Data acquisition and data mining techniques for metabolite identification using LC coupled to high-resolution MS

Bioanalysis

Volumn 5, Issue 10, 2013, Pages 1285-1297

  Ma, Shuguang ^a   Chowdhury, Swapan K ^a  

^a GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG METABOLITE; TALINOLOL;

ACCURACY; ACCURATE MASS INCLUSION LIST DEPENDENT ACQUISITION; BIOASSAY; DATA ANALYSIS SOFTWARE; DATA COLLECTION METHOD; DATA DEPENDENT ACQUISITION; DATA MINING; DRUG DETERMINATION; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; INTERMETHOD COMPARISON; ION INTENSITY DEPENDENT ACQUISITION; ISOTOPE PATTERN DEPENDENT ACQUISITION; LIQUID CHROMATOGRAPHY; MASS DEFECT DEPENDENT ACQUISITION; MASS SPECTROMETRY; NONHUMAN; PROCESS DEVELOPMENT; QUADRUPOLE TIME OF FLIGHT MASS SPECTROMETRY; REVIEW; TANDEM MASS SPECTROMETRY; TIME OF FLIGHT MASS SPECTROMETRY;

BIOLOGICAL MARKERS; CHROMATOGRAPHY, LIQUID; DATA MINING; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MASS SPECTROMETRY; METABOLOMICS;

EID: 84878501262     PISSN: 17576180     EISSN: 17576199     Source Type: Journal    
DOI: 10.4155/bio.13.103     Document Type: Review

References (41)

