Mass-spectrometry based metabolomics: an overview of workflows, strategies, data analysis and applications

Oliver SG, Winson MK, Kell DB, Baganz F. Systematic functional analysis of the yeast genome. Trends Biotechnol. 1998;16:373–8.

Article  CAS  PubMed  Google Scholar 

Nicholson JK, Lindon JC, Holmes E. “Metabonomics”: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica. 1999;29:1181–9.

Article  CAS  PubMed  Google Scholar 

Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L. Metabolite profiling for plant functional genomics. Nat Biotechnol. 2000;18:1157–61.

Article  CAS  PubMed  Google Scholar 

Holmes E, Wilson ID, Nicholson JK. Metabolic phenotyping in health and disease. Cell. 2008;134:714–7.

Article  CAS  PubMed  Google Scholar 

Fiehn O. Metabolomics–the link between genotypes and phenotypes. Plant Mol Biol. 2002;48:155–71.

Article  CAS  PubMed  Google Scholar 

Beger RD. A review of applications of metabolomics in cancer. Metabolites. 2013;3:552–74.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics. 2001;2:155–68.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clarke CJ, Haselden JN. Metabolic profiling as a tool for understanding mechanisms of toxicity. Toxicol Pathol. 2008;36:140–7.

Article  CAS  PubMed  Google Scholar 

Yi L, Shi S, Wang Y, Huang W, Xia ZA, Xing Z, Peng W, Wang Z. Serum Metabolic Profiling Reveals Altered Metabolic Pathways in Patients with Post-traumatic Cognitive Impairments. Sci Rep. 2016;6:21320.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koslinski P, Daghir-Wojtkowiak E, Szatkowska-Wandas P, Markuszewski M, Markuszewski MJ. The metabolic profiles of pterin compounds as potential biomarkers of bladder cancer-Integration of analytical-based approach with biostatistical methodology. J Pharm Biomed Anal. 2016;127:256–62.

Article  CAS  PubMed  Google Scholar 

Ganti S, Weiss RH. Urine metabolomics for kidney cancer detection and biomarker discovery. Urol Oncol. 2011;29:551–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Van Gulik WM, Canelas AB, Taymaz-Nikerel H, Douma RD, de Jonge LP, Heijnen JJ. Fast sampling of the cellular metabolome. Methods Mol Biol. 2012;881:279–306.

Article  PubMed  Google Scholar 

Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem. 2017;86:277–304.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hernandez Bort JA, Shanmukam V, Pabst M, Windwarder M, Neumann L, Alchalabi A, Krebiehl G, Koellensperger G, Hann S, Sonntag D, et al. Reduced quenching and extraction time for mammalian cells using filtration and syringe extraction. J Biotechnol. 2014;182–183:97–103.

Article  PubMed  PubMed Central  Google Scholar 

Faijes M, Mars AE, Smid EJ. Comparison of quenching and extraction methodologies for metabolome analysis of Lactobacillus plantarum. Microb Cell Fact. 2007;6:27.

Article  PubMed  PubMed Central  Google Scholar 

Lorenz MA, Burant CF, Kennedy RT. Reducing time and increasing sensitivity in sample preparation for adherent mammalian cell metabolomics. Anal Chem. 2011;83:3406–14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang B, Young JD. (13)C-Isotope-Assisted Assessment of Metabolic Quenching During Sample Collection from Suspension Cell Cultures. Anal Chem. 2022;94:7787–94.

Article  CAS  PubMed  Google Scholar 

Spicer RA, Salek R, Steinbeck C. A decade after the metabolomics standards initiative it’s time for a revision. Sci Data. 2017;4:170138.

Article  PubMed  PubMed Central  Google Scholar 

Masson P, Alves AC, Ebbels TM, Nicholson JK, Want EJ. Optimization and evaluation of metabolite extraction protocols for untargeted metabolic profiling of liver samples by UPLC-MS. Anal Chem. 2010;82:7779–86.

Article  CAS  PubMed  Google Scholar 

Dettmer K, Nurnberger N, Kaspar H, Gruber MA, Almstetter MF, Oefner PJ. Metabolite extraction from adherently growing mammalian cells for metabolomics studies: optimization of harvesting and extraction protocols. Anal Bioanal Chem. 2011;399:1127–39.

Article  CAS  PubMed  Google Scholar 

Kirkwood JS, Maier C, Stevens JF: Simultaneous, untargeted metabolic profiling of polar and nonpolar metabolites by LC-Q-TOF mass spectrometry. Curr Protoc Toxicol. 2013;56:4.39.1–4.39.12.

Tambellini NP, Zaremberg V, Turner RJ, Weljie AM. Evaluation of extraction protocols for simultaneous polar and non-polar yeast metabolite analysis using multivariate projection methods. Metabolites. 2013;3:592–605.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Folch J, Lees M, Sloane Stanley GH. A simple method for the isolation and purification of total lipides from animal tissues. J Biol Chem. 1957;226:497–509.

Article  CAS  PubMed  Google Scholar 

Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol. 1959;37:911–7.

Article  CAS  PubMed  Google Scholar 

Sostare J, Di Guida R, Kirwan J, Chalal K, Palmer E, Dunn WB, Viant MR. Comparison of modified Matyash method to conventional solvent systems for polar metabolite and lipid extractions. Anal Chim Acta. 2018;1037:301–15.

Article  CAS  PubMed  Google Scholar 

Sana TR, Gordon DB, Fischer SM, Tichy SE, Kitagawa N, Lai C, Gosnell WL, Chang SP. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum. PLoS ONE. 2013;8:e60840.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang ZH, Vaziri ND, Wei F, Cheng XL, Bai X, Zhao YY. An integrated lipidomics and metabolomics reveal nephroprotective effect and biochemical mechanism of Rheum officinale in chronic renal failure. Sci Rep. 2016;6:22151.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Castro C, Sar F, Shaw WR, Mishima M, Miska EA, Griffin JL. A metabolomic strategy defines the regulation of lipid content and global metabolism by Delta9 desaturases in Caenorhabditis elegans. BMC Genomics. 2012;13:36.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sysi-Aho M, Katajamaa M, Yetukuri L, Oresic M. Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics. 2007;8:93.

Article  PubMed  PubMed Central  Google Scholar 

Lei Z, Huhman DV, Sumner LW. Mass spectrometry strategies in metabolomics. J Biol Chem. 2011;286:25435–42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kirwan JA, Gika H, Beger RD, Bearden D, Dunn WB, Goodacre R, Theodoridis G, Witting M, Yu LR, Wilson ID, et al. Quality assurance and quality

Comments (0)

No login
gif