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Lee HHL, Ha SK, Kim Y, Hur J. Simultaneous analysis of advanced glycation end products using dansyl derivatization. Food Chem 2024; 432:137186. [PMID: 37657336 DOI: 10.1016/j.foodchem.2023.137186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023]
Abstract
Herein, new pre-column derivatization based on dansylation is present to resolve analytical difficulties, such as chromatographic separation difficulty, in identifying and quantifying advanced glycation end products (AGEs) owing to their high hydrophilicity, wide variety, and structural similarity. The proposed analytical method facilitated the separation of 14 AGEs, including structural isomers. Limits of detection of 1.0-43.3 ng/mL and linear ranges of the double- or triple-digit were achieved. Intra- and inter-day precisions of 1.1-3.0% and 1.3-3.1%, respectively, were achieved for standard solutions, while those for food specimens were 1.4-11.2% and 1.7-15.7%, respectively. The matrix effect was insignificant with regard to the percent recoveries and differences between slopes for both the standard solutions and food specimens. Furthermore, the quantitation results of AGEs in foods (coffee, beer, and sausage) and glycated proteins revealed the potential applicability of the developed method in various fields of food chemistry and biochemistry.
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Affiliation(s)
- Hyun Hee L Lee
- Agency for Defense Development, Daejeon 34186, Republic of Korea.
| | - Sang Keun Ha
- Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Division of Food Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Yoonsook Kim
- Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jinyoung Hur
- Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Division of Food Biotechnology, University of Science and Technology, Daejeon, Republic of Korea.
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2
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Zheng J, Yang J, Liang X, Fang M, Wang Y. Dual strategy for 13C-Metabolic flux analysis of central carbon and energy metabolism in Mammalian cells based on LC-isoMRM-MS. Talanta 2024; 266:125074. [PMID: 37651912 DOI: 10.1016/j.talanta.2023.125074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
Central carbon and energy metabolism are the most concerned metabolic pathways in 13C-Metabolic flux analysis (13C-MFA). However, some α-keto acids, ribonucleoside triphosphate (NTPs) and deoxyribonucleoside triphosphate (dNTPs) involved in central carbon and energy metabolism pathways were unstable or reactive, leading to inaccurate metabolic flux analysis. To achieve accurate 13C-MFA of central carbon and energy metabolism, we proposed a dual strategy for the detection of 101 metabolites in glucose metabolism pathways. N-Methylphenylethylamine (MPEA) was utilized for derivatization of 4 carboxyl (α-keto acids) and 8 phosphate metabolites (NTPs and dNTPs). After derivatization, the MPEA derivatives were investigated to be stable for 4 weeks under 4 °C and detected with high intensity in ∼104 cells. On the other hand, we analyzed an additional 89 metabolites in central carbon and energy metabolic pathways were directly analyzed by liquid chromatography tandem mass spectrometry (LC-MRM-MS). The limit of detection (LODs) of our method were as low as 0.05 ng/mL and the linear range was at least two orders of magnitude with determination coefficient (R2) > 0.9701. The relative standard divisions (RSDs) of intra- and inter-day of 95% metabolites were below 20%. In addition, the isotope list of 82 detected metabolites in central carbon and energy metabolism were generated according to isotopologues and isotopomers for each metabolite resulting from 13C incorporation. Accurate assessment of mass isotopomer distributions (MIDs) of intracellular 13C-labeled metabolites was achieved in [U-13C]-glucose cultured HepG2 cells by our dual strategy. Finally, we performed MID analysis of 101 metabolites in central carbon and energy metabolism. Overall, this dual method is reproducible and robust for application on 13C-MFA and has a great potential for studying clinical isotope labeled samples.
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Affiliation(s)
- Jie Zheng
- Singapore Phenome Center, Nanyang Technological University, 639798, Singapore
| | - Junjie Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore; Nanyang Environment & Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Xu Liang
- Singapore Phenome Center, Nanyang Technological University, 639798, Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore; Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China.
| | - Yulan Wang
- Singapore Phenome Center, Nanyang Technological University, 639798, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 639798, Singapore.
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3
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Gao S, Zhou X, Yue M, Zhu S, Liu Q, Zhao XE. Advances and perspectives in chemical isotope labeling-based mass spectrometry methods for metabolome and exposome analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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4
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Tao WB, Xie NB, Cheng QY, Feng YQ, Yuan BF. Sensitive determination of inosine RNA modification in single cell by chemical derivatization coupled with mass spectrometry analysis. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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5
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Jiang D, Qi R, Lyu S, Wang W, Liu J, Jia Q. Preparation of Cerium Dioxide Functionalized Magnetic Layered Double Hydroxides for High-efficiency Phosphopeptide Enrichment. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2165-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Chen D, Chan W, Zhao S, Li L, Li L. High-Coverage Quantitative Metabolomics of Human Urine: Effects of Freeze-Thaw Cycles on the Urine Metabolome and Biomarker Discovery. Anal Chem 2022; 94:9880-9887. [PMID: 35758637 DOI: 10.1021/acs.analchem.2c01816] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Urine sample storage after collection at ultra-low-temperature (e.g., -80 °C) is normally required for comparative metabolome analysis of many samples, and therefore, freeze-thaw cycles (FTCs) are unavoidable. However, the reported effects of FTCs on the urine metabolome are controversial. Moreover, there is no report on the study of how urine FTCs affect biomarker discovery. Herein, we present our study of the FTC effects on the urine metabolome and biomarker discovery using a high-coverage quantitative metabolomics platform. Our study involved two centers located in Hangzhou, China, and Edmonton, Canada, to perform metabolome analysis of two separate cohorts of urine samples. The same workflow of sample preparation and dansylation isotope labeling LC-MS was used for in-depth analysis of the amine/phenol submetabolome. The analysis of 320 samples from the Hangzhou cohort consisting of 80 healthy subjects with each urine being subjected to four FTCs resulted in relative quantification of 3682 metabolites with 3307 identified or mass-matched. The analysis of 176 samples from the Edmonton cohort of 44 subjects with four FTCs quantified 3516 metabolites with 3166 identified or mass-matched. Multivariate and univariate analyses indicated that significant variations (fold change ≥ 1.5 with q-value ≤ 0.05) from FTCs were only observed in a very small fraction of the metabolites (<0.3%). Moreover, various metabolites did not show a consistent pattern of concentration changes from one to four FTCs, allowing the use of two separate cohorts of samples to remove these randomly changed metabolites. Three metabolite biomarkers for separating males and females were discovered, and FTC did not influence their discovery.
