Analytical methodology for metabolomics study of adherent mammalian cells using NMR, GC-MS and LC-HRMS

Analytical and Bioanalytical Chemistry

Volumn 407, Issue 29, 2015, Pages 8861-8872

  Madji Hounoum, Blandine ^a   Blasco, Hélène ^a   Nadal Desbarats, Lydie ^a   Diémé, Binta ^a   Montigny, Frédéric ^a   Andres, Christian R ^a   Emond, Patrick ^a   Mavel, Sylvie ^a  

^a Université de Tours   (France)

Author keywords

Bioanalytical methods; Cell systems single cell analysis; Mass spectrometry ICP MS; NMR ESR

Indexed keywords

BIOMOLECULES; CELLS; CHROMATOGRAPHY; CYTOLOGY; EXTRACTION; GAS CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MAMMALS; MASS SPECTROMETRY; METABOLISM; METABOLITES; QUENCHING; RELIABILITY ANALYSIS; SPECTROMETRY;

ANALYTICAL METHODOLOGY; BIOANALYTICAL METHODS; CELL SYSTEMS/SINGLE-CELL ANALYSIS; HIGH RESOLUTION MASS SPECTROMETRY; INTRACELLULAR METABOLITES; MASS SPECTROMETRY/ICP-MS; RELATIVE STANDARD DEVIATIONS; REVERSED PHASE LIQUID-CHROMATOGRAPHY;

NUCLEAR MAGNETIC RESONANCE;

ANIMAL; CELL LINE; LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; MOUSE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROCEDURES; REPRODUCIBILITY; SINGLE CELL ANALYSIS;

ANIMALS; CELL LINE; CHROMATOGRAPHY, LIQUID; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; METABOLOMICS; MICE; REPRODUCIBILITY OF RESULTS; SINGLE-CELL ANALYSIS;

EID: 84947128941     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-015-9047-x     Document Type: Article

References (46)

