51
|
Alexandre-Gouabau MC, Courant F, Le Gall G, Moyon T, Darmaun D, Parnet P, Coupé B, Antignac JP. Offspring Metabolomic Response to Maternal Protein Restriction in a Rat Model of Intrauterine Growth Restriction (IUGR). J Proteome Res 2011; 10:3292-302. [DOI: 10.1021/pr2003193] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Cécile Alexandre-Gouabau
- INRA and University of Nantes, UMR-1280 Physiologie des Adaptations Nutritionnelles CHU Hôtel Dieu, 44093 Nantes cedex 1, France
| | - Frédérique Courant
- ONIRIS, USC 2013, Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Nantes, France
| | - Gwénaëlle Le Gall
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, United Kingdom
| | - Thomas Moyon
- INRA and University of Nantes, UMR-1280 Physiologie des Adaptations Nutritionnelles CHU Hôtel Dieu, 44093 Nantes cedex 1, France
| | - Dominique Darmaun
- INRA and University of Nantes, UMR-1280 Physiologie des Adaptations Nutritionnelles CHU Hôtel Dieu, 44093 Nantes cedex 1, France
| | - Patricia Parnet
- INRA and University of Nantes, UMR-1280 Physiologie des Adaptations Nutritionnelles CHU Hôtel Dieu, 44093 Nantes cedex 1, France
| | - Bérengère Coupé
- INRA and University of Nantes, UMR-1280 Physiologie des Adaptations Nutritionnelles CHU Hôtel Dieu, 44093 Nantes cedex 1, France
| | - Jean-Philippe Antignac
- ONIRIS, USC 2013, Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Nantes, France
| |
Collapse
|
52
|
Shen F, Ying Y, Li B, Zheng Y, Zhuge Q. Multivariate classification of rice wines according to ageing time and brand based on amino acid profiles. Food Chem 2011; 129:565-569. [PMID: 30634268 DOI: 10.1016/j.foodchem.2011.04.062] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/26/2011] [Accepted: 04/22/2011] [Indexed: 11/26/2022]
Abstract
Discrimination of Chinese rice wines according to ageing time and brand using amino acid profiles was presented in this study. Free amino acids (16) in 98 rice wines were simultaneously determined using high-performance liquid chromatograph-diode array detection (HPLC-DAD). Then the experimental data was subjected to multivariate analysis. Principal component analysis (PCA) was employed to differentiate samples from various ageing times (3, 9, 11 and 15months) and brands ("pagoda", "kuaijishan", and "guyuelongshan"). Partial least square discriminant analysis (PLS-DA) and full (leave-one-out) cross-validation were used to develop classification models. The overall correct classification rate for different ageing times and brands was 99.7% and 94.9%, respectively. The proposed method shows an effective strategy for the detection of mislabelling of rice wines.
Collapse
Affiliation(s)
- Fei Shen
- College of Biosystems Engineering and Food Science, Zhejiang University, 268 Kaixuan Street, Hangzhou 310029, People's Republic of China
| | - Yibin Ying
- College of Biosystems Engineering and Food Science, Zhejiang University, 268 Kaixuan Street, Hangzhou 310029, People's Republic of China.