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Affiliation(s)
- Deying Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Wan Chan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Liang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.,Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Guo C, Hu Y, Cao X, Wang Y. HILIC-MS/MS for the Determination of Methylated Adenine Nucleosides in Human Urine. Anal Chem 2021; 93:17060-17068. [PMID: 34902250 PMCID: PMC8751233 DOI: 10.1021/acs.analchem.1c03829] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
N6-methyl-2'-deoxyadenosine (m6dA) is a newly discovered DNA epigenetic mark in mammals. N6-methyladenosine (m6A), 2'-O-methyladenosine (Am), N6,2'-O-dimethyladenosine (m6Am), and N6,N6-dimethyladenosine (m62A) are common RNA modifications. Previous studies illustrated the associations between the aberrations of these methylated adenosines in nucleic acids and cancer. Herein, we developed Fe3O4/graphene-based magnetic dispersive solid-phase extraction for the enrichment and hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS/MS) for the measurements of m6dA, m6A, Am, m6Am, and m62A in human urine samples. We found that malic acid could improve the HILIC-based separation of these modified nucleosides and markedly enhance the sensitivity of their MS detection. With this method, we accurately quantified the contents of these modified adenine nucleosides in urine samples collected from gastric and colorectal cancer patients as well as healthy controls. We found that, relative to healthy controls, urinary m6dA and Am levels are significantly lower for gastric and colorectal cancer patients; while gastric cancer patients also exhibited lower levels of urinary m6A, the trend was opposite for colorectal cancer patients. Together, we developed a robust analytical method for simultaneous measurements of five methylated adenine nucleosides in human urine, and our results revealed an association between the levels of urinary methylated adenine nucleosides and the occurrence of gastric as well as colorectal cancers, suggesting the potential applications of these modified nucleosides as biomarkers for the early detection of these cancers.
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Affiliation(s)
- Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yiqiu Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Xiaoji Cao
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521, United States
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Chen D, Zhang JX, Cui WQ, Zhang JW, Wu DQ, Yu XR, Luo YB, Jiang XY, Zhu FP, Hussain D, Xu X. A simultaneous extraction/derivatization strategy coupled with liquid chromatography-tandem mass spectrometry for the determination of free catecholamines in biological fluids. J Chromatogr A 2021; 1654:462474. [PMID: 34438300 DOI: 10.1016/j.chroma.2021.462474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023]
Abstract
The current study presents a convenient, rapid and effective simultaneous extraction/derivatization (SEDP) strategy for effective pretreatment of catecholamines (CAs). Commercial zirconium oxide (ZrO2) nanoparticles were employed for the selective capturing of cis-diol containing CAs to remove the biological interferences and phenyl isothiocyanate (PITC) was used for derivatization to improve the ionization and to improve the chromatographic separation. The extraction and derivatization procedures were integrated into one step to simplify the sample pretreatment. Excessive derivatization reagents were removed as well, reducing the degree of contaminations in mass spectrometry. The factors affecting the SEDP process were optimized and the results showed that the detection sensitivity and chromatographic separation of CAs greatly improved compared with underivatized CAs, during LC-MS/MS analysis. Combined with ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), quantifying the concentration of norepinephrine (NE), epinephrine (E) and dopamine (DA) in biological fluids was validated in ranges of 1-200.0 ng/mL with a satisfactory correlation coefficient (R2 > 0.997). The obtained recoveries were in the range of 91.0-109.5% with RSDs less than 9.4%. Finally, significant changes in CAs levels in urine samples of healthy people and pheochromocytoma patients were detected. The developed method offers comparative advantages in terms of sensitivity, specificity and selectivity.
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Affiliation(s)
- Di Chen
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jing-Xian Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Wei-Qi Cui
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jun-Wei Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - De-Qiao Wu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xin-Rui Yu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yan-Bo Luo
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, No.6 Cuizhu Street, Zhengzhou 450001, China
| | - Xing-Yi Jiang
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, No.6 Cuizhu Street, Zhengzhou 450001, China
| | - Feng-Peng Zhu
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, No.6 Cuizhu Street, Zhengzhou 450001, China
| | - Dilshad Hussain
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences University of Karachi, Pakistan
| | - Xia Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
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9
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Guo B, Bi S, Zhang B, Tong Y, Chen X, Tian M. Synthesis of nanoparticles with a combination of metal chelation and molecular imprinting for efficient and selective extraction of glycoprotein. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Guo B, Tong Y, Zhang B, Tian M. Double affinity based molecularly imprinted polymers for selective extraction of luteolin: A combination of synergistic metal chelating and boronate affinity. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105670] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Zhao S, Li L. Chemical Isotope Labeling LC-MS for Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:1-18. [PMID: 33791971 DOI: 10.1007/978-3-030-51652-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Due to the great diversity of chemical and physical properties of metabolites as well as a wide range of concentrations of metabolites present in metabolomic samples, performing comprehensive and quantitative metabolome analysis is a major analytical challenge. Conventional approach of combining various techniques and methods with each detecting a fraction of the metabolome can lead to the increase in overall metabolomic coverage. However, this approach requires extensive investment in equipment and analytical expertise with still relatively low coverage and low sample throughput. Chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) offers an alternative means of increasing metabolomic coverage while maintaining high quantification precision and accuracy. This chapter describes the CIL LC-MS method and its key features for metabolomic analysis.
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Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada.
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12
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Arismendi D, Díaz K, Aguilera-Marabolí N, Sepúlveda B, Richter P. Rotating-disk sorptive extraction for the determination of sex hormones and triclosan in urine by gas chromatography-mass spectrometry: Clean-up integrated steps and improved derivatization. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ścigalski P, Kosobucki P. Recent Materials Developed for Dispersive Solid Phase Extraction. Molecules 2020; 25:E4869. [PMID: 33105561 PMCID: PMC7659476 DOI: 10.3390/molecules25214869] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022] Open
Abstract
Solid phase extraction (SPE) is an analytical procedure developed with the purpose of separating a target analyte from a complex sample matrix prior to quantitative or qualitative determination. The purpose of such treatment is twofold: elimination of matrix constituents that could interfere with the detection process or even damage analytical equipment as well as enriching the analyte in the sample so that it is readily available for detection. Dispersive solid phase extraction (dSPE) is a recent development of the standard SPE technique that is attracting growing attention due to its remarkable simplicity, short extraction time and low requirement for solvent expenditure, accompanied by high effectiveness and wide applicability. This review aims to thoroughly survey recently conducted analytical studies focusing on methods utilizing novel, interesting nanomaterials as dSPE sorbents, as well as known materials that have been only recently successfully applied in dSPE techniques, and evaluate their performance and suitability based on comparison with previously reported analytical procedures.
