Citation: | Lili Hong, Wei Wang, Shiyu Wang, Wandi Hu, Yuyang Sha, Xiaoyan Xu, Xiaoying Wang, Kefeng Li, Hongda Wang, Xiumei Gao, Dean Guo, Wenzhi Yang. Software-aided efficient identification of the components of compound formulae and their metabolites in rats by UHPLC/IM-QTOF-MS and an in-house high-definition MS2 library: Sishen Formula as a case[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2024.100994 |
[1] |
H.Y. Xu, Y.Q. Zhang, P. Wang, et al., A comprehensive review of integrative pharmacology-based investigation: a paradigm shift in traditional Chinese medicine, Acta Pharm. Sin. B 11 (2021) 1379-1399.
|
[2] |
R.D. Beger, W. Dunn, M.A. Schmidt, et al., Metabolomics enables precision medicine: “A white paper, community perspective.”, Metabolomics 12 (2016) 149.
|
[3] |
Y.H. Chen, J.H. Bi, M. Xie, et al., Classification-based strategies to simplify complex traditional Chinese medicine (TCM) researches through liquid chromatography-mass spectrometry in the last decade (2011-2020): Theory, technical route and difficulty, J. Chromatogr. A 1651 (2021) 462307.
|
[4] |
M.L. Huang, S.J. Yu, Q. Shao, et al., Comprehensive profiling of Lingzhihuang capsule by liquid chromatography coupled with mass spectrometry-based molecular networking and target prediction, Acupunct. Herb. Med. 2 (2022) 58-67.
|
[5] |
X. Gao, J.J. Wang, X.L. Chen, et al., Reduning Injection prevents carrageenan-induced inflammation in rats by serum and urine metabolomics analysis, Chin. Herb. Med. 14 (2022) 583-591.
|
[6] |
S. Ma, S.K. Chowdhury, Data acquisition and data mining techniques for metabolite identification using LC coupled to high-resolution MS, Bioanalysis 5 (2013) 1285-1297.
|
[7] |
X. Li, J. Liu, T.T. Zuo, et al., Advances and challenges in ginseng research from 2011 to 2020: the phytochemistry, quality control, metabolism, and biosynthesis, Nat. Prod. Rep. 39 (2022) 875-909.
|
[8] |
X.Y. Wang, M.T. Jiang, J. Lou, et al., Pseudotargeted metabolomics approach enabling the classification-induced ginsenoside characterization and differentiation of ginseng and its compound formulation products, J. Agric. Food Chem. 71 (2023) 1735-1747.
|
[9] |
X.Y. Zhang, Z.Z. Jiang, L. Zhang, et al., Identification of prototype compounds and their metabolites in rats’ serum from Xuefu Zhuyu Decoction by UPLC-Q-TOF/MS, Chin. Herb. Med. 15 (2023) 139-150.
|
[10] |
K.Y. Feng, S.M. Wang, L.F. Han, et al., Configuration of the ion exchange chromatography, hydrophilic interaction chromatography, and reversed-phase chromatography as off-line three-dimensional chromatography coupled with high-resolution quadrupole-orbitrap mass spectrometry for the multicomponent characterization of Uncaria sessilifructus, J. Chromatogr. A 1649 (2021) 462237.
|
[11] |
H.D. Wang, C.X. Zhang, T.T. Zuo, et al., In-depth profiling, characterization, and comparison of the ginsenosides among three different parts (the root, stem leaf, and flower bud) of Panax quinquefolius L. by ultra-high performance liquid chromatography/quadrupole-orbitrap mass spectrometry, Anal. Bioanal. Chem. 411 (2019) 7817-7829.
|
[12] |
C.X. Zhang, M.Y. Liu, X.Y. Xu, et al., Application of large-scale molecular prediction for creating the preferred precursor ions list to enhance the identification of ginsenosides from the flower buds of Panax ginseng, J. Agric. Food Chem. 70 (2022) 5932-5944.
|
[13] |
M.X. Sun, X.H. Li, M.T. Jiang, et al., A practical strategy enabling more reliable identification of ginsenosides from Panax quinquefolius flower by dimension-enhanced liquid chromatography/mass spectrometry and quantitative structure-retention relationship-based retention behavior prediction, J. Chromatogr. A 1706 (2023) 464243.
