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Review

Post-Acquisition Data Mining Techniques for LC–MS/MS-Acquired Data in Drug Metabolite Identification

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Pages 1265-1278 | Received 09 Mar 2017, Accepted 20 Jun 2017, Published online: 17 Aug 2017

References

  • Wen B , ZhuM. Applications of mass spectrometry in drug metabolism: 50 years of progress. Drug Metab. Rev. 47 (1), 71–87 (2015).
  • Tolonen A , TurpeinenM, PelkonenO. Liquid chromatography-mass spectrometry in in vitro drug metabolite screening. Drug Discov. Today14 (3–4), 120–133 (2009).
  • Prasad B , GargA, TakwaniH, SinghS. Metabolite identification by liquid chromatography–mass spectrometry. Trends Anal. Chem. 30 (2), 360–387 (2011).
  • Huang M-Q , LinZ, WengN. Applications of high-resolution MS in bioanalysis. Bioanalysis5 (10), 1269–1276 (2013).
  • Ma S , ChowdhurySK. Application of LC–high-resolution MS with ‘intelligent’ data mining tools for screening reactive drug metabolites. Bioanalysis4 (5), 501–510 (2012).
  • Rathahao-Paris E , AlvesS, JunotC, TabetJ-C. High resolution mass spectrometry for structural identification of metabolites in metabolomics. Metabolomics12 (1), 1–15 (2016).
  • Ma S , ChowdhurySK. Data acquisition and data mining techniques for metabolite identification using LC coupled to high-resolution MS. Bioanalysis5 (10), 1285–1297 (2013).
  • Xing J , ZangM, ZhangH, ZhuM. The application of high-resolution mass spectrometry-based data-mining tools in tandem to metabolite profiling of a triple drug combination in humans. Anal. Chim. Acta897, 34–44 (2015).
  • Zhu M , ZhangH, HumphreysWG. Drug metabolite profiling and identification by high-resolution mass spectrometry. J. Biol. Chem. 286 (29), 25419–25425 (2011).
  • Zhang H , ZhangD, RayK, ZhuM. Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry. J. Mass Spectrom. 44 (7), 999–1016 (2009).
  • Gu M , WangY, ZhaoXG, GuZM. Accurate mass filtering of ion chromatograms for metabolite identification using a unit mass resolution liquid chromatography/mass spectrometry system. Rapid Commun. Mass Spectrom. 20 (5), 764–770 (2006).
  • Koulman A , WoffendinG, NarayanaVK, WelchmanH, CroneC, VolmerDA. High-resolution extracted ion chromatography, a new tool for metabolomics and lipidomics using a second-generation orbitrap mass spectrometer. Rapid Commun. Mass Spectrom. 23 (10), 1411–1418 (2009).
  • Du F , RuanQ, ZhuM, XingJ. Detection and characterization of ticlopidine conjugates in rat bile using high-resolution mass spectrometry: applications of various data acquisition and processing tools. J. Mass Spectrom. 48 (3), 413–422 (2013).
  • He C , ZhouD, LiJet al. Identification of 20 (S)-protopanaxatriol metabolites in rats by ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry and nuclear magnetic resonance spectroscopy. J. Pharm. Biomed. Anal. 88, 497–508 (2014).
  • Zhang H , ZhangD, RayK. A software filter to remove interference ions from drug metabolites in accurate mass liquid chromatography/mass spectrometric analyses. J. Mass Spectrom. 38 (10), 1110–1112 (2003).
  • Zhu M , MaL, ZhangDet al. Detection and characterization of metabolites in biological matrices using mass defect filtering of liquid chromatography/high resolution mass spectrometry data. Drug Metab. Dispos. 34 (10), 1722–1733 (2006).
  • Sleno L . The use of mass defect in modern mass spectrometry. J. Mass Spectrom. 47 (2), 226–236 (2012).
  • Yang A , ZangM, LiuH, FanP, XingJ. Metabolite identification of the antimalarial piperaquine in vivo using liquid chromatography–high-resolution mass spectrometry in combination with multiple data-mining tools in tandem. Biomed. Chromatogr. 30 (8), 1324–1330 (2016).
  • Gandhi AS , WohlfarthA, ZhuMet al. High-resolution mass spectrometric metabolite profiling of a novel synthetic designer drug, N-(adamantan-1-yl)-1-(5-fluoropentyl)-1H-indole-3-carboxamide (STS-135), using cryopreserved human hepatocytes and assessment of metabolic stability with human liver microsomes. Drug Test Anal. 7 (3), 187–198 (2015).
  • Kalariya PD , PatelPN, KavyaPet al. Rapid structural characterization of in vivo and in vitro metabolites of tinoridine using UHPLC–QTOF–MS/MS and in silico toxicological screening of its metabolites. J. Mass Spectrom. 50 (11), 1222–1233 (2015).