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Affiliation(s)
- Piotr Ścigalski
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland;
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Chen D, Zhao S, Han W, Lo E, Su X, Li L, Li L. High tolerance to instrument drifts by differential chemical isotope labeling LC-MS: A case study of the effect of LC leak in long-term sample runs on quantitative metabolome analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4589. [PMID: 32639693 DOI: 10.1002/jms.4589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Metabolomics study of a biological system often involves the analysis of many comparative samples over a period of several days or weeks. This process of long-term sample runs can encounter unexpected instrument drifts such as small leaks in liquid chromatography-mass spectrometry (LC-MS), degradation of column performance, and MS signal intensity change. A robust analytical method should ideally tolerate these instrumental drifts as much as possible. In this work, we report a case study to demonstrate the high tolerance of differential chemical isotope labeling (CIL) LC-MS method for quantitative metabolome analysis. In a study of using a rat model to examine the metabolome changes during rheumatoid arthritis (RA) disease development and treatment, over 468 samples were analyzed over a period of 15 days in three batches. During the sample runs, a small leak in LC was discovered after a batch of analyses was completed. Reanalysis of these samples was not an option as sample amounts were limited. To overcome the problem caused by the small leak, we applied a method of retention time correction to the LC-MS data to align peak pairs from different runs with different degrees of leak, followed by peak ratio calculation and analysis. Herein, we illustrate that using 12 C-/13 C-peak pair intensity values in CIL LC-MS as a measurement of concentration changes in different samples could tolerate the signal drifts, while using the absolute intensity values (ie, 12 C-peak as in conventional LC-MS) was not as reliable. We hope that the case study illustrated and the method of overcoming the small-leak-caused signal drifts can be helpful to others who may encounter this kind of situation in long-term sample runs.
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Affiliation(s)
- Deying Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | - Wei Han
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | - Elvis Lo
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Liang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Chen D, Han W, Huan T, Li L, Li L. Effects of Freeze–Thaw Cycles of Blood Samples on High-Coverage Quantitative Metabolomics. Anal Chem 2020; 92:9265-9272. [DOI: 10.1021/acs.analchem.0c01610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deying Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Wei Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tao Huan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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Chemical labeling – Assisted mass spectrometry analysis for sensitive detection of cytidine dual modifications in RNA of mammals. Anal Chim Acta 2020; 1098:56-65. [DOI: 10.1016/j.aca.2019.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/13/2019] [Accepted: 11/10/2019] [Indexed: 12/15/2022]
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17
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Current trends in isotope‐coded derivatization liquid chromatographic‐mass spectrometric analyses with special emphasis on their biomedical application. Biomed Chromatogr 2020; 34:e4756. [DOI: 10.1002/bmc.4756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
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18
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Cheng QY, Xiong J, Ma CJ, Dai Y, Ding JH, Liu FL, Yuan BF, Feng YQ. Chemical tagging for sensitive determination of uridine modifications in RNA. Chem Sci 2020; 11:1878-1891. [PMID: 34123281 PMCID: PMC8148390 DOI: 10.1039/c9sc05094a] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base or in the 2′-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m5U) has not been discovered in mRNA of eukaryotes. In the current study, we established a method of N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide p-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1408 fold upon CMCT labelling. Using the developed method, we identified the distinct existence of m5U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methyl group of m5U originated from S-adenosyl-l-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m5U will further uncover the functional roles of m5U in mRNA of mammals. The discovery of dynamic and reversible modifications in messenger RNA is opening new directions in RNA modification-mediated regulation of biological processes.![]()
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Affiliation(s)
- Qing-Yun Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Cheng-Jie Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Yi Dai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Jiang-Hui Ding
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Fei-Long Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P.R. China +86-27-68755595 +86-27-68755595
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19
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Godoy AT, Eberlin MN, Simionato AVC. Targeted metabolomics: Liquid chromatography coupled to mass spectrometry method development and validation for the identification and quantitation of modified nucleosides as putative cancer biomarkers. Talanta 2019; 210:120640. [PMID: 31987192 DOI: 10.1016/j.talanta.2019.120640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 12/29/2022]
Abstract
A notable change in the body fluids nucleosides of cancer patients has been actively highlighted in searches for new biomarkers to early cancer detection. For this reason, improvements of bioanalytical methods for these compounds focused on a noninvasive sampling trend are of great importance. Therefore, this work aimed firstly to develop efficient methods for nucleoside analysis in urine and serum by liquid chromatography-tandem mass spectrometry (LC-MS/MS), applying different strategies to quantify nine nucleosides, and further identify other untargeted nucleosides. Sample preparation was based on protein precipitation and affinity-solid phase extraction (SPE), whereas quantification was performed using a triple quadrupole (QqQ) mass analyzer operating in the selected reaction monitoring (SRM) mode. Surrogates matrices were proposed as an alternative to standard addition calibration. Specifically, to quantitate creatinine, a simple LC-MS/MS method was validated and used for normalization of urinary metabolites quantitation. To identify the other nucleosides, LC methods using different MS scans modes were evaluated on a quadrupole-time of flight (Q-TOF) or a hybrid triple quadrupole linear ion trap (Q-trap). Validation was performed for nucleosides quantification using the synthetic matrices of urine and serum, and selectivity, linearity, accuracy, reproducibility, matrix effect, LOD's and LOQ's were accessed, providing trustworthy results for bioanalysis purposes. Both LC-Q-Trap/MS and LC-Q-TOF/MS methods showed proper sensitivity for structural characterization on assays with urine and serum samples from healthy volunteers and could also be used in the identification of untargeted nucleosides. The investigated approaches delivered in-depth results and seem promising for future applications on urine and serum samples analyses aiming to validate nucleosides as cancer biomarkers.
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Affiliation(s)
- Adriana Teixeira Godoy
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas, 13083-970, Campinas, SP, Brazil.
| | - Marcos Nogueira Eberlin
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas, 13083-970, Campinas, SP, Brazil; Mackenzie Presbyterian University, MackMass Laboratory, Scholl of Engineering, 01302-907, São Paulo, SP, Brazil
| | - Ana Valéria Colnaghi Simionato
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas, 13083-970, Campinas, SP, Brazil.