| | - Bobin Li
- Shaoxing Testing Institute of Quality Technical Supervision, Shaoxing 312071, People's Republic of China
| | - Yunfeng Zheng
- Shaoxing Testing Institute of Quality Technical Supervision, Shaoxing 312071, People's Republic of China
| | - Qing Zhuge
- Shaoxing Testing Institute of Quality Technical Supervision, Shaoxing 312071, People's Republic of China
| |
Collapse
|
53
|
Rappaport SM, Li H, Grigoryan H, Funk WE, Williams ER. Adductomics: characterizing exposures to reactive electrophiles. Toxicol Lett 2011; 213:83-90. [PMID: 21501670 DOI: 10.1016/j.toxlet.2011.04.002] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/04/2011] [Indexed: 01/13/2023]
Abstract
To understand environmental causes of disease, unbiased methods are needed to characterize the human exposome, which represents all toxicants to which people are exposed from both exogenous and endogenous sources. Because they directly modify DNA and important proteins, reactive electrophiles are probably the most important constituents of the exposome. Exposures to reactive electrophiles can be characterized by measuring adducts from reactions between circulating electrophiles and blood nucleophiles. We define an 'adductome' as the totality of such adducts with a given nucleophilic target. Because of their greater abundance and residence times in human blood, adducts of hemoglobin (Hb) and human serum albumin (HSA) are preferable to those of DNA and glutathione for characterizing adductomes. In fact, the nucleophilic hotspot represented by the only free sulfhydryl group in HSA (HSA-Cys(34)) offers particular advantages for adductomic experiments. Although targeted adducts of HSA-Cys(34) have been monitored for decades, an unbiased method has only recently been reported for visualizing the HSA-Cys(34) 'subadductome'. The method relies upon a novel mass spectrometry application, termed fixed-step selected reaction monitoring (FS-SRM), to profile Cys(34) adducts in tryptic digests of HSA. Here, we selectively review the literature regarding the potential of adductomics to partially elucidate the human exposome, with particular attention to the HSA-Cys(34) subadductome.
Collapse
Affiliation(s)
- Stephen M Rappaport
- Center for Exposure Biology, School of Public Health and College of Chemistry, University of California, Berkeley, CA 94720-7356, USA.
| | | | | | | | | |
Collapse
|
54
|
Analysis of polar metabolites by hydrophilic interaction chromatography–MS/MS. Bioanalysis 2011; 3:899-912. [DOI: 10.4155/bio.11.51] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Increasing emphasis has been placed on quantitative characterization of drug metabolites during drug discovery and development. Due to the more polar nature of drug metabolites, quantitative analysis using traditional reversed-phase liquid chromatography tandem mass spectrometry (RPLC–MS/MS) can be quite challenging. As an alternative chromatographic mode, hydrophilic interaction chromatography (HILIC) offers unique advantages for analysis of polar metabolites, providing better retention/separation, higher sensitivity, higher efficiency and potential for ultra-fast analysis to improve throughput. In this article, selected case studies from the authors’ own laboratory, and examples from current literature, will be discussed to demonstrate some practical considerations for method development of HILIC–MS/MS assays. The effectiveness of using HILIC–MS/MS for mitigating analytical challenges associated with quantitation of polar metabolites, including phase I and II metabolites of drugs, as well as endogenous metabolites, will be exhibited.
Collapse
|
55
|
Database searching for structural identification of metabolites in complex biofluids for mass spectrometry-based metabonomics. Bioanalysis 2011; 1:1627-43. [PMID: 21083108 DOI: 10.4155/bio.09.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MS and HPLC are commonly used for compound characterization and obtaining structural information; in the field of metabonomics, these two analytical techniques are often combined to characterize unknown endogenous or exogenous metabolites present in complex biological samples. Since the structures of a majority of these metabolites are not actually identified, the result of most metabonomic studies is a list of m/z values and retention times. However, without knowing actual structures, the biological significance of these 'features' cannot be determined. The process of identifying the structures of unknown compounds can be time intensive, costly and frequently requires the use of multiple orthogonal analytical techniques - this laborious procedure seems insurmountable for the long lists of unknowns that must be identified for each study. In addition, the limited sample volume and the extremely low concentration of most endogenous analytes frequently make purification and identification by other instrumentation nearly impossible. This review is intended to explore the problems and progress with current tools that are available for MS-based structure identification for both endogenous and exogenous metabolites.
