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Untargeted Metabolomics Methods to Analyze Blood-Derived Samples

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Part of the book series: Neuromethods ((NM,volume 159))

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Untargeted metabolomics is applied to a wide range of preclinical and clinical studies. The metabolome is the furthest downstream product of the genome and is considered to provide a direct measure of the phenotype at the molecular level. Therefore, metabolomics seeks for the comprehensive detection and offers the broadest possible metabolome coverage in type of molecules and level of concentration. Nevertheless, the large number of molecules with physicochemical and structural diversity constituting the metabolome possess a bottleneck and is pointed as one of the greatest analytical challenges. Due to its high sensitivity and throughput, a commonly used mass spectrometry (MS) platform is often considered as a “gold standard” that plays a crucial role in untargeted metabolomics methods. Furthermore, the combination of separation techniques (LC, liquid chromatography; GC, gas chromatography; or CE, capillary electrophoresis) with mass spectrometry tremendously expands the capability of the analysis of highly complex biological samples with the highest metabolite coverage. This chapter exemplifies the strategies used for untargeted metabolomics analysis of blood derived samples. It gives experimental details on basic steps like blood plasma/serum withdrawal, metabolite extraction and analysis for LC-MS, GC-MS, and CE-MS untargeted metabolomic studies.

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  1. Patti GJ, Yanes O, Siuzdak G (2012) Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 13:263–269.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL (2011) Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem Soc Rev 40:387–426.

    Article  CAS  PubMed  Google Scholar 

  3. García-Cañaveras JC, López S, Castell JV, Donato MT, Lahoz A (2016) Extending metabolome coverage for untargeted metabolite profiling of adherent cultured hepatic cells. Anal Bioanal Chem 408:1217–1230.

    Article  CAS  PubMed  Google Scholar 

  4. Wang Y, Liu S, Hu Y, Wan J (2015) Current state of the art of mass spectrometry- based metabolomics studies – a review focusing on wide coverage, high throughput and easy. RSC Adv 5:78728–78737.

    Article  CAS  Google Scholar 

  5. Ortmayr K, Causon TJ, Hann S, Koellensperger G (2016) Increasing selectivity and coverage in LC-MS based metabolome analysis. TrAC Trends Anal Chem 82:358–366.

    Article  CAS  Google Scholar 

  6. Haggarty J, Burgess KE (2017) Recent advances in liquid and gas chromatography methodology for extending coverage of the metabolome. Curr Opin Biotechnol 43:77–85.

    Article  CAS  PubMed  Google Scholar 

  7. Yanes O, Tautenhahn R, Patti GJ, Siuzdak G (2011) Expanding coverage of the metabolome for global metabolite profiling. Anal Chem 83:2152–2161.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hernandes VV, Barbas C, Dudzik D (2017) A review of blood sample handling and pre-processing for metabolomics studies. Electrophoresis 38(18):2232–2241.

    Article  CAS  PubMed  Google Scholar 

  9. Dudzik D, Barbas-Bernardos C, García A, Barbas C (2018) Quality assurance procedures for mass spectrometry untargeted metabolomics. A review. J Pharm Biomed Anal 147:149–173.

    Article  CAS  PubMed  Google Scholar 

  10. Dunn WB, Wilson ID, Nicholls AW, Broadhurst D (2012) The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans. Bioanalysis 4:2249–2264.

    Article  CAS  PubMed  Google Scholar 

  11. Dudzik D, Zorawski M, Skotnicki M, Zarzycki W, Kozlowska G, Bibik-Malinowska K, Vallejo M, García A, Barbas C, Ramos MP (2014) Metabolic fingerprint of gestational diabetes mellitus. J Proteome 103:57–71.

    Article  CAS  Google Scholar 

  12. Dudzik D, Zorawski M, Skotnicki M, Zarzycki W, García A, Angulo S, Lorenzo MP, Barbas C, Ramos MP (2017) GC–MS based gestational diabetes mellitus longitudinal study: identification of 2-and 3-hydroxybutyrate as potential prognostic biomarkers. J Pharm Biomed Anal 144:90–98.

    Article  CAS  PubMed  Google Scholar 

  13. Naz S, Garcia A, Rusak M, Barbas C (2013) Method development and validation for rat serum fingerprinting with CE-MS: application to ventilator-induced-lung-injury study. Anal Bioanal Chem 405:4849–4858.

    Article  CAS  PubMed  Google Scholar 

  14. Mastrangelo A, Ferrarini A, Rey-Stolle F, García A, Barbas C (2015) From sample treatment to biomarker discovery: a tutorial for untargeted metabolomics based on GC-(EI)-Q-MS. Anal Chim Acta 900:21–35.

    Article  CAS  PubMed  Google Scholar 

  15. Sangster T, Major H, Plumb R, Wilson AJ, Wilson ID (2006) A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MS-based metabonomic analysis. Analyst 131:1075–1078.

    Article  CAS  PubMed  Google Scholar 

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The authors would like to express their gratitude to the financial support received from the Spanish Ministry of Science, Innovation and Universities (RTI2018-095166-B-I00) and Fondo Europeo de Desarrollo Regional (FEDER) and the Polish National Science Center (No 04-0225/09/529; DEC-2018/29/B/NZ7/02489). .

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Correspondence to Danuta Dudzik .

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Dudzik, D., García, A. (2021). Untargeted Metabolomics Methods to Analyze Blood-Derived Samples. In: Wood, P.L. (eds) Metabolomics . Neuromethods, vol 159. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0863-0

  • Online ISBN: 978-1-0716-0864-7

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