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20
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Qi C, Ding J, Yuan B, Feng Y. Analytical methods for locating modifications in nucleic acids. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Zhao S, Li H, Han W, Chan W, Li L. Metabolomic Coverage of Chemical-Group-Submetabolome Analysis: Group Classification and Four-Channel Chemical Isotope Labeling LC-MS. Anal Chem 2019; 91:12108-12115. [DOI: 10.1021/acs.analchem.9b03431] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Hao Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wei Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wan Chan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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22
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Mohyuddin A, Hussain D, Fatima B, Athar M, Ashiq MN, Najam-ul-Haq M. Gallic acid functionalized UiO-66 for the recovery of ribosylated metabolites from human urine samples. Talanta 2019; 201:23-32. [DOI: 10.1016/j.talanta.2019.03.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
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23
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Zhang YF, Qi CB, Yuan BF, Feng YQ. Determination of cytidine modifications in human urine by liquid chromatography - Mass spectrometry analysis. Anal Chim Acta 2019; 1081:103-111. [PMID: 31446947 DOI: 10.1016/j.aca.2019.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
Both DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC) and RNA cytosine methylation (5-methylcytidine, m5rC) are important epigenetic marks that play regulatory roles in diverse biological processes. m5dC and m5rC can be further oxidized by the ten-eleven translocation (TET) proteins to form 5-hydroxymethyl-2'-deoxycytidine (hm5dC) and 5-hydroxymethylcytidine (hm5rC), respectively. 2'-O-methyl-5-hydroxymethylcytidine (hm5rCm) was recently also identified as a second oxidative metabolite of m5rC in RNA. Previous studies showed that the dysregulation of cytidine modifications in both DNA and RNA are closely related to a variety of human diseases. These cytidine modifications are generally excreted from cell into urine. If these cytidine modifications exhibit specific features related to certain diseases, determination of the cytidine modifications in urine could be utilized as non-invasive diagnostic of diseases. Here, we established a solid-phase extraction in combination with liquid chromatography-mass spectrometry (LC-MS/MS) analysis for simultaneous detection of these cytidine modifications in human urine samples. The developed method enabled the distinct detection of these cytidine modifications. We reported, for the first time, the presence of hm5rCm in human urine. Furthermore, we found that compared to the healthy controls, the contents of hm5dC, hm5rC, and hm5rCm showed significant increases in urine samples of cancer patients, including lymphoma patients, gastric cancer patients, and esophageal cancer patients. This study indicates that the urinary hydroxylmethylation modifications of hm5dC, hm5rC, and hm5rCm may serve as potential indicator of cancers.
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Affiliation(s)
- Yu-Fan Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Sauvage Center for Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Sauvage Center for Molecular Sciences, Wuhan University, Wuhan, 430072, PR China.
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
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Huang S, Chen G, Ye N, Kou X, Zhu F, Shen J, Ouyang G. Solid-phase microextraction: An appealing alternative for the determination of endogenous substances - A review. Anal Chim Acta 2019; 1077:67-86. [PMID: 31307724 DOI: 10.1016/j.aca.2019.05.054] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023]
Abstract
The determination of endogenous substances is of great significance for obtaining important biotic information such as biological components, metabolic pathways and disease biomarkers in different living organisms (e.g. plants, insects, animals and humans). However, due to the complex matrix and the trace concentrations of target analytes, the sample preparation procedure is an essential step before the analytes of interest are introduced into a detection instrument. Solid-phase microextraction (SPME), an emerging sample preparation technique that integrates sampling, extraction, concentration, and sample introduction into one step, has gained wide acceptance in various research fields, including in the determination of endogenous compounds. In this review, recent developments and applications of SPME for the determination of endogenous substances over the past five years are summarized. Several aspects, including the design of SPME devices (sampling configuration and coating), applications (in vitro and in vivo sampling), and coupling with emerging instruments (comprehensive two-dimensional gas chromatography (GC × GC), ambient mass spectrometry (AMS) and surface enhanced Raman scattering (SERS)) are involved. Finally, the challenges and opportunities of SPME methods in endogenous substances analysis are also discussed.
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Affiliation(s)
- Siming Huang
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No. 107 Yanjiang Road West, Guangzhou, 510120, China
| | - Guosheng Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Niru Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoxue Kou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jun Shen
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No. 107 Yanjiang Road West, Guangzhou, 510120, China.
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China; College of Chemistry & Molecular Engineering, Center of Advanced Analysis and Computational Science, Zhengzhou University, Kexue Avenue 100, Zhengzhou, 450001, PR China.
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25
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Zheng J, Zheng SJ, Cai WJ, Yu L, Yuan BF, Feng YQ. Stable isotope labeling combined with liquid chromatography-tandem mass spectrometry for comprehensive analysis of short-chain fatty acids. Anal Chim Acta 2019; 1070:51-59. [PMID: 31103167 DOI: 10.1016/j.aca.2019.04.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Short-chain fatty acids (SCFAs) are one class of bacterial metabolites mainly formed by gut microbiota from undigested fibers and proteins. These molecules are able to mediate signal conduction processes of cells, acting as G protein-coupled receptors (GPR) activators and histone deacetylases (HDAC) inhibitors. It was reported that SCFAs were closely associated with various human diseases. However, it is still challenging to analyze SCFAs because of their diverse structures and broad range of concentrations. In this study, we developed a highly sensitive method for simultaneous detection of 34 SCFAs by stable isotope labeling coupled with ultra-high performance liquid chromatography-electrospray ionization-mass spectrometry (UHPLC-ESI-MS/MS) analysis. In this respect, a pair of isotope labeling reagents, N-(4-(aminomethyl)benzyl)aniline (4-AMBA) and N-(4-(aminomethyl)benzyl)aniline-d5 (4-AMBA-d5), were synthesized to label SCFAs from the feces of mice and SCFA standards, respectively. The 4-AMBA-d5 labeled SCFAs were used as internal standards to compensate the ionization variances resulting from matrix effect and thus minimize quantitation deviation in MS detection. After 4-AMBA labeling, the retention of SCFAs on the reversed-phase column increased and the separation resolution of isomers were improved. In addition, the MS responses of most SCFAs were enhanced by up to three orders of magnitude compared to unlabeled SCFAs. The limits of detection (LODs) of SCFAs were as low as 0.005 ng/mL. Moreover, good linearity for 34 SCFAs was obtained with the coefficient of determination (R2) ranging from 0.9846 to 0.9999 and the intra- and inter-day relative standard deviations (RSDs) were <17.8% and 15.4%, respectively, indicating the acceptable reproducibility of the developed method. Using the developed method, we successfully quantified 21 SCFAs from the feces of mice. Partial least squares discriminant analysis (PLS-DA) and t-test analysis showed that the contents of 9 SCFAs were significantly different between Alzheimer's disease (AD) and wide type (WT) mice fecal samples. Compared to WT mice, the contents of propionic acid, isobutyric acid, 3-hydroxybutyric acid, and 3-hydroxyisocaleric acid were decreased in AD mice, while lactic acid, 2-hydroxybutyric acid, 2-hydroxyisobutyric acid, levulinic acid, and valpronic acid were increased in AD mice. These significantly changed SCFAs in the feces of AD mice may afford to a better understanding of the pathogenesis of AD. Taken together, the developed UHPLC-ESI-MS/MS method could be applied for the sensitive and comprehensive determination of SCFAs from complex biological samples.