1. Ma S, Chowdhury SK, Alton KB. Application of mass spectrometry for metabolite identifcation. Curr. Drug Metab. 7(5), 503-523 (2006).
2. Zhu M, Zhang H, Humphreys WG. Drug metabolite profling and identifcation by high-resolution mass spectrometry. J. Biol. Chem. 286(29), 25419-25425 (2011).
3. Xie C, Zhong D, Yu K, Chen X. Recent advances in metabolite identifcation and quantitative bioanalysis by LC-Q-TOF MS. Bioanalysis 4(8), 937-959 (2012).
4. Andrews GL, Simons BL, Young JB, Hawkridge AM, Muddiman DC. Performance characteristics of a new hybrid quadrupole time-of-fight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 83(13), 5442-5446 (2011).
5. Perry RH, Cooks RG, Noll RJ. Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom. Rev. 27(6), 661-699 (2008).
6. Makarov A, Denisov E, Kholomeev A et al. Performance evaluation of a hybrid linear ion trap/Orbitrap mass spectrometer. Anal. Chem. 78(7), 2113-2120 (2006).
7. Zhang H, Zhang D, Ray K, Zhu M. Mass defect flter technique and its applications to drug metabolite identifcation by high-resolution mass spectrometry. J. Mass Spectrom. 44(7), 999-1016 (2009).
8. Zhang H, Zhang D, Ray K. A software flter to remove interference ions from drug metabolites in accurate mass liquid chromatography/mass spectrometric analyses. J. Mass Spectrom. 38 (10), 1110-1112 (2003).
9. Zhang H, Yang Y. An algorithm for thorough background subtraction from high-resolution LC-MS data: application for detection of glutathione-trapped reactive metabolites. J. Mass Spectrom. 43(9), 1181-1190 (2008).
10. Zhu P, Ding W, Tong W, Ghosal A, Alton K, Chowdhury S. A retention-time-shift-tolerant background subtraction and noise reduction algorithm (BgS-NoRA) for extraction of drug metabolites in liquid chromatography/mass spectrometry data from biological matrices. Rapid Commun. Mass Spectrom. 23(11), 1563-1572 (2009).
11. Zhu P, Tong W, Alton K, Chowdhury S. An accurate-mass-based spectral-averaging isotope-pattern-fltering algorithm for extraction of drug metabolites possessing a distinct isotope pattern from LC-MS data. Anal. Chem. 81(14), 5910-5917 (2009).
12. Campbell JL, Le Blanc JC. Using high-resolution quadrupole TOF technology in DMPK analyses. Bioanalysis 4(5), 487-500 (2012).
13. Peterman SM, Duczak N Jr, Kalgutkar AS, Lame ME, Soglia JR. Application of a linear ion trap/Orbitrap mass spectrometer in metabolite characterization studies: examination of the human liver microsomal metabolism of the non-tricyclic anti-depressant nefazodone using data-dependent accurate mass measurements. J. Am. Soc. Mass Spectrom. 17(3), 363-375 (2006).
14. Anari MR, Sanchez RI, Bakhtiar R, Franklin RB, Baillie TA. Integration of knowledge-based metabolic predictions with liquid chromatography data-dependent tandem mass spectrometry for drug metabolism studies: application to studies on the biotransformation of indinavir. Anal. Chem. 76(3), 823-832 (2004).
15. Lim HK, Chen J, Sensenhauser C, Cook K, Subrahmanyam V. Metabolite identifcation by data-dependent accurate mass spectrometric analysis at resolving power of 60, 000 in external calibration mode using an LTQ/Orbitrap. Rapid Commun. Mass Spectrom. 21(12), 1821-1832 (2007).
16. Ma L, Wen B, Ruan Q, Zhu M. Rapid screening of glutathione-trapped reactive metabolites by linear ion trap mass spectrometry with isotope pattern-dependent scanning and postacquisition data mining. Chem. Res. Toxicol. 21(7), 1477-1483 (2008).
17. Lim HK, Chen J, Cook K, Sensenhauser C, Silva J, Evans DC. A generic method to detect electrophilic intermediates using isotopic pattern triggered data-dependent high-resolution accurate mass spectrometry. Rapid Commun. Mass Spectrom. 22(8), 1295-1311 (2008).
18. Castro-Perez J, Plumb R, Liang L, Yang E. A high-throughput liquid chromatography/tandem mass spectrometry method for screening glutathione conjugates using exact mass neutral loss acquisition. Rapid Commun. Mass Spectrom. 19(6), 798-804 (2005).
19. Zhu M, Ma L, Zhang D et al. Detection and characterization of metabolites in biological matrices using mass defect fltering of liquid chromatography/high resolution mass spectrometry data. Drug Metab. Dispos. 34(10), 1722-1733 (2006).
20. Tiller PR, Yu S, Castro-Perez J, Fillgrove KL, Baillie TA. High-throughput, accurate mass liquid chromatography/tandem mass spectrometry on a quadrupole time-of-fight system as a 'frst-line' approach for metabolite identifcation studies. Rapid Commun. Mass Spectrom. 22(7), 1053-1061 (2008).