Collapse
|
56
|
|
57
|
Kiss A, Jacquet AL, Paisse O, Flament-Waton MM, de Ceaurriz J, Bordes C, Gauvrit JY, Lantéri P, Cren-Olivé C. Urinary signature of anabolic steroids and glucocorticoids in humans by LC–MS. Talanta 2011; 83:1769-73. [DOI: 10.1016/j.talanta.2010.10.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 10/17/2010] [Accepted: 10/26/2010] [Indexed: 10/18/2022]
|
58
|
Roux A, Lison D, Junot C, Heilier JF. Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review. Clin Biochem 2011; 44:119-35. [DOI: 10.1016/j.clinbiochem.2010.08.016] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 01/01/2023]
|
59
|
Li H, Grigoryan H, Funk WE, Lu SS, Rose S, Williams ER, Rappaport SM. Profiling Cys34 adducts of human serum albumin by fixed-step selected reaction monitoring. Mol Cell Proteomics 2010; 10:M110.004606. [PMID: 21193536 DOI: 10.1074/mcp.m110.004606] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A method is described for profiling putative adducts (or other unknown covalent modifications) at the Cys34 locus of human serum albumin (HSA), which represents the preferred reaction site for small electrophilic species in human serum. By comparing profiles of putative HSA-Cys34 adducts across populations of interest it is theoretically possible to explore environmental causes of degenerative diseases and cancer caused by both exogenous and endogenous chemicals. We report a novel application of selected-reaction-monitoring (SRM) mass spectrometry, termed fixed-step SRM (FS-SRM), that allows detection of essentially all HSA-Cys34 modifications over a specified range of mass increases (added masses). After tryptic digestion, HSA-Cys34 adducts are contained in the third largest peptide (T3), which contains 21 amino acids and an average mass of 2433.87 Da. The FS-SRM method does not require that exact masses of T3 adducts be known in advance but rather uses a theoretical list of T3-adduct m/z values separated by a fixed increment of 1.5. In terms of added masses, each triply charged parent ion represents a bin of ±2.3 Da between 9.1 Da and 351.1 Da. Synthetic T3 adducts were used to optimize FS-SRM and to establish screening rules based upon selected b- and y-series fragment ions. An isotopically labeled T3 adduct is added to protein digests to facilitate quantification of putative adducts. We used FS-SRM to generate putative adduct profiles from six archived specimens of HSA that had been pooled by gender, race, and smoking status. An average of 66 putative adduct hits (out of a possible 77) were detected in these samples. Putative adducts covered a wide range of concentrations, were most abundant in the mass range below 100 Da, and were more abundant in smokers than in nonsmokers. With minor modifications, the FS-SRM methodology can be applied to other nucleophilic sites and proteins.
Collapse
Affiliation(s)
- He Li
- Center for Exposure Biology, Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | | | | | | | | | | |
Collapse
|
60
|
Dwivedi P, Schultz AJ, Hill HH. Metabolic Profiling of Human Blood by High Resolution Ion Mobility Mass Spectrometry (IM-MS). INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2010; 298:78-90. [PMID: 21113320 PMCID: PMC2990699 DOI: 10.1016/j.ijms.2010.02.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A high resolution ion mobility time-of-flight mass spectrometer with electrospray ionization source (ESI-IM-MS) was evaluated as an analytical method for rapid analysis of complex biological samples such as human blood metabolome was investigated. The hybrid instrument (IM-MS) provided an average ion mobility resolving power of ~90 and a mass resolution of ~1500 (at m/z 100). A few µL of whole blood was extracted with methanol, centrifuged and infused into the IM-MS via an electrospray ionization source. Upon IM-MS profiling of the human blood metabolome approximately 1,100 metabolite ions were detected and 300 isomeric metabolites separated in short analyses time (30 minutes). Estimated concentration of the metabolites ranged from the low micromolar to the low nanomolar level. Various classes of metabolites (amino acids, organic acids, fatty acids, carbohydrates, purines and pyrimidines etc) were found to form characteristic mobility-mass correlation curves (MMCC) that aided in metabolite identification. Peaks corresponding to various sterol derivatives, estrogen derivatives, phosphocholines, prostaglandins, and cholesterol derivatives detected in the blood extract were found to occupy characteristic two dimensional IM-MS space. Low abundance metabolite peaks that can be lost in MS random noise were resolved from noise peaks by differentiation in mobility space. In addition, the peak capacity of MS increased six fold by coupling IMS prior to MS analysis.