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Affiliation(s)
- Jie Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Shu-Jian Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Wen-Jing Cai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Lei Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China.
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26
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Xiong J, Yuan BF, Feng YQ. Mass Spectrometry for Investigating the Effects of Toxic Metals on Nucleic Acid Modifications. Chem Res Toxicol 2019; 32:808-819. [PMID: 30920205 DOI: 10.1021/acs.chemrestox.9b00042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The extensive use of toxic metals in industry and agriculture leads to their wide distribution in the environment, which raises critical concerns over their toxic effects on human health. Many toxic metals are reported to be mildly mutagenic or non-mutagenic, indicating that genetic-based mechanisms may not be primarily responsible for toxic metal-induced carcinogenesis. Increasing evidence has demonstrated that exposure to toxic metals can alter epigenetic modifications, which may lead to the dysregulation of gene expression and disease susceptibility. It is now becoming clear that a full understanding of the effects of toxic metals on cellular toxicity and carcinogenesis will need to consider both genetic- and epigenetic-based mechanisms. Uncovering the effects of toxic metals on epigenetic modifications in nucleic acids relies on the detection and quantification of these modifications. Mass spectrometry (MS)-based methods for deciphering epigenetic modifications have substantially advanced over the past decade, and they are now becoming widely used and essential tools for evaluating the effects of toxic metals on nucleic acid modifications. This Review provides an overview of MS-based methods for analysis of nucleic acid modifications. In addition, we also review recent advances in understanding the effects of exposure to toxic metals on nucleic acid modifications.
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Affiliation(s)
- Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
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27
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Xu J, Zhang QF, Zheng J, Yuan BF, Feng YQ. Mass spectrometry-based fecal metabolome analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Profiling of carboxyl-containing metabolites in smokers and non-smokers by stable isotope labeling combined with LC-MS/MS. Anal Biochem 2019; 569:1-9. [DOI: 10.1016/j.ab.2018.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 12/16/2022]
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29
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Wang X, Han W, Yang J, Westaway D, Li L. Development of chemical isotope labeling LC-MS for tissue metabolomics and its application for brain and liver metabolome profiling in Alzheimer's disease mouse model. Anal Chim Acta 2019; 1050:95-104. [DOI: 10.1016/j.aca.2018.10.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/18/2022]
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30
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Deciphering nucleic acid modifications by chemical derivatization-mass spectrometry analysis. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.04.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Development of a simple and efficient method of harvesting and lysing adherent mammalian cells for chemical isotope labeling LC-MS-based cellular metabolomics. Anal Chim Acta 2018; 1037:97-106. [DOI: 10.1016/j.aca.2017.11.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/10/2017] [Accepted: 11/18/2017] [Indexed: 02/08/2023]
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32
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Zhao S, Li L. Dansylhydrazine Isotope Labeling LC-MS for Comprehensive Carboxylic Acid Submetabolome Profiling. Anal Chem 2018; 90:13514-13522. [DOI: 10.1021/acs.analchem.8b03435] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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33
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Guo C, Xie C, Chen Q, Cao X, Guo M, Zheng S, Wang Y. A novel malic acid-enhanced method for the analysis of 5-methyl-2'-deoxycytidine, 5-hydroxymethyl-2'-deoxycytidine, 5-methylcytidine and 5-hydroxymethylcytidine in human urine using hydrophilic interaction liquid chromatography-tandem mass spectrometry. Anal Chim Acta 2018; 1034:110-118. [PMID: 30193624 DOI: 10.1016/j.aca.2018.06.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 12/30/2022]
Abstract
5-Methyl-2'-deoxycytidine (5-mdC), 5-hydroxymethyl-2'-deoxycytidine (5-hmdC), 5-methylcytidine (5-mrC) and 5-hydroxymethylcytidine (5-hmrC) are epigenetic marks of DNA and RNA, and aberrant levels of these modified nucleosides were found to be associated with various cancers. Urine is a preferred source of biological fluid for biomarker discovery because the sample collection process is not invasive to patients. Herein, we developed a novel malic acid-enhanced hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method for sensitive and simultaneous quantification of the modified cytosine nucleosides in human urine. Malic acid markedly increased the detection sensitivities of all four cytosine nucleosides, with the limits of detection (LODs) for 5-mdC, 5-hmdC, 5-mrC and 5-hmrC being 0.025, 0.025, 0.025 and 0.050 fmol, respectively. By using this method, we demonstrated, for the first time, the presence of 5-hmrC in human urine, and we successfully quantified 5-mdC, 5-hmdC, 5-mrC and 5-hmrC in urine samples collected from 90 patients with colorectal cancer (CRC) and 90 healthy controls. We found that the levels of 5-mdC, 5-hmdC, 5-mrC and 5-hmrC in urine were all substantially decreased in CRC patients, suggesting that these modified nucleosides might have great potential to be noninvasive biomarkers for early detection and prognosis of CRC. Together, we established a novel and sensitive method for detecting 5-methylated and 5-hydroxymethylated cytosine nucleosides in human urine and the results from this study may stimulate future investigations about the regulatory roles of these cytosine derivatives in the initiation and development of CRC.
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Affiliation(s)
- Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
| | - Cong Xie
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China; College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Qin Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Xiaoji Cao
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical College, Xuzhou, Jiangsu, 221004, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, 92521, United States.
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Zheng SJ, Liu SJ, Zhu QF, Guo N, Wang YL, Yuan BF, Feng YQ. Establishment of Liquid Chromatography Retention Index Based on Chemical Labeling for Metabolomic Analysis. Anal Chem 2018; 90:8412-8420. [DOI: 10.1021/acs.analchem.8b00901] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shu-Jian Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Shi-Jie Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Quan-Fei Zhu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Ning Guo
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Ya-Lan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
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35
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Wang YL, Zhu QF, Cheng LM, Wang ST, Qin SS, Zheng SJ, Xiao HM, Li JJ, Liu SM, Yuan BF, Feng YQ. Stable isotope labeling - dispersive solid phase extraction - liquid chromatography - tandem mass spectrometry for quantitative analysis of transsulfuration pathway thiols in human serum. J Chromatogr B Analyt Technol Biomed Life Sci 2018. [DOI: 10.1016/j.jchromb.2018.02.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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36
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Cheng QY, Xiong J, Wang F, Yuan BF, Feng YQ. Chiral derivatization coupled with liquid chromatography/mass spectrometry for determining ketone metabolites of hydroxybutyrate enantiomers. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.06.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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Immobilization of zirconium-glycerolate nanowires on magnetic nanoparticles for extraction of urinary ribonucleosides. Mikrochim Acta 2017; 185:43. [PMID: 29594396 DOI: 10.1007/s00604-017-2596-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
The authors have immobilized nanowires made from zirconium glycerolate (ZrGly) on magnetite (Fe3O4) nanoparticles by applying a solvothermal growth process using metal-glycerolate as a precursor. The structure and the dissolution-recrystallization mechanism of the resulting Fe3O4@ZrGly composite were investigated by attenuated total reflection-FTIR, energy-dispersive X-ray analysis, thermogravimetric analysis and solid-state cross polarization/magic angle spinning 13C NMR spectroscopy. The interaction between the zirconium glycerolate in Fe3O4@ZrGly and cis-diols leads to efficient adsorption of riboncleosides which then can be quantified by HPLC with UV detection. The sorbent was successfully applied to the selective enrichment of adenosine, cytidine, uridine and guanosine from spiked human urine samples. The detection limit of the method is in the range from 1.7 to 19 ng·mL-1 of nucleosides in spiked human urine, with relative standard deviations of lower than 12.4% and recoveries ranging from 90.6 to 113%. Graphical abstract Fe3O4@ZrGly with high selectivity towards ribonucleosides was designed and applied for quantitation of urinary ribonucleosides.