21. E with mass defect fltering for in vitro and in vivo metabolite identifcation. Rapid Commun. Mass Spectrom. 21(9), 1485-1496 (2007).
22. Wrona M, Mauriala T, Bateman KP, Mortishire-Smith RJ, O'Connor D. 'All-in-one' analysis for metabolite identifcation using liquid chromatography/hybrid quadrupole time-of-fight mass spectrometry with collision energy switching. Rapid Commun. Mass Spectrom. 19(18), 2597-2602 (2005).
23. Bateman K P, Kellmann M, Muenster H, Papp R, Taylor L. Quantitative-qualitative data acquisition using a benchtop Orbitrap mass spectrometer. J. Am. Soc. Mass Spectrom. 20 (8), 1441-1450 (2009).
24. M, an effcient workfow for metabolite identifcation using hybrid linear ion trap Orbitrap mass spectrometer. J. Am. Soc. Mass Spectrom. 23(5), 880-888 (2012).
25. Ruan Q, Peterman S, Szewc MA et al. An integrated method for metabolite detection and identifcation using a linear ion trap/Orbitrap mass spectrometer and multiple data processing techniques: application to indinavir metabolite detection. J. Mass Spectrom. 43(2), 251-261 (2008).
26. Zhang H, Grubb M, Wu W, Josephs J, Humphreys WG. Algorithm for thorough background subtraction of high-resolution LC-MS data: application to obtain clean product ion spectra from nonselective collision-induced dissociation experiments. Anal. Chem. 81(7), 2695-2700 (2009).
27. Zhu X, Kalyanaraman N, Subramanian R. Enhanced screening of glutathione-trapped reactive metabolites by in-source collision-induced dissociation and extraction of product ion using UHPLC-high resolution mass spectrometry. Anal. Chem. 83(24), 9516-9523 (2011).
28. Hopfgartner G, Tonoli D, Varesio E. High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices. Anal. Bioanal. Chem. 402(8), 2587-2596 (2012).
29. Li AC, Ding J, Jiang X, Denissen J. Two-injection workfow for a liquid chromatography/LTQ-Orbitrap system to complete in vivo biotransformation characterization: demonstration with buspirone metabolite identifcation. Rapid Commun. Mass Spectrom. 23(18), 3003-3012 (2009).
30. Liu DQ, Hop CE. Strategies for characterization of drug metabolites using liquid chromatography-tandem mass spectrometry in conjunction with chemical derivatization and on-line H/D exchange approaches. J. Pharm. Biomed. Anal. 37(1), 1-18 (2005).
31. Penner NA, Ho G, Bercovici A, Chowdhury SK, Alton KB. Identifcation of two novel metabolites of SCH 486757, a nociceptin/orphanin FQ peptide receptor agonist, in humans. Drug Metab. Dispos. 38(11), 2067-2074 (2010).
32. Kulanthaivel P, Barbuch RJ, Davidson RS et al. Selective reduction of N-oxides to amines: application to drug metabolism. Drug Metab. Dispos. 32(9), 966-972 (2004).
33. E and a semi-automated software for structural elucidation. Rapid Commun. Mass Spectrom. 24(21), 3127-3138 (2010).
34. Li AC, Chovan JP, Yu E, Zamora I. Update on hydrocodone metabolites in rats and dogs aided with a semi-automatic software for metabolite identifcation Mass-MetaSite. Xenobiotica 43(4), 390-398 (2013).
35. Pelander A, Tyrkko E, Ojanpera I. In silico methods for predicting metabolism and mass fragmentation applied to quetiapine in liquid1 chromatography/time-of-fight mass spectrometry urine drug screening. Rapid Commun. Mass Spectrom. 23(4), 506-514 (2009).
36. Heinonen M, Rantanen A, Mielikainen T et al. FiD: a software for ab initio structural identifcation of product ions from tandem mass spectrometric data. Rapid Commun. Mass Spectrom. 22(19), 3043-3052 (2008).
37. Leclercq L, Mortishire-Smith RJ, Huisman M, Cuyckens F, Hartshorn MJ, Hill A. IsoScore: automated localization of biotransformations by mass spectrometry using product ion scoring of virtual regioisomers. Rapid Commun. Mass Spectrom. 23(1), 39-50 (2009).
38. Ramanathan R, Korfmacher W. The emergence of high-resolution MS as the premier analytical tool in the pharmaceutical bioanalysis arena. Bioanalysis 4(5), 467-469 (2012).
39. Korfmacher W. High-resolution mass spectrometry will dramatically change our drug-discovery bioanalysis procedures. Bioanalysis 3 (11), 1169-1171 (2011).
40. Ranasinghe A, Ramanathan R, Jemal M, D'Arienzo CJ, Humphreys WG, Olah TV. Integrated quantitative and qualitative workfow for in vivo bioanalytical support in drug discovery using hybrid Q-TOF-MS. Bioanalysis 4(5), 511-528 (2012).
41. Ma S, Li Z, Lee KJ, Chowdhury SK. Determination of exposure multiples of human metabolites for MIST assessment in preclinical safety species without using reference standards or radiolabeled compounds. Chem. Res. Toxicol. 23(12), 1871-1873 (2010).