Collapse
Affiliation(s)
- Prabha Dwivedi
- Washington State University, Pullman, WA, 99163 USA
- to whom correspondence should be addressed, () (Phone: 509-335-5648) (Fax: 509-335-8867), () (Phone: 509-335-7752) (Fax: 509-335-8867)
| | | | - Herbert H. Hill
- Washington State University, Pullman, WA, 99163 USA
- to whom correspondence should be addressed, () (Phone: 509-335-5648) (Fax: 509-335-8867), () (Phone: 509-335-7752) (Fax: 509-335-8867)
| |
Collapse
|
61
|
Dwivedi P, Puzon G, Tam M, Langlais D, Jackson S, Kaplan K, Siems WF, Schultz AJ, Xun L, Woods A, Hill HH. Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1383-93. [PMID: 20967735 PMCID: PMC3012737 DOI: 10.1002/jms.1850] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Comprehensive metabolome analysis using mass spectrometry (MS) often results in a complex mass spectrum and difficult data analysis resulting from the signals of numerous small molecules in the metabolome. In addition, MS alone has difficulty measuring isobars and chiral, conformational and structural isomers. When a matrix-assisted laser desorption ionization (MALDI) source is added, the difficulty and complexity are further increased. Signal interference between analyte signals and matrix ion signals produced by MALDI in the low mass region (<1500 Da) cause detection and/or identification of metabolites difficult by MS alone. However, ion mobility spectrometry (IMS) coupled with MS (IM-MS) provides a rapid analytical tool for measuring subtle structural differences in chemicals. IMS separates gas-phase ions based on their size-to-charge ratio. This study, for the first time, reports the application of MALDI to the measurement of small molecules in a biological matrix by ion mobility-time of flight mass spectrometry (IM-TOFMS) and demonstrates the advantage of ion-signal dispersion in the second dimension. Qualitative comparisons between metabolic profiling of the Escherichia coli metabolome by MALDI-TOFMS, MALDI-IM-TOFMS and electrospray ionization (ESI)-IM-TOFMS are reported. Results demonstrate that mobility separation prior to mass analysis increases peak-capacity through added dimensionality in measurement. Mobility separation also allows detection of metabolites in the matrix-ion dominated low-mass range (m/z < 1500 Da) by separating matrix signals from non-matrix signals in mobility space.
Collapse
|
62
|
Djukovic D, Baniasadi HR, Kc R, Hammoud Z, Raftery D. Targeted serum metabolite profiling of nucleosides in esophageal adenocarcinoma. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3057-3062. [PMID: 20872639 DOI: 10.1002/rcm.4739] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleosides are indicators of the whole-body turnover of transfer RNA. Based on the activity of cancer cells these molecules could potentially be used as cancer biomarkers, and several studies have determined that the metabolic levels of nucleosides are significantly altered in cancer patients compared to control groups. Here we report a targeted metabolite investigation of serum nucleosides in esophageal adenocarcinoma specimens. We quantified eight nucleosides using high-performance liquid chromatography/triple quadrupole mass spectrometry (HPLC/TQMS) and determined that the metabolic levels of 1-methyladenosine (p <2.14 × 10(-7)), N(2),N(2)-dimethylguanosine (p <2.78 × 10(-7)), N(2)-methylguanosine (p <2.48 × 10(-6)) and cytidine (p <6.98 × 10(-4)) were significantly elevated while the concentration of uridine (p <3.74 × 10(-3)) was significantly lowered in serum samples from cancer patients compared to those of control group. Our results suggest that nucleosides could potentially serve as useful biomarkers to identify esophageal adenocarcinoma.
