem 2009;81(16):6656-67
- Schmidt A, Karas M, Dulcks T. Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI? J Am Soc Mass Spectrom 2003;14(5):492-500
- Tang K, Page JS, Smith RD. Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. J Am Soc Mass Spectrom 2004;15(10):1416-23
- Metz TO, Page JS, Baker ES, High-resolution separations and improved ion production and transmission in metabolomics. Trends Anal Chem 2008;27(3):205-14
- Granger J, Plumb R, Castro-Perez J, Wilson ID. Metabonomic studies comparing capillary and conventional HPLC-oa-TOF MS for the analysis of urine from Zucker obese rats. Chromatographia 2005;61(7/8):375-80
- Buscher JM, Czernik D, Ewald JC, Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal Chem 2009;81(6):2135-43
- Alpert AJ. Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J Chromatogr 1990;499:177-96
- Tolstikov Vladimir V, Fiehn O. Analysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Anal Biochem 2002;301(2):298-307
- Bruce SJ, Tavazzi I, Parisod V, Investigation of human blood plasma sample preparation for performing metabolomics using ultrahigh performance liquid chromatography/mass spectrometry. Anal Chem 2009;81(9):3285-96
- Uehara T, Yokoi A, Aoshima K, Quantitative phosphorus metabolomics using nanoflow liquid chromatography-tandem mass spectrometry and culture-derived comprehensive global internal standards. Anal Chem 2009;81(10):3836-42
- Wu L, Mashego Mlawule R, van Dam Jan C, Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. Anal Biochem 2005;336(2):164-71
- Sas B, Peys E, Helsen M. Efficient method for (lyso)phospholipid class separation by high-performance liquid chromatography using an evaporative light-scattering detector. J Chromatogr A 1999;864(1):179-82
- Jaaskelainen I, Urtti A. Liquid chromatography determination of liposome components using a light-scattering evaporative detector. J Pharm Biomed Anal 1994;12(8):977-82
- Taguchi R, Houjou T, Nakanishi H, Focused lipidomics by tandem mass spectrometry. J Chromatography B Analyt Technol Biomed Life Sci 2005;823(1):26-36
- Han X, Gross RW. Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics. J Lipid Res 2003;44(6):1071-9
- Han X, Gross RW. Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 2005;24(3):367-412
- Han X, Gross RW. Shotgun lipidomics: multidimensional MS analysis of cellular lipidomes. Expert Rev Proteomics 2005;2(2):253-64
- Han X, Yang J, Cheng H, Toward fingerprinting cellular lipidomes directly from biological samples by two-dimensional electrospray ionization mass spectrometry. Anal Biochem 2004;330(2):317-31
- Taguchi R. Systems for lipidomics: metabolomics focused on lipids. Tanpakushitsu Kakusan Koso 2004;49(Suppl 11):1911-6
- Houjou T, Yamatani K, Nakanishi H, Rapid and selective identification of molecular species in phosphatidylcholine and sphingomyelin by conditional neutral loss scanning and MS3. Rapid Commun Mass Spectrom 2004;18(24):3123-30
- Houjou T, Yamatani K, Imagawa M, A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 2005;19(5):654-66
- Milne S, Ivanova P, Forrester J, Alex Brown H. Lipidomics: an analysis of cellular lipids by ESI-MS. Methods 2006;39(2):92-103
- Han X, Yang K, Yang J, Shotgun lipidomics of cardiolipin molecular species in lipid extracts of biological samples. J Lipid Res 2006;47(4):864-79
- Han X, D MH, McKeel DW Jr, Substantial sulfatide deficiency and ceramide elevation in very early Alzheimer's disease: potential role in disease pathogenesis. J Neurochem 2002;82(4):809-18
- Fuller M, Sharp PC, Rozaklis T, Urinary lipid profiling for the identification of fabry hemizygotes and heterozygotes. Clin Chem 2005;51(4):688-94
- Zamfir A, Vakhrushev S, Sterling A, Fully automated chip-based mass spectrometry for complex carbohydrate system analysis. Anal Chem 2004;76(7):2046-54
- Taguchi R, Nishijima M, Shimizu T. Basic analytical systems for lipidomics by mass spectrometry in Japan. Methods Enzymol 2007;432:185-211
- Ikeda K, Oike Y, Shimizu T, Taguchi R. Global analysis of triacylglycerols including oxidized molecular species by reverse-phase high resolution LC/ESI-QTOF MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2009;877(25):2639-47
- Rainville PD, Stumpf CL, Shockcor JP, Novel application of reversed-phase UPLC-oaTOF-MS for lipid analysis in complex biological mixtures: a new tool for lipidomics. J Proteome Res 2007;6(2):552-8
- Yetukuri L, Katajamaa M, Medina-Gomez G, Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. BMC Syst Biol 2007;1:12