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Zheng SJ, Wang YL, Liu P, Zhang Z, Yu L, Yuan BF, Feng YQ. Stable isotope labeling-solid phase extraction-mass spectrometry analysis for profiling of thiols and aldehydes in beer. Food Chem 2017; 237:399-407. [DOI: 10.1016/j.foodchem.2017.05.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 01/08/2023]
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Luo X, Li L. Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells. Anal Chem 2017; 89:11664-11671. [DOI: 10.1021/acs.analchem.7b03100] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xian Luo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Yu L, Ye T, Bai YL, Cai WJ, Ding J, Yuan BF, Feng YQ. Profiling of potential brassinosteroids in different tissues of rape flower by stable isotope labeling - liquid chromatography/mass spectrometry analysis. Anal Chim Acta 2017; 1037:55-62. [PMID: 30292315 DOI: 10.1016/j.aca.2017.08.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
Brassinosteroids (BRs) play crucial roles in a variety of physiological processes in plants. The full elucidation of the functions of RBs relies on sensitive detection and accurate measurement of BRs in plants. However, the identification and quantification of BRs are challenging due to their low abundance as well as poor ionization efficiencies during mass spectrometry-based analysis. Herein, we developed a highly sensitive and selective strategy for profiling potential BRs in plants by stable isotope labeling liquid chromatography multiple reaction monitoring scan mass spectrometry (SIL-LC-MRM-MS) analysis. In the strategy, we used a pair of stable isotope labeling reagents 4-phenylaminomethyl-benzeneboronic acid (4-PAMBA) and d5-4-phenylaminomethyl-benzeneboronic acid (4-PAMBA-d5) that can react with C22-C23 cis-diol on BRs for profiling potential BRs in plant tissues. The 4-PAMBA and 4-PAMBA-d5 labeled BRs could generate two characteristic neutral loss under collision induced dissociation (CID), respectively, which is used to establish the MRM-based detection and screening. The precursor ions of BRs labeled with 4-PAMBA and 4-PAMBA-d5 were set according to the reported structures of BRs, and the corresponding product ions were predicted by subtracting the lost neutral loss. In this respect, corresponding precursor ions and product ions in MRM transitions are formed. The peak pairs with a fixed mass difference, similar retention times and intensities were assigned as potential BRs. Using the developed SIL-LC-MRM-MS strategy, we successfully found 13 potential BR in different tissues of rape flower. Taken together, the SIL-LC-MRM-MS analytical strategy is promising for profiling potential BRs as well as other compounds that have the same functional moiety from complex biological samples.
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Affiliation(s)
- Lei Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Tiantian Ye
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Ya-Li Bai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Wen-Jing Cai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Jun Ding
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China.
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Chen D, Han W, Su X, Li L, Li L. Overcoming Sample Matrix Effect in Quantitative Blood Metabolomics Using Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry. Anal Chem 2017; 89:9424-9431. [PMID: 28787119 DOI: 10.1021/acs.analchem.7b02240] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Blood is widely used for discovery metabolomics to search for disease biomarkers. However, blood sample matrix can have a profound effect on metabolome analysis, which can impose an undesirable restriction on the type of blood collection tubes that can be used for blood metabolomics. We investigated the effect of blood sample matrix on metabolome analysis using a high-coverage and quantitative metabolome profiling technique based on differential chemical isotope labeling (CIL) LC-MS. We used 12C-/13C-dansylation LC-MS to perform relative quantification of the amine/phenol submetabolomes of four types of samples (i.e., serum, EDTA plasma, heparin plasma, and citrate plasma) collected from healthy individuals and compare their metabolomic results. From the analysis of 80 plasma and serum samples in experimental triplicate, we detected a total of 3651 metabolites with an average of 1818 metabolites per run (n = 240). The number of metabolites detected and the precision and accuracy of relative quantification were found to be independent of the sample type. Within each sample type, the metabolome data set could reveal biological variation (e.g., sex separation). Although the relative concentrations of some individual metabolites might be different in the four types of samples, for sex separation, all 66 significant metabolites with larger fold-changes (FC ≥ 2 and p < 0.05) found in at least one sample type could be found in the other types of samples with similar or somewhat reduced, but still significant, fold-changes. Our results indicate that CIL LC-MS could overcome the sample matrix effect, thereby greatly broadening the scope of blood metabolomics; any blood samples properly collected in routine clinical settings, including those in biobanks originally used for other purposes, can potentially be used for discovery metabolomics.
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Affiliation(s)
- Deying Chen
- State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, Zhejiang 310003, China
| | - Wei Han
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Xiaoling Su
- State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, Zhejiang 310003, China
| | - Liang Li
- State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, Zhejiang 310003, China.,Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Lanjuan Li
- State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, Zhejiang 310003, China
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HE YL, LUO YB, CHEN H, HOU HW, HU QY. Research Progress in Analysis of Small Molecule Metabolites in Bio-matrices by Stable Isotope Coded Derivatization Combining with Liquid Chromatography–tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61026-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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43
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Zheng L, Zhao XE, Zhu S, Tao Y, Ji W, Geng Y, Wang X, Chen G, You J. A new combined method of stable isotope-labeling derivatization-ultrasound-assisted dispersive liquid–liquid microextraction for the determination of neurotransmitters in rat brain microdialysates by ultra high performance liquid chromatography tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1054:64-72. [DOI: 10.1016/j.jchromb.2017.03.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/18/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
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44
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Zhao S, Dawe M, Guo K, Li L. Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Carbonyl Submetabolome. Anal Chem 2017; 89:6758-6765. [PMID: 28505421 DOI: 10.1021/acs.analchem.7b01098] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential 12C- and 13C-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with 12C-labeling and spiked with a 13C-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 12C-/13C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl metabolites with each containing MS, retention time (RT), and MS/MS information. This library and an online search program for labeled carbonyl metabolite identification based on MS, RT, and MS/MS matches have been implemented in a freely available Website, www.mycompoundid.org . Using this library, out of the 1737 peak pairs detected in urine, 33 metabolites were positively identified. In addition, 1333 peak pairs could be matched to the metabolome databases with most of them belonging to the carbonyl metabolites. These results show that 12C-/13C-DnsHz labeling LC-MS is a useful tool for profiling the carbonyl submetabolome of complex samples with high coverage.
