Mass spectrometry-based metabolomics diagnostics – myth or reality?

References

• Trivedi DK, Hollywood KA, Goodacre R. Metabolomics for the masses: the future of metabolomics in a personalized world. New Horizons Transl Med. 2017;3(6):294–305.
   PubMed Web of Science ®Google Scholar
• Wishart DS. Emerging applications of metabolomics in drug discovery and precision medicine. Nat Rev Drug Discov. 2016;15(7):473–484.
   PubMed Web of Science ®Google Scholar
• Kennedy AD, Wittmann BM, Evans AM, et al. Metabolomics in the clinic: a review of the shared and unique features of untargeted metabolomics for clinical research and clinical testing. J Mass Spectrom. 2018;53(11):1143–1154.
   PubMed Web of Science ®Google Scholar
• Pinu FR, Beale DJ, Paten AM, et al. Systems biology and multi-omics integration: viewpoints from the metabolomics research community. Metabolites. 2019;9(4):76.
   PubMed Web of Science ®Google Scholar
• Pinu FR, Goldansaz SA, Jaine J. Translational metabolomics: current challenges and future opportunities. Metabolites. 2019;9(6):108.
   PubMed Web of Science ®Google Scholar
• Trifonova O, Lokhov P, Archakov A. Postgenomics diagnostics: metabolomics approaches to human blood profiling. OMICS. 2013;17:550–559.
   PubMed Web of Science ®Google Scholar
• Fiehn O. Metabolomics — the link between genotypes and phenotypes. Funct Genomics. 2002;48(1–2):155–171.
   Google Scholar
• Macel M, Van Dam NM, Keurentjes JJB. Metabolomics: the chemistry between ecology and genetics. Mol Ecol Resour. 2010;10(4):583–593.
   PubMed Web of Science ®Google Scholar
• Beger RD, Dunn W, Schmidt MA, et al. Metabolomics enables precision medicine: “A White Paper, Community Perspective.”. Metabolomics. 2016;12(10):149.
   PubMedGoogle Scholar
• Perez De Souza L, Alseekh S, Brotman Y, et al. Network-based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation. Expert Rev Proteomics. 2020;17(4):243–255.
   PubMed Web of Science ®Google Scholar
• Cobb J, Gall W, Adam KP, et al. A novel fasting blood test for insulin resistance and prediabetes. J Diabetes Sci Technol. 2013;7(1):100–110.
   PubMedGoogle Scholar
• Jelonek K, Widłak P. Metabolome-based biomarkers: their potential role in the early detection of lung cancer. Contemp Oncol (Pozn). 2018;22(3):135–140.
   PubMed Web of Science ®Google Scholar
• Mehta KY, Wu H-J, Menon SS, et al. Metabolomic biomarkers of pancreatic cancer: a meta-analysis study. Oncotarget. 2017;8(40):68899–68915.
   PubMedGoogle Scholar
• Lokhov PG, Maslov DL, Balashova EE. et al. Mass spectrometry analysis of blood plasma lipidome as the method of disease diagnostics, evalution of effectiveness and optimization of drug therapy. Biochem Suppl Ser B Biomed Chem. 2015;9(2):95–105.
   Google Scholar
• Lokhov PG, Balashova EE, Voskresenskaya AA, et al. Mass spectrometric signatures of the blood plasma metabolome for disease diagnostics. Biomed Reports. 2016;4(1):122–126.
   PubMed Web of Science ®Google Scholar
• Johnson CH, Ivanisevic J, Siuzdak G. Metabolomics: beyond biomarkers and towards mechanisms. Nat Rev Mol Cell Biol. 2016;17(7):451–459.
   PubMed Web of Science ®Google Scholar
• Zhang XW, Li QH, Di XZ, et al. Mass spectrometry-based metabolomics in health and medical science: a systematic review. RSC Adv. 2020;10:3092–3104.
   Web of Science ®Google Scholar
• Considine EC. The search for clinically useful biomarkers of complex disease: a data analysis perspective. Metabolites. 2019;9(7):126.
   Web of Science ®Google Scholar
• Kern SE. Why your new cancer biomarker may never work: recurrent patterns and remarkable diversity in biomarker failures. Cancer Res. 2012;72(23):6097–6101.
   PubMed Web of Science ®Google Scholar
• Ioannidis JPA, Bossuyt PMM. Waste, leaks, and failures in the biomarker pipeline. Clin Chem. 2017;63(5):963–972.
   PubMed Web of Science ®Google Scholar
• Nicholson JK, Holmes E, Lindon JC, et al. The challenges of modeling mammalian biocomplexity. Nat Biotechnol. 2004;22(10):1268–1274.