  • Liu S , CheY, WangFet al. Identification of metabolites of 6′-hydroxy-3, 4, 5, 2′, 4′-pentamethoxychalcone in rats by a combination of ultra-high-performance liquid chromatography with linear ion trap-orbitrap mass spectrometry based on multiple data processing techniques. Molecules21 (10), 1266 (2016).
  • Zhang J , CaiW, ZhouYet al. Profiling and identification of the metabolites of baicalin and study on their tissue distribution in rats by ultra-high-performance liquid chromatography with linear ion trap-orbitrap mass spectrometer. J. Chromatogr. B985, 91–102 (2015).
  • Xie C , ZhongD, YuK, ChenX. Recent advances in metabolite identification and quantitative bioanalysis by LC–Q-TOF MS. Bioanalysis4 (8), 937–959 (2012).
  • Gao Y , ZhangR, BaiJet al. Targeted data-independent acquisition and mining strategy for trace drug metabolite identification using liquid chromatography coupled with tandem mass spectrometry. Anal. Chem. 87 (15), 7535–7539 (2015).
  • Zhang H , ZhuM. Drug metabolite identification with high-resolution mass spectrometry. In:Handbook of Metabolic Pathways of Xenobiotics (1st edition). LeePW ( Ed.). John Wiley & Sons, NJ, USA, 1–23 (2014).
  • Ruan Q , PetermanS, SzewcMAet al. An integrated method for metabolite detection and identification 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).
  • Perry SJ , NászS, SaeedM. A high-resolution accurate mass (HR/AM) approach to identification, profiling and characterization of in vitro nefazodone metabolites using a hybrid quadrupole orbitrap (Q-Exactive). Rapid Commun. Mass Spectrom. 29 (17), 1545–1555 (2015).
  • Brink A , FontaineF, MarschmannMet al. Post-acquisition analysis of untargeted accurate mass quadrupole time-of-flight MSE data for multiple collision-induced neutral losses and fragment ions of glutathione conjugates. Rapid Commun. Mass Spectrom. 28 (24), 2695–2703 (2014).
  • Jian W , LiuH-F, ZhaoW, JonesE, ZhuM. Simultaneous screening of glutathione and cyanide adducts using precursor ion and neutral loss scans-dependent product ion spectral acquisition and data mining tools. J. Am. Soc. Mass Spectrom. 23 (5), 964–976 (2012).
  • Cuyckens F , HurkmansR, Castro-PerezJM, LeclercqL, Mortishire-SmithRJ. Extracting metabolite ions out of a matrix background by combined mass defect, neutral loss and isotope filtration. Rapid Commun. Mass Spectrom. 23 (2), 327–332 (2009).
  • Zhu P , TongW, AltonK, ChowdhuryS. An accurate-mass-based spectral-averaging isotope-pattern-filtering algorithm for extraction of drug metabolites possessing a distinct isotope pattern from LC–MS data. Anal. Chem. 81 (14), 5910–5917 (2009).
  • Lu D , ZhangS, WangDet al. Identification of flurochloridone metabolites in rat urine using liquid chromatography/high resolution mass spectrometry. J. Chromatogr. A1445, 80–92 (2016).
  • Leblanc A , ShiaoTC, RoyR, SlenoL. Improved detection of reactive metabolites with a bromine-containing glutathione analog using mass defect and isotope pattern matching. Rapid Commun. Mass Spectrom. 24 (9), 1241–1250 (2010).
  • Du F , RuanQ, ZhuM, XingJ. Detection and characterization of ticlopidine conjugates in rat bile using high-resolution mass spectrometry: applications of various data acquisition and processing tools. J. Mass Spectrom. 48 (3), 413–422 (2013).
  • Barbara JE , Castro-PerezJM. High-resolution chromatography/time-of-flight MSE with in silico data mining is an information-rich approach to reactive metabolite screening. Rapid Commun. Mass Spectrom. 25 (20), 3029–3040 (2011).
  • Afzal A , ZhongY, SarfrazMet al. Identification and characterization of in vivo metabolites of asulacrine using advanced mass spectrophotometry technique in combination with improved data mining strategy. J. Chromatogr. A1444, 74–85 (2016).
  • Jhajra S , PrasadB, ShahJ, SinghS. High-resolution MS for drug metabolite identification. In : Applications of High-Resolution Mass Spectrometry in Drug Discovery and Development. SlenoL ( Ed.). Future Science Group, London, UK, 22–40 (2013).
  • Zhang H , YangY. 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).