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Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Margot Dawe
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Kevin Guo
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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45
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Guo N, Peng CY, Zhu QF, Yuan BF, Feng YQ. Profiling of carbonyl compounds in serum by stable isotope labeling - Double precursor ion scan - Mass spectrometry analysis. Anal Chim Acta 2017; 967:42-51. [DOI: 10.1016/j.aca.2017.03.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/16/2017] [Accepted: 03/12/2017] [Indexed: 10/19/2022]
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46
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Wan L, Zhu H, Guan Y, Huang G. Nanocoating cellulose paper based microextraction combined with nanospray mass spectrometry for rapid and facile quantitation of ribonucleosides in human urine. Talanta 2017; 169:209-215. [PMID: 28411814 DOI: 10.1016/j.talanta.2017.03.085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/14/2017] [Accepted: 03/26/2017] [Indexed: 10/19/2022]
Abstract
A rapid and facile analytical method for quantification of ribonucleosides in human urine was developed by the combination of nanocoating cellulose paper based microextraction and nanoelectrospray ionization-tandem mass spectrometry (nESI-MS/MS). Cellulose paper used for microextraction was modified by nano-precision deposition of uniform ultrathin zirconia gel film using a sol-gel process. Due to the large surface area of the cellulose paper and the strong affinity between zirconia and the cis-diol compounds, the target analytes were selectively extracted from the complex matrix. Thus, the detection sensitivity was greatly improved. Typically, the nanocoating cellulose paper was immersed into the diluted urine for selective extraction of target analytes, then the extracted analytes were subjected to nESI-MS/MS detection. The whole analytical procedure could be completed within 10min. The method was evaluated by the determination of ribonucleosides (adenosine, cytidine, uridine, guanosine) in urine sample. The signal intensities of the ribonuclesides extracted by the nanocoating cellulose paper were greatly enhanced by 136-459-folds compared with the one of the unmodified cellulose paper based microextraction. The limits of detection (LODs) and the limits of quantification (LOQs) of the four ribonucleosides were in the range of 0.0136-1.258μgL-1 and 0.0454-4.194μgL-1, respectively. The recoveries of the target nucleosides from spiked human urine were in the range of 75.64-103.49% with the relative standard deviations (RSDs) less than 9.36%. The results demonstrate the potential of the proposed method for rapid and facile determination of endogenous ribonucleosides in urine sample.
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Affiliation(s)
- Lingzhong Wan
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China (USTC), Hefei 230026, China
| | - Haijing Zhu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China (USTC), Hefei 230026, China
| | - Yafeng Guan
- Department of Instrumentation and Analytical Chemistry, Key Laboratory of Separation Science for Analytical Chemistry of CAS, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guangming Huang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China (USTC), Hefei 230026, China.
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Zeng H, Qi CB, Liu T, Xiao HM, Cheng QY, Jiang HP, Yuan BF, Feng YQ. Formation and Determination of Endogenous Methylated Nucleotides in Mammals by Chemical Labeling Coupled with Mass Spectrometry Analysis. Anal Chem 2017; 89:4153-4160. [PMID: 28271879 DOI: 10.1021/acs.analchem.7b00052] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Methylcytosine (5-mC) is an important epigenetic mark that plays critical roles in a variety of cellular processes. To properly exert physiological functions, the distribution of 5-mC needs to be tightly controlled in both DNA and RNA. In addition to methyltransferase-mediated DNA and RNA methylation, premethylated nucleotides can be potentially incorporated into DNA and RNA during replication and transcription. To exclude the premodified nucleotides into DNA and RNA, endogenous 5-methyl-2'-deoxycytidine monophosphate (5-Me-dCMP) generated from nucleic acids metabolism can be enzymatically deaminated to thymidine monophosphate (TMP). Therefore, previous studies failed to detect 5-Me-dCMP or 5-methylcytidine monophosphate (5-Me-CMP) in cells. In the current study, we established a method by chemical labeling coupled with liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS/MS) for sensitive and simultaneous determination of 10 nucleotides, including 5-Me-dCMP and 5-Me-CMP. As N,N-dimethyl-p-phenylenediamine (DMPA) was utilized for labeling, the detection sensitivities of nucleotides increased by 88-372-fold due to the introduction of a tertiary amino group and a hydrophobic moiety from DMPA. Using this method, we found that endogenous 5-Me-dCMP and 5-Me-CMP widely existed in cultured human cells, human tissues, and human urinary samples. The presence of endogenous 5-Me-dCMP and 5-Me-CMP indicates that deaminases may not fully deaminate these methylated nucleotides. Consequently, the remaining premethylated nucleosides could be converted to nucleoside triphosphates as building blocks for DNA and RNA synthesis. Furthermore, we found that the contents of 5-Me-dCMP and 5-Me-CMP exhibited significant decreases in renal carcinoma tissues and urine samples of lymphoma patients compared to their controls, probably due to more reutilization of methylated nucleotides in DNA and RNA synthesis. This study is, to the best of our knowledge, the first report for detecting endogenous 5-Me-dCMP and 5-Me-CMP in mammals. The detectable endogenous methylated nucleotides indicate the potential deleterious effects of premodified nucleotides on aberrant gene regulation in cancers.