   PubMed Web of Science ®Google Scholar
• Nicholson JK, Holmes E, Wilson ID. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol. 2005;3(5):431–438.
   PubMed Web of Science ®Google Scholar
• Lindon JC, Nicholson JK. The emergent role of metabolic phenotyping in dynamic patient stratification. Expert Opin Drug Metab Toxicol. 2014;10(7):915–919.
   PubMed Web of Science ®Google Scholar
• Kowalczyk T, Ciborowski M, Kisluk J, et al. Mass spectrometry based proteomics and metabolomics in personalized oncology. Biochim Biophys Acta - Mol Basis Dis. 2020;1866(5):165690.
   PubMed Web of Science ®Google Scholar
• López-López Á, López-Gonzálvez Á, Barker-Tejeda TC, et al. A review of validated biomarkers obtained through metabolomics. Expert Rev Mol Diagn. 2018;18(6):557–575.
   PubMed Web of Science ®Google Scholar
• Cheung PK, Ma MH, Tse HF, et al. The applications of metabolomics in the molecular diagnostics of cancer. Expert Rev Mol Diagn. 2019;19(9):785–793.
   PubMed Web of Science ®Google Scholar
• Lokhov PG, Dashtiev MI, Moshkovskii SI, et al. Metabolite profiling of blood plasma of patients with prostate cancer. Metabolomics. 2010;6:156–163.
   Web of Science ®Google Scholar
• Lokhov PG, Kharybin ON, Archakov AI. Diagnosis of lung cancer based on direct-infusion electrospray mass spectrometry of blood plasma metabolites. Int J Mass Spectrom. 2012;309:200–205.
   Web of Science ®Google Scholar
• Haznadar M, Cai Q, Krausz KW, et al. Urinary metabolite risk biomarkers of lung cancer: a prospective cohort study. Cancer Epidemiol Biomarkers Prev. 2016;25(6):978–986.
   PubMed Web of Science ®Google Scholar
• Mu Y, Zhou Y, Wang Y, et al. Serum metabolomics study of nonsmoking female patients with non-small cell lung cancer using gas chromatography-mass spectrometry. J Proteome Res. 2019;18(5):2175–2184.
   PubMed Web of Science ®Google Scholar
• Xiang C, Jin S, Zhang J, et al. Cortisol, cortisone, and 4-methoxyphenylacetic acid as potential plasma biomarkers for early detection of non-small cell lung cancer. Int J Biol Markers. 2018;33(3):314–320.
   PubMed Web of Science ®Google Scholar
• Chen Y, Ma Z, Zhong J, et al. Simultaneous quantification of serum monounsaturated and polyunsaturated phosphatidylcholines as potential biomarkers for diagnosing non-small cell lung cancer. Sci Rep. 2018;8(1):7137.
   PubMed Web of Science ®Google Scholar
• Zhuang J, Tang X, Du Z, et al. Prediction of biomarkers of therapeutic effects of patients with lung adenocarcinoma treated with gefitinib based on progression-free-survival by metabolomic fingerprinting. Talanta. 2016;160:636–644.
   PubMed Web of Science ®Google Scholar
• Lokhov PG, Trifonova OP, Maslov DL, et al. Blood plasma metabolites and the risk of developing lung cancer in Russia. Eur J Cancer Prev. 2013;22(4):335–341.
   PubMed Web of Science ®Google Scholar
• Pallares-Méndez R, Aguilar-Salinas CA, Cruz-Bautista I, et al. Metabolomics in diabetes, a review. Ann Med. 2016;48(1–2):89–102.
   PubMed Web of Science ®Google Scholar
• Guasch-Ferré M, Hruby A, Toledo E, et al. Metabolomics in prediabetes and diabetes: a systematic review and meta-analysis. Diabetes Care. 2016;39(5):833–846.
   PubMed Web of Science ®Google Scholar
• Rebholz CM, Yu B, Zheng Z, et al. Serum metabolomic profile of incident diabetes. Diabetologia. 2018;61(5):1046–1054.
   PubMed Web of Science ®Google Scholar
• Lokhov PG, Trifonova OP, Maslov DL, et al. Diagnosing impaired glucose tolerance using direct infusion mass spectrometry of blood plasma. PLoS One. 2014;9(9):e105343.
   PubMed Web of Science ®Google Scholar
• Fan Y, Li Y, Chen Y, et al. Comprehensive metabolomic characterization of coronary artery diseases. J Am Coll Cardiol. 2016;68(12):1281–1293.