  • Zhang H , MaL, HeK, ZhuM. An algorithm for thorough background subtraction from high-resolution LC/MS data: application to the detection of troglitazone metabolites in rat plasma, bile, and urine. J. Mass Spectrom. 43 (9), 1191–1200 (2008).
  • Zhu P , DingW, TongW, GhosalA, AltonK, ChowdhuryS. 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).
  • Shekar V , ShahA, ShadidM, WuJ-T, BolleddulaJ, ChowdhuryS. An accelerated background subtraction algorithm for processing high-resolution MS data and its application to metabolite identification. Bioanalysis8 (16), 1693–1707 (2016).
  • Xing J , ZangM, ZhangH, ZhuM. The application of high-resolution mass spectrometry-based data-mining tools in tandem to metabolite profiling of a triple drug combination in humans. Anal. Chim. Acta897, 34–44 (2015).
  • Nijenhuis CM , LucasL, RosingHet al. Metabolite profiling of 14C-omacetaxine mepesuccinate in plasma and excreta of cancer patients. Xenobiotica46 (12), 1122–1132 (2016)
  • Wang J , QiP, HouJet al. The profiling of the metabolites of hirsutine in rat by ultra-high performance liquid chromatography coupled with linear ion trap orbitrap mass spectrometry: an improved strategy for the systematic screening and identification of metabolites in multi-samples in vivo. J. Pharm. Biomed. Anal. 134, 149–157 (2017).
  • Johnson CH , PattersonAD, IdleJR, GonzalezFJ. Xenobiotic metabolomics: major impact on the metabolome. Annu. Rev. Pharmacol. Toxicol. 52, 37–56 (2012).
  • Plumb RS , StumpfCL, GrangerJH, Castro-PerezJ, HaseldenJN, DearGJ. Use of liquid chromatography/time-of-flight mass spectrometry and multivariate statistical analysis shows promise for the detection of drug metabolites in biological fluids. Rapid Commun. Mass Spectrom. 17 (23), 2632–2638 (2003).
  • Beyoğlu D , IdleJR. Metabolomics and its potential in drug development. Biochem. Pharmacol. 85 (1), 12–20 (2013).
  • Giri S , IdleJR, ChenC, ZabriskieTM, KrauszKW, GonzalezFJ. A metabolomic approach to the metabolism of the areca nut alkaloids arecoline and arecaidine in the mouse. Chem. Res. 19 (6), 818–827 (2006).
  • Chen C , GonzalezFJ, IdleJR. LC–MS-based metabolomics in drug metabolism. Drug Metab. Rev. 39 (2–3), 581–597 (2007).
  • Barnes S , BentonHP, CasazzaKet al. Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future. J. Mass Spectrom. 51 (8), 535–548 (2016).
  • Wishart DS . Advances in metabolite identification. Bioanalysis3 (15), 1769–1782 (2011).
  • Wang X , WangD, WangY, ZhangP, ZhouZ, ZhuW. A combined non-targeted and targeted metabolomics approach to study the stereoselective metabolism of benalaxyl enantiomers in mouse hepatic microsomes. Environ. Pollut. 212, 358–365 (2016).
  • Bonner R , HopfgartnerG. SWATH acquisition mode for drug metabolism and metabolomics investigations. Bioanalysis8 (16), 1735–1750 (2016).
  • Guo J , ZhangM, ElmoreCS, VishwanathanK. An integrated strategy for in vivo metabolite profiling using high-resolution mass spectrometry based data processing techniques. Anal. Chim. Acta780, 55–64 (2013).
  • Huan T , TangC, LiR, ShiY, LinG, LiL. MyCompoundID MS/MS Search: metabolite identification using a library of predicted fragment-ion-spectra of 383,830 possible human metabolites. Anal. Chem. 87 (20), 10619–10626 (2015).
  • van der Hooft JJ , PadmanabhanS, BurgessKE, BarrettMP. Urinary antihypertensive drug metabolite screening using molecular networking coupled to high-resolution mass spectrometry fragmentation. Metabolomics12 (7), 1–15 (2016).
  • Hufsky F , BöckerS. Mining molecular structure databases: identification of small molecules based on fragmentation mass spectrometry data. Mass Spectrom. Rev. 9999, 1–10 (2016).
  • Knolhoff AM , CroleyTR. Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry. J. Chromatogr. A1428, 86–96 (2016).
  • Vaniya A , FiehnO. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics. Trends Anal. Chem. 69, 52–61 (2015).
  • Zhou J , YinY. Strategies for large-scale targeted metabolomics quantification by liquid chromatography–mass spectrometry. Analyst141 (23), 6362–6373 (2016).
  • Quinn RA , NothiasL-F, ViningO, MeehanM, EsquenaziE, DorresteinPC. Molecular networking as a drug discovery, drug metabolism, and precision medicine strategy. Trends Pharmacol. Sci. 38 (2), 143–154 (2016).

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