1. Patti GJ, Yanes O, Siuzdak G (2012) Innovation: metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 13(4):263-269
2. Chrysanthopoulos PK, Goudar CT, Klapa MI (2010) Metabolomics for high-resolution monitoring of the cellular physiological state in cell culture engineering. Metab Eng 12:212-222
3. Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21:692-696
4. Wang J-R, Zhang H, Yau LF, Mi J-N, Lee S, Lee KC, Hu P, Liu L, Jiang Z-H (2014) Improved sphingolipidomic approach based on ultra-high performance liquid chromatography and multiple mass spectrometries with application to cellular neurotoxicity. Anal Chem 86:5688-5696
5. Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R (2008) Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem 80:2939-2948
6. Bayet-Robert M, Morvan D, Chollet P, Barthomeuf C (2010) Pharmacometabolomics of docetaxel-treated human MCF7 breast cancer cells provides evidence of varying cellular responses at high and low doses. Breast Cancer Res Treat 120:613-626
7. Cao B, Aa J, Wang G, Wu X, Liu L, Li M, Shi J, Wang X, Zhao C, Zheng T, Guo S, Duan J (2011) GC-TOFMS analysis of metabolites in adherent MDCK cells and a novel strategy for identifying intracellular metabolic markers for use as cell amount indicators in data normalization. Anal Bioanal Chem 400:2983-2993
8. León Z, García-Cañaveras JC, Donato MT, Lahoz A (2013) Mammalian cell metabolomics: experimental design and sample preparation. Electrophoresis 34:2762-2775
9. Martineau E, Tea I, Loaëc G, Giraudeau P, Akoka S (2011) Strategy for choosing extraction procedures for NMR-based metabolomic analysis of mammalian cells. Anal Bioanal Chem 401(7):2133-2142
10. Teng Q, Huang W, Collette T, Ekman D, Tan C (2009) A direct cell quenching method for cell-culture based metabolomics. Metabolomics 5(2):199-208
11. 1H TOCSY. Metabolomics 3(2):79-86
12. Danielsson AP, Moritz T, Mulder H, Spegel P (2010) Development and optimization of a metabolomic method for analysis of adherent cell cultures. Anal Biochem 404(1):30-39
13. Sellick CA, Hansen R, Maqsood AR, Dunn WB, Stephens GM, Goodacre R, Dickson AJ (2009) Effective quenching processes for physiologically valid metabolite profiling of suspension cultured mammalian cells. Anal Chem 81(1):174-183
14. Lorenz MA, Burant CF, Kennedy RT (2011) Reducing time and increasing sensitivity in sample preparation for adherent mammalian cell metabolomics. Anal Chem 83(9):3406-3414
15. Vuckovic D (2012) Current trends and challenges in sample preparation for global metabolomics using liquid chromatography-mass spectrometry. Anal Bioanal Chem 403(6):1523-1548
16. Want EJ, Masson P, Michopoulos F, Wilson ID, Theodoridis G, Plumb RS, Shockcor J, Loftus N, Holmes E, Nicholson JK (2013) Global metabolic profiling of animal and human tissues via UPLC-MS. Nat Protoc 8(1):17-32
17. Naz S, García A, Barbas C (2013) Multiplatform analytical methodology for metabolic fingerprinting of lung tissue. Anal Chem 85(22):10941-10948
18. Vinaixa M, Rodriguez MA, Samino S, Díaz M, Beltran A, Mallol R, Bladé C, Ibañez L, Correig X, Yanes O (2011) Metabolomics reveals reduction of metabolic oxidation in women with polycystic ovary syndrome after pioglitazone-flutamide-metformin polytherapy. PLoS One 6(12):e29052
19. Goodpaster AM, Ramadas EH, Kennedy MA (2011) Potential effect of diaper and cotton ball contamination on NMR- and LC/MS-based metabonomics studies of urine from newborn babies. Anal Chem 83(3):896-902
20. Emond P, Mavel S, Aïdoud N, Nadal-Desbarats L, Montigny F, Bonnet-Brilhault F, Barthélémy C, Merten M, Sarda P, Laumonnier F, Vourc'h P, Blasco H, Andres C (2013) GC-MS-based urine metabolic profiling of autism spectrum disorders. Anal Bioanal Chem 405(15):5291-5300
21. 13C HSQC-NMR to improve urinary screening in autism spectrum disorders. Analyst 139(13):3460-3468
22. Chan EC, Pasikanti KK, Nicholson JK (2011) Global urinary metabolic profiling procedures using gas chromatography-mass spectrometry. Nat Protoc 6(10):1483-1499
23. 13C NMR-based urine metabolic profiling in autism spectrum disorders. Talanta 114:95-102
24. Martano G, Delmotte N, Kiefer P, Christen P, Kentner D, Bumann D, Vorholt JA (2015) Fast sampling method for mammalian cell metabolic analyses using liquid chromatography-mass spectrometry. Nat Protoc 10(1):1-11
25. 1H-NMR spectroscopy. NMR Biomed 15(1):37-44
26. Dettmer K, Nurnberger N, Kaspar H, Gruber MA, Almstetter MF, Oefner PJ (2011) Metabolite extraction from adherently growing mammalian cells for metabolomics studies: optimization of harvesting and extraction protocols. Anal Bioanal Chem 399(3):1127-1139
27. Ritter JB, Genzel Y, Reichl U (2008) Simultaneous extraction of several metabolites of energy metabolism and related substances in mammalian cells: optimization using experimental design. Anal Biochem 373(2):349-369
28. Dietmair S, Timmins NE, Gray PP, Nielsen LK, Kromer JO (2010) Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol. Anal Biochem 404(2):155-164
29. Loizides-Mangold U (2013) On the future of mass-spectrometry-based lipidomics. FEBS J 280(12):2817-2829
30. Fan TM, Lane A, Higashi R, Yan J (2011) Stable isotope resolved metabolomics of lung cancer in a SCID mouse model. Metabolomics 7(2):257-269
31. Čuperlović-Culf M, Barnett DA, Culf AS, Chute I (2010) Cell culture metabolomics: applications and future directions. Drug Discov Today 15:610-621
32. Li X, Long D, Ji J, Yang W, Zeng Z, Guo S, Ji Z, Qi G, Chen S (2013) Sample preparation for the metabolomics investigation of poly-gamma-glutamate-producing Bacillus licheniformis by GC-MS. J Microbiol Meth 94(1):61-67
33. Sellick C, Knight D, Croxford A, Maqsood A, Stephens G, Goodacre R, Dickson A (2010) Evaluation of extraction processes for intracellular metabolite profiling of mammalian cells: matching extraction approaches to cell type and metabolite targets. Metabolomics 6(3):427-438
34. Sana TR, Waddell K, Fischer SM (2008) A sample extraction and chromatographic strategy for increasing LC/MS detection coverage of the erythrocyte metabolome. J Chromatogr B Analyt Technol Biomed Life Sci 871(2):314-321
35. Cequier-Sanchez E, Rodriguez C, Ravelo AG, Zarate R (2008) Dichloromethane as a solvent for lipid extraction and assessment of lipid classes and fatty acids from samples of different natures. J Agric Food Chem 56(12):4297-4303
36. Kanani H, Chrysanthopoulos PK, Klapa MI (2008) Standardizing GC-MS metabolomics. J Chromatogr B 871:191-201
37. Hu X, Li H, Tang P, Sun J, Yuan Q, Li C (2013) GC-MS-based metabolomics study of the responses to arachidonic acid in Blakeslea trispora. Fungal Genet Biol 57:33-41
38. Gullberg J, Jonsson P, Nordström A, Sjöström M, Moritz T (2004) Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331(2):283-295
39. Koek M, Jellema R, van der Greef J, Tas A, Hankemeier T (2011) Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives. Metabolomics 7(3):307-328
40. Bi H, Krausz KW, Manna SK, Li F, Johnson CH, Gonzalez FJ (2013) Optimization of harvesting, extraction, and analytical protocols for UPLC-ESI-MS-based metabolomic analysis of adherent mammalian cancer cells. Anal Bioanal Chem 405(15):5279-5289
41. Fei F, Bowdish DME, McCarry BE (2014) Comprehensive and simultaneous coverage of lipid and polar metabolites for endogenous cellular metabolomics using HILIC-TOF-MS. Anal Bioanal Chem 406(15):3723-3733
42. Gangl ET, Annan M, Spooner N, Vouros P (2001) Reduction of signal suppression effects in ESI-MS using a nanosplitting device. Anal Chem 73(23):5635-5644
43. Gika HG, Theodoridis GA, Plumb RS, Wilson ID (2014) Current practice of liquid chromatography-mass spectrometry in metabolomics and metabonomics. J Pharm Biomed 87:12-25
44. Paglia G, Hrafnsdóttir S, Magnúsdóttir M, Fleming RT, Thorlacius S, Palsson B, Thiele I (2012) Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Anal Bioanal Chem 402(3):1183-1198
45. Abdel Rahman AM, Pawling J, Ryczko M, Caudy AA, Dennis JW (2014) Targeted metabolomics in cultured cells and tissues by mass spectrometry: method development and validation. Anal Chim Acta 845:53-61
46. Lu W, Clasquin MF, Melamud E, Amador-Noguez D, Caudy AA, Rabinowitz JD (2010) Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal Chem 82(8):3212-3221