   PubMed Web of Science ®Google Scholar
• McGranaghan P, Saxena A, Rubens M, et al. Predictive value of metabolomic biomarkers for cardiovascular disease risk: a systematic review and meta-analysis. Biomarkers. 2020;25(2):101–111.
   PubMed Web of Science ®Google Scholar
• Kim M, Snowden S, Suvitaival T, et al. Primary fatty amides in plasma associated with brain amyloid burden, hippocampal volume, and memory in the European medical information framework for alzheimer’s disease biomarker discovery cohort. Alzheimer’s Dement. 2019;15(6):817–827.
   PubMed Web of Science ®Google Scholar
• Havelund JF, Heegaard NHH, Færgeman NJK, et al. Biomarker research in parkinson’s disease using metabolite profiling. Metabolites. 2017;7(3):42.
   Web of Science ®Google Scholar
• Balashova EE, Lokhov PG, Maslov DL, et al. Plasma metabolome signature in patients with early-stage Parkinson disease. Curr Metabolomics. 2018;6(1):75–82.
   Web of Science ®Google Scholar
• Nagana Gowda GA, Djukovic D. Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol Biol. 2014;1198:3–12.
   PubMedGoogle Scholar
• Beale DJ, Pinu FR, Kouremenos KA, et al. Review of recent developments in GC–MS approaches to metabolomics-based research. Metabolomics. 2018;14(11):152.
   PubMed Web of Science ®Google Scholar
• Fiehn O. Metabolomics by gas chromatography-mass spectrometry: combined targeted and untargeted profiling. Curr Protoc Mol Biol. 2016;114:30.4.1–30.4.32.
   PubMedGoogle Scholar
• Vinaixa M, Schymanski EL, Neumann S, et al. Mass spectral databases for LC/MS- and GC/MS-based metabolomics: state of the field and future prospects. TrAC - Trends Anal Chem. 2016;78:23–35.
   Web of Science ®Google Scholar
• Nassar AF, Wu T, Nassar SF, et al. UPLC–MS for metabolomics: a giant step forward in support of pharmaceutical research. Drug Discov Today. 2017;22(2):463–470.
   PubMed Web of Science ®Google Scholar
• Kim YM, Heyman HM. Mass spectrometry-based metabolomics. Methods Mol Biol. 2018;1775:107–118.
   PubMedGoogle Scholar
• Maier TV, Schmitt-Kopplin P. Capillary electrophoresis in metabolomics. Methods Mol Biol. 2016;1483:437–470.
   PubMedGoogle Scholar
• Sasaki K, Sagawa H, Suzuki M, et al. Metabolomics platform with capillary electrophoresis coupled with high-resolution mass spectrometry for plasma analysis. Anal Chem. 2019;91(2):1295–1301.
   PubMed Web of Science ®Google Scholar
• Ellis DI, Dunn WB, Griffin JL, et al. Metabolic fingerprinting as a diagnostic tool. Pharmacogenomics. 2007.
   Google Scholar
• Armitage EG, Ciborowski M. Applications of metabolomics in cancer studies. Adv Exp Med Biol. 2017;8(9):1243–1266.
   Google Scholar
• Lynn KS, Cheng ML, Chen YR, et al. Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information. Anal Chem. 2015;87(4):2143–2151.
   PubMed Web of Science ®Google Scholar
• Kwak M, Kang K, Wang Y Methods of metabolite identification using MS/MS data. J Comput Inf Syst. 2019; DOI: 10.1080/08874417.2019.1681328.
   Google Scholar
• Kirwan JA, Brennan L, Broadhurst D, et al. Preanalytical processing and biobanking procedures of biological samples for metabolomics research: a white paper, community perspective (for “Precision medicine and pharmacometabolomics task group”—the metabolomics society initiative). Clin Chem. 2018;64(8):1158–1182.
   PubMed Web of Science ®Google Scholar
• Gong ZG, Hu J, Wu X, et al. The recent developments in sample preparation for mass spectrometry-based metabolomics. Crit Rev Anal Chem. 2017;47(4):325–331.
   PubMed Web of Science ®Google Scholar
• Pinu FR, Villas-Boas SG, Aggio R. Analysis of intracellular metabolites from microorganisms: quenching and extraction protocols. Metabolites. 2017;7(4):53.
   PubMed Web of Science ®Google Scholar
• Edwards P. Questionnaires in clinical trials: guidelines for optimal design and administration. Trials. 2010;11:2.
   PubMed Web of Science ®Google Scholar
• Genzen JR. Regulation of laboratory-developed tests. Am J Clin Pathol. 2019;152(2):122–131.
   PubMed Web of Science ®Google Scholar