- Kolak M, Westerbacka J, Velagapudi VR, Adipose tissue inflammation and increased ceramide content characterize subjects with high liver fat content independent of obesity. Diabetes 2007;56(8):1960-8
- Kirsch S, Muthing J, Peter-Katalinic J, Bindila L. On-line nano-HPLC/ESI QTOF MS monitoring of alpha2-3 and alpha2-6 sialylation in granulocyte glycosphingolipidome. Biol Chem 2009;390(7):657-72
- Kim H, Ahn E, Moon MH. Profiling of human urinary phospholipids by nanoflow liquid chromatography/tandem mass spectrometry. Analyst 2008;133(12):1656-63
- Ahn EJ, Kim H, Chung BC, Quantitative profiling of phosphatidylcholine and phosphatidylethanolamine in a steatosis/fibrosis model of rat liver by nanoflow liquid chromatography/tandem mass spectrometry. J Chromatogr A 2008;1194(1):96-102
- Bang DY, Ahn E, Moon MH. Shotgun analysis of phospholipids from mouse liver and brain by nanoflow liquid chromatography/tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2007;852(1-2):268-77
- He H, Conrad CA, Nilsson CL, Method for lipidomic analysis: p53 expression modulation of sulfatide, ganglioside, and phospholipid composition of U87 MG glioblastoma cells. Anal Chem 2007;79(22):8423-30
- Bang DY, Kang D, Moon MH. Nanoflow liquid chromatography-tandem mass spectrometry for the characterization of intact phosphatidylcholines from soybean, bovine brain, and liver. J Chromatogr A 2006;1104(1-2):222-9
- Katajamaa M, Oresic M. Data processing for mass spectrometry-based metabolomics. J Chromatogr A 2007;1158(1-2):318-28
- Smith CA, Want EJ, O'Maille G, XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 2006;78(3):779-87
- Baran R, Kochi H, Saito N, MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics 2006;7:530-8
- Neuweger H, Albaum SP, Dondrup M, MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics 2008;24(23):2726-32
- Xia J, Psychogios N, Young N, Wishart DS. MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res 2009;37(Web Server):W652-60
- Mendes P. Emerging bioinformatics for the metabolome. Brief Bioinform 2002;3(2):134-45
- Sumner Lloyd W, Mendes P, Dixon Richard A. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 2003;62(6):817-36
- Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000;97(18):10101-6
- Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95(25):14863-8
- Churchill GA. Using ANOVA to analyze microarray data. BioTechniques 2004;37(2):173-5, 7
- Musumarra G, Barresi V, Condorelli DF, Scire S. A bioinformatic approach to the identification of candidate genes for the development of new cancer diagnostics. Biol Chem 2003;384(2):321-7
- Faber NM, Rajko R. How to avoid over-fitting in multivariate calibration–The conventional validation approach and an alternative. Anal Chim Acta 2007;595(1-2):98-106
- Kind T, Fiehn O. Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 2006;7:234-44
- Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res 2002;30(1):42-6
- Okuda S, Yamada T, Hamajima M, KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 2008; 36(Web Server):W423-6
- Wishart David S. Applications of metabolomics in drug discovery and development. Drugs R D 2008;9(5):307-22
- Robertson DG. Metabonomics in toxicology: a review. Toxicol Sci 2005;85(2):809-22
- Griffin JL, Nicholls AW. Metabolomics as a functional genomic tool for understanding lipid dysfunction in diabetes, obesity and related disorders. Pharmacogenomics 2006;7(7):1095-107
- Zivkovic Angela M, German JB. Metabolomics for assessment of nutritional status. Curr Opin Clin Nutr Metab Care 2009;12(5):501-7
- Serkova Natalie J, Glunde K. Metabolomics of cancer. Methods Mol Biol 2009;520:273-95
- Barba I, Fernandez-Montesinos R, Garcia-Dorado D, Pozo D. Alzheimer's disease beyond the genomic era: nuclear magnetic resonance (NMR) spectroscopy-based metabolomics. J Cell Mol Med 2008;12(5A):1477-85
- Quinones MP, Kaddurah-Daouk R. Metabolomics tools for identifying biomarkers for neuropsychiatric diseases. Neurobiol Dis 2009;35(2):165-76
- Lewis Gregory D, Asnani A, Gerszten Robert E. Application of metabolomics to cardiovascular biomarker and pathway discovery. J Am Coll Cardiol 2008;52(2):117-23
- Sreekumar A, Poisson Laila M, Rajendiran Thekkelnaycke M, Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 2009;457(7231):910-4
- Investigational New Drug Application. 2009; Available from: http://www.fda.gov/Drugs/DevelopmentApprovalProcess [cited]
- Beloqui A, Guazzaroni M-E, Pazos F, Reactome array: forging a link between metabolome and genome. Science 2009;326(5950):252-7