|
[14] |
Z.X. Yan, R. Yan, Improved data-dependent acquisition for untargeted metabolomics using gas-phase fractionation with staggered mass range, Anal. Chem. 87 (2015) 2861-2868.
|
[15] |
F.Y. Zhong, M.Y. Xu, J.J. Zhu, Development and application of time staggered/mass staggered-globally optimized targeted mass spectrometry, J. Chromatogr. B 1120 (2019) 80-88.
|
[16] |
Y. Wang, R.B. Feng, R.B. Wang, et al., Enhanced MS/MS coverage for metabolite identification in LC-MS-based untargeted metabolomics by target-directed data dependent acquisition with time-staggered precursor ion list, Anal. Chim. Acta 992 (2017) 67-75.
|
[17] |
D. Mehta, S. Scandola, R.G. Uhrig, BoxCar and library-free data-independent acquisition substantially improve the depth, range, and completeness of label-free quantitative proteomics, Anal. Chem. 94 (2022) 793-802.
|
[18] |
J.Z. Zhao, Y. Yang, H. Xu, et al., Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota, NPJ Biofilms Microbiomes 9 (2023) 4.
|
[19] |
N.H. Anh, Y.C. Yoon, Y.J. Min, et al., Caenorhabditis elegans deep lipidome profiling by using integrative mass spectrometry acquisitions reveals significantly altered lipid networks, J. Pharm. Anal. 12 (2022) 743-754.
|
[20] |
J. Guo, S. Shen, S.P. Xing, et al., DaDIA: Hybridizing data-dependent and data-independent acquisition modes for generating high-quality metabolomic data, Anal. Chem. 93 (2021) 2669-2677.
|
[21] |
Y.X. Qian, D.X. Zhao, H.D. Wang, et al., An ion mobility-enabled and high-efficiency hybrid scan approach in combination with ultra-high performance liquid chromatography enabling the comprehensive characterization of the multicomponents from Carthamus tinctorius, J. Chromatogr. A 1667 (2022) 462904.
|
[22] |
H.D. Wang, H.M. Wang, X.Y. Wang, et al., A novel hybrid scan approach enabling the ion-mobility separation and the alternate data-dependent and data-independent acquisitions (HDDIDDA): Its combination with off-line two-dimensional liquid chromatography for comprehensively characterizing the multicomponents from Compound Danshen Dripping Pill,Anal. Chim. Acta 1193 (2022) 339320.
|
[23] |
W.D. Hu, X.Y. Xu, Y.X. Qian, et al., Integration of a hybrid scan approach and in-house high-resolution MS2 spectral database for charactering the multicomponents of Xuebijing Injection, Arab. J. Chem. 16 (2023) 104519.
|
[24] |
M. Giera, O. Yanes, G. Siuzdak, Metabolite discovery: Biochemistry's scientific driver, Cell Metab. 34 (2022) 21-34.
|
[25] |
H.C. Lan, S.Z. Li, K. Li, et al., In vitro human intestinal microbiota biotransformation of nobiletin using liquid chromatography-mass spectrometry analysis and background subtraction strategy, J. Sep. Sci. 44 (2021) 2046-2053.
|
[26] |
W.L. Wei, H.J. Li, W.Z. Yang, et al., An integrated strategy for comprehensive characterization of metabolites and metabolic profiles of bufadienolides from Venenum Bufonis in rats, J. Pharm. Anal. 12 (2022) 136-144.
|
[27] |
J. Wu, W.F. Gou, Z.Y. Wang, et al., Discovery of the radio-protecting effect of Ecliptae Herba, its constituents and targeting p53-mediated apoptosis in vitro and in vivo, Acta Pharm. Sin. B 13 (2023) 1216-1230.
|
[28] |
H.Q. Lai, Y. Ouyang, G.H. Tian, et al., Rapid characterization and identification of the chemical constituents and the metabolites of Du-zhi pill using UHPLC coupled with quadrupole time-of-flight mass spectrometry, J. Chromatogr. B 1209 (2022) 123433.
|
[29] |
C.X. Zhang, X.Y. Wang, Z.Z. Lin, et al., Highly selective monitoring of in-source fragmentation sapogenin product ions in positive mode enabling group-target ginsenosides profiling and simultaneous identification of seven Panax herbal medicines, J. Chromatogr. A 1618 (2020) 460850.