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Affiliation(s)
- Huan Zeng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China.,Department of Pathology, Hubei Cancer Hospital , Wuhan, Hubei 430079, People's Republic of China
| | - Ting Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
| | - Hua-Ming Xiao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
| | - Qing-Yun Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
| | - Han-Peng Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, People's Republic of China
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Lu Z, Wang Q, Wang M, Fu S, Zhang Q, Zhang Z, Zhao H, Liu Y, Huang Z, Xie Z, Yu H, Gao X. Using UHPLC Q-Trap/MS as a complementary technique to in-depth mine UPLC Q-TOF/MS data for identifying modified nucleosides in urine. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1051:108-117. [PMID: 28340480 DOI: 10.1016/j.jchromb.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/25/2022]
Abstract
Modified nucleosides, metabolites of RNA, are potential biomarkers of cancer before the appearance of morphological abnormalities. It is of great significance to comprehensively detect and identify nucleosides in human urine for discovery of cancer biomarkers. However, the lower abundance, the greater polarity and the matrix effects make it difficult to detect urinary nucleosides. In this paper, an integrated method consisted of sample preparation followed by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS) detection and primary identification, then ultra-high performance liquid chromatography coupled with hybrid triple quadrupole linear ion trap mass spectrometer (UHPLC Q-Trap/MS) further identification and validation were introduced. Firstly, to enrich the nucleosides and eliminate the urine matrix effects, different sorbent materials of solid phase extraction (SPE) and the elution conditions were screened. Secondly, UPLC Q-TOF/MS was used to acquire mass data in MSE mode. The structural formulas of nucleosides in urine sample were primarily identified according to retention time, accurate mass precursor ions and fragment ions from in-house database and online database. Thirdly, the preliminary identified nucleoside structures lacking of characteristic fragment ions were verified by UHPLC Q-Trap/MS in multiple reaction monitoring trigger enhanced product ion scan (MRM-EPI) and neutral loss scan (NL). At last, phenylboronic acid (PBA)-based SPE was utilized due to its higher MS signal and weaker matrix effects under optimized extraction conditions. Fifty-five nucleosides were primarily identified by UPLC Q-TOF/MS, among which 50 nucleosides were confirmed by UHPLC Q-Trap/MS. Five nucleosides, namely 4',5'-didehydro-5'-deoxyadenosine, 4',5'-didehydro-5'-deoxyinosine, isonicotinamide riboside, peroxywybutosine and hydroxywybutosine, were found from urine for the first time. The results will expand the Human Metabolome Database (HMDB).
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Affiliation(s)
- Zhiwei Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Qing Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Meiling Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Shuang Fu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Qingqing Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Zhixin Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Huizhen Zhao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Yuehong Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Zhenhai Huang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Ziye Xie
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Honghong Yu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Xiaoyan Gao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
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Metal oxide-based dispersive solid-phase extraction coupled with mass spectrometry analysis for determination of ribose conjugates in human follicular fluid. Talanta 2017; 167:506-512. [PMID: 28340751 DOI: 10.1016/j.talanta.2017.02.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/22/2017] [Accepted: 02/26/2017] [Indexed: 01/06/2023]
Abstract
Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility. The pathogenesis of PCOS remains unclear and early diagnosis of PCOS is challenging. Follicular fluid provides a unique window in the critical processes during oocyte and follicular maturation, and the metabolic level of follicular fluid has important impact on the developmental potential of oocytes and subsequent embryos. Previous studies demonstrated some modified ribonucleosides in biological fluids were diseases related metabolites. In this respect, analysis of endogenous modified ribonucleosides in follicular fluids will facilitate the investigation of follicular development. Here, we developed a strategy for determination of ribose conjugates from follicular fluid using metal oxide-based dispersive solid-phase extraction (DSPE) coupled with liquid chromatography-multiple reaction monitoring-mass spectrometry analysis (DSPE-LC-MRM-MS/MS). Cerium dioxide (CeO2) was used to selectively recognize and capture cis-diol containing ribose conjugates from complex biological samples under basic environment. The trapped ribose conjugates were then easily released under acidic environment. The results showed that 50 potential ribose conjugates were detected in follicular fluid by the developed DSPE-LC-MRM-MS/MS method. We then further investigated the contents change of the detected ribose conjugates in follicular fluid from PCOS patients. The results indicated that the follicular fluid from healthy controls and PCOS patients can be clearly differentiated with the partial least squares-discriminate analysis (PLS-DA) based on the detected ribose conjugates. In addition, the contents of 8 ribose conjugates were significantly different between PCOS patients and healthy controls, which could potentially serve as the indicator of PCOS.
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50
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Budelier MM, Cheng WWL, Bergdoll L, Chen ZW, Abramson J, Krishnan K, Qian M, Covey DF, Janetka JW, Evers AS. Click Chemistry Reagent for Identification of Sites of Covalent Ligand Incorporation in Integral Membrane Proteins. Anal Chem 2017; 89:2636-2644. [PMID: 28194953 DOI: 10.1021/acs.analchem.6b05003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identifying sites of protein-ligand interaction is important for structure-based drug discovery and understanding protein structure-function relationships. Mass spectrometry (MS) has emerged as a useful tool for identifying residues covalently modified by ligands. Current methods use database searches that are dependent on acquiring interpretable fragmentation spectra (MS2) of peptide-ligand adducts. This is problematic for identifying sites of hydrophobic ligand incorporation in integral membrane proteins (IMPs), where poor aqueous solubility and ionization of peptide-ligand adducts and collision-induced adduct loss hinder the acquisition of quality MS2 spectra. To address these issues, we developed a fast ligand identification (FLI) tag that can be attached to any alkyne-containing ligand via Cu(I)-catalyzed cycloaddition. The FLI tag adds charge to increase solubility and ionization, and utilizes stable isotope labeling for MS1 level identification of hydrophobic peptide-ligand adducts. The FLI tag was coupled to an alkyne-containing neurosteroid photolabeling reagent and used to identify peptide-steroid adducts in MS1 spectra via the stable heavy isotope pair. Peptide-steroid adducts were not identified in MS2-based database searches because collision-induced adduct loss was the dominant feature of collision-induced dissociation (CID) fragmentation, but targeted analysis of MS1 pairs using electron transfer dissociation (ETD) markedly reduced adduct loss. Using the FLI tag and ETD, we identified Glu73 as the site of photoincorporation of our neurosteroid ligand in the IMP, mouse voltage-dependent anion channel-1 (mVDAC1), and top-down MS confirmed a single site of photolabeling.
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Affiliation(s)
- Melissa M Budelier
- Department of Anesthesiology, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Lucie Bergdoll
- Department of Physiology, David Geffen School of Medicine at UCLA, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Zi-Wei Chen
- Department of Anesthesiology, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,The Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine at UCLA, University of California at Los Angeles , Los Angeles, California 90095, United States.,The Institute for Stem Cell Biology and Regenerative Medicine (instem), National Centre for Biological Sciences-Tata Institute of Fundamental Research , Bangalore 560065, Karnataka India
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Mingxing Qian
- Department of Developmental Biology, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Douglas F Covey
- Department of Anesthesiology, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,The Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,Department of Developmental Biology, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,Department of Psychiatry, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Alex S Evers
- Department of Anesthesiology, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,The Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis , St. Louis, Missouri 63110, United States.,Department of Developmental Biology, Washington University in St. Louis , St. Louis, Missouri 63110, United States
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