Metabolomics and Isotope Tracing

被引:603
作者
Jang, Cholsoon [1 ,2 ]
Chen, Li [1 ,2 ]
Rabinowitz, Joshua D. [1 ,2 ]
机构
[1] Princeton Univ, Lewis Sigler Inst Integrat Genom, Washington Rd, Princeton, NJ 08544 USA
[2] Princeton Univ, Dept Chem, Washington Rd, Princeton, NJ 08544 USA
基金
美国国家卫生研究院;
关键词
CELL LUNG-CANCER; MASS-SPECTROMETRY; NMR-SPECTROSCOPY; METABOLITE CONCENTRATIONS; LIQUID-CHROMATOGRAPHY; GLUTAMINE-METABOLISM; ESCHERICHIA-COLI; TUMOR-CELLS; PROTEIN; FLUX;
D O I
10.1016/j.cell.2018.03.055
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Great strides have been made over the past decade toward comprehensive study of metabolism. Mass spectrometry (MS) has played a central role by enabling measurement of many metabolites simultaneously. Tracking metabolite labeling from stable isotope tracers can in addition reveal pathway activities. Here, we describe the basics of metabolite measurement by MS, including sample preparation, metabolomic analysis, and data interpretation. In addition, drawing on examples of successful experiments, we highlight the ways in which metabolomics and isotope tracing can illuminate biology.
引用
收藏
页码:822 / 837
页数:16
相关论文
共 99 条
[1]   Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry [J].
Bajad, Sunil U. ;
Lu, Wenyun ;
Kimball, Elizabeth H. ;
Yuan, Jie ;
Peterson, Celeste ;
Rabinowitz, Joshua D. .
JOURNAL OF CHROMATOGRAPHY A, 2006, 1125 (01) :76-88
[2]   Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts [J].
Beckonert, Olaf ;
Keun, Hector C. ;
Ebbels, Timothy M. D. ;
Bundy, Jacob G. ;
Holmes, Elaine ;
Lindon, John C. ;
Nicholson, Jeremy K. .
NATURE PROTOCOLS, 2007, 2 (11) :2692-2703
[3]   Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach [J].
Bennett, Bryson D. ;
Yuan, Jie ;
Kimball, Elizabeth H. ;
Rabinowitz, Joshua D. .
NATURE PROTOCOLS, 2008, 3 (08) :1299-1311
[4]   IMAGING MASS SPECTROMETRY: INSTRUMENTATION, APPLICATIONS, AND COMBINATION WITH OTHER VISUALIZATION TECHNIQUES [J].
Bodzon-Kulakowska, Anna ;
Suder, Piotr .
MASS SPECTROMETRY REVIEWS, 2016, 35 (01) :147-169
[5]   Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations [J].
Boer, Viktor M. ;
Crutchfield, Christopher A. ;
Bradley, Patrick H. ;
Botstein, David ;
Rabinowitz, Joshua D. .
MOLECULAR BIOLOGY OF THE CELL, 2010, 21 (01) :198-211
[6]   Measurement of protein turnover rates by heavy water labeling of nonessential amino acids [J].
Busch, Robert ;
Kim, Yoo-Kyeong ;
Neese, Richard A. ;
Schade-Serin, Valerie ;
Collins, Michelle ;
Awada, Mohamad ;
Gardner, James L. ;
Beysen, Carine ;
Marino, Michael E. ;
Misell, Lisa M. ;
Hellerstein, Marc K. .
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 2006, 1760 (05) :730-744
[7]   NMR spectroscopy as a tool to close the gap on metabolite characterization under MIST [J].
Caceres-Cortes, Janet ;
Reily, Michael D. .
BIOANALYSIS, 2010, 2 (07) :1263-1276
[8]   High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions [J].
Caldana, Camila ;
Degenkolbe, Thomas ;
Cuadros-Inostroza, Alvaro ;
Klie, Sebastian ;
Sulpice, Ronan ;
Leisse, Andrea ;
Steinhauser, Dirk ;
Fernie, Alisdair R. ;
Willmitzer, Lothar ;
Hannah, Matthew A. .
PLANT JOURNAL, 2011, 67 (05) :869-884
[9]   The MetaCyc database of metabolic pathways and enzymes [J].
Caspi, Ron ;
Billington, Richard ;
Fulcher, Carol A. ;
Keseler, Ingrid M. ;
Kothari, Anamika ;
Krummenacker, Markus ;
Latendresse, Mario ;
Midford, Peter E. ;
Ong, Quang ;
Ong, Wai Kit ;
Paley, Suzanne ;
Subhraveti, Pallavi ;
Karp, Peter D. .
NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) :D633-D639
[10]   Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism [J].
Chen, Walter W. ;
Freinkman, Elizaveta ;
Wang, Tim ;
Birsoy, Kivanc ;
Sabatini, David M. .
CELL, 2016, 166 (05) :1324-+