|
[30] |
H.Y. Wang, H.M. Zhao, Y. Wang, et al., Sishen Wan® ameliorated trinitrobenzene-sulfonic-acid-induced chronic colitis via NEMO/NLK signaling pathway, Front. Pharmacol. 10 (2019) 170.
|
[31] |
F. Chen, Y.T. Yin, H.M. Zhao, et al., Sishen pill treatment of DSS-induced colitis via regulating interaction with inflammatory dendritic cells and gut microbiota, Front. Physiol. 9 (2020) 801.
|
[32] |
X.L. Su, Y.P. Tang, J. Zhang, et al., Curative effect of warming renal and fortifying spleen recipe on diarrhea-predominant irritable bowel syndrome, J. Tradit. Chin. Med. 33 (2013) 615-619.
|
[33] |
L. Liu, S. Wang, Q.X. Xu, et al., Poly-pharmacokinetic strategy represented the synergy effects of bioactive compounds in a traditional Chinese medicine formula, Si Shen Wan and its separated recipes to normal and colitis rats, J. Sep. Sci. 44 (2021) 2065-2077.
|
[34] |
G. Paglia, P. Angel, J.P. Williams, et al., Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification, Anal. Chem. 87 (2015) 1137-1144.
|
[35] |
J. Liu, Y.T. Li, Y.J. Chen, Advances in high-resolution mass spectrometric-based data-mining technologies for detecting and characterizing the components and metabolites of Chinese materia medica, Acta Pharm. Sin. 56 (2021) 113-129.
|
[36] |
F. Fenaille, P.B. Saint-Hilaire, K. Rousseau, et al., Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?, J. Chromatogr. A 1526 (2017) 1-12.
|
[37] |
R. Franski, B. Gierczyk, T. Kozik, et al., Signals of diagnostic ions in the product ion spectra of [M-H]- ions of methoxylated flavonoids, Rapid Commun. Mass Spectrom. 33 (2019) 125-132.
|
[38] |
Y. Gao, S.M. Wu, R.H. Cong, et al., Characterization of lignans in Schisandra chinensis oil with a single analysis process by UPLC-Q/TOF-MS, Chem. Phys. Lipids 218 (2019) 158-167.
|
[39] |
Z.W. Zhang, T.Z. Fang, H.Y. Zhou, et al., Characterization of the in vitro metabolic profile of evodiamine in human liver microsomes and hepatocytes by UHPLC-Q Exactive mass spectrometer, Front. Pharmacol. 9 (2018) 130.
|
[40] |
Y.F. Zhang, Yuan J, Wang Y, et al., LC-MS/MS determination and pharmacokinetics study of puerarin and daidzein in rat plasma after oral administration of Gegenqinlian decoction and Radix Puerariae extract, Pharmacogn. Mag. 10 (2014) 241-248.
|
[41] |
D.W. Lee, Y. Kang, M.J. Kang, et al., Phase I and phase II metabolite identification of rutaecarpine in freshly isolated hepatocytes from male Sprague-Dawley rats, Arch. Pharm. Res. 40 (2017) 972-979.
|
[42] |
H. Ren, S. Guo, Y.Y. Zhang, Metabolite identification and metabolic pathway analysis of Bufei Huoxue Capsules in rats, Chin. Tradit. Herb. Drugs 54 (2023) 1051-1063.
|
[43] |
H.D. Wang, L. Zhang, X.H. Li, et al., Machine learning prediction for constructing a universal multidimensional information library of Panax saponins (ginsenosides), Food Chem. 439 (2024) 138106.
|
[44] |
D.H. Ross, L.B. Xu, Determination of drugs and drug metabolites by ion mobility-mass spectrometry: A review, Anal. Chim. Acta 1154 (2021) 338270.
|
[45] |
C. Chalet, B. Hollebrands, H.G. Janssen, et al., Identification of phase-II metabolites of flavonoids by liquid chromatography-ion-mobility spectrometry-mass spectrometry, Anal. Bioanal. Chem. 410 (2018) 471-482.
|
[46] |
J.-J. Xu, M.-S. Li, Z.-H. Yao, et al. In vitro metabolic mapping of neobavaisoflavone in human cytochromes P450 and UDP-glucuronosyltransferase enzymes by ultra high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry, J. Pharm. Biomed. Anal. 158 (2018) 351-360.
|