Collapse
Affiliation(s)
- Danijel Djukovic
- Department of Chemistry, Purdue University, 506 Oval Dr., W. Lafayette, IN 47906, USA
| | | | | | | | | |
Collapse
|
63
|
Thomas A, Déglon J, Lenglet S, Mach F, Mangin P, Wolfender JL, Steffens S, Staub C. High-Throughput Phospholipidic Fingerprinting by Online Desorption of Dried Spots and Quadrupole-Linear Ion Trap Mass Spectrometry: Evaluation of Atherosclerosis Biomarkers in Mouse Plasma. Anal Chem 2010; 82:6687-6694. [DOI: 10.1021/ac101421b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aurélien Thomas
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - Julien Déglon
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - Sébastien Lenglet
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - François Mach
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - Patrice Mangin
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - Sabine Steffens
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| | - Christian Staub
- Unit of Toxicology, CURML, Geneva University Hospitals, Geneva, Switzerland, Division of Cardiology, Department of Internal Medicine, University Hospital, Foundation for Medical Researches, Geneva, Switzerland, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland, and Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland
| |
Collapse
|
64
|
Beger RD, Sun J, Schnackenberg LK. Metabolomics approaches for discovering biomarkers of drug-induced hepatotoxicity and nephrotoxicity. Toxicol Appl Pharmacol 2010; 243:154-66. [DOI: 10.1016/j.taap.2009.11.019] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/10/2009] [Accepted: 11/13/2009] [Indexed: 12/23/2022]
|
65
|
Kim SH, Kim DH, Park JH, Choi EJ, Park S, Lee KY, Jeon MJ, Kim YC, Sung SH. Discrimination of Scrophularia spp. according to geographic origin with HPLC-DAD combined with multivariate analysis. Microchem J 2010. [DOI: 10.1016/j.microc.2009.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
66
|
Junot C, Madalinski G, Tabet JC, Ezan E. Fourier transform mass spectrometry for metabolome analysis. Analyst 2010; 135:2203-19. [DOI: 10.1039/c0an00021c] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
67
|
Tsukube H, Yano K, Shinoda S. Near-Infrared Luminescence Sensing of Glutamic Acid, Aspartic Acid, and Their Dipeptides with Tris(β-diketonato)lanthanide Probes. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900112] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
68
|
Rubino FM, Pitton M, Di Fabio D, Colombi A. Toward an "omic" physiopathology of reactive chemicals: thirty years of mass spectrometric study of the protein adducts with endogenous and xenobiotic compounds. MASS SPECTROMETRY REVIEWS 2009; 28:725-84. [PMID: 19127566 DOI: 10.1002/mas.20207] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cancer and degenerative diseases are major causes of morbidity and death, derived from the permanent modification of key biopolymers such as DNA and regulatory proteins by usually smaller, reactive molecules, present in the environment or generated from endogenous and xenobiotic components by the body's own biochemical mechanisms (molecular adducts). In particular, protein adducts with organic electrophiles have been studied for more than 30 [see, e.g., Calleman et al., 1978] years essentially for three purposes: (a) as passive monitors of the mean level of individual exposure to specific chemicals, either endogenously present in the human body or to which the subject is exposed through food or environmental contamination; (b) as quantitative indicators of the mean extent of the individual metabolic processing which converts a non-reactive chemical substance into its toxic products able to damage DNA (en route to cancer induction through genotoxic mechanisms) or key proteins (as in the case of several drugs, pesticides or otherwise biologically active substances); (c) to relate the extent of protein modification to that of biological function impairment (such as enzyme inhibition) finally causing the specific health damage. This review describes the role that contemporary mass spectrometry-based approaches employed in the qualitative and quantitative study of protein-electrophile adducts play in the discovery of the (bio)chemical mechanisms of toxic substances and highlights the future directions of research in this field. A particular emphasis is given to the measurement of often high levels of the protein adducts of several industrial and environmental pollutants in unexposed human populations, a phenomenon which highlights the possibility that a number of small organic molecules are generated in the human organism through minor metabolic processes, the imbalance of which may be the cause of "spontaneous" cases of cancer and of other degenerative diseases of still uncharacterized etiology. With all this in mind, it is foreseen that a holistic description of cellular functions will take advantage of new analytical methods based on time-integrated metabolomic measurements of a new biological compartment, the "adductome," aimed at better understanding integrated organism response to environmental and endogenous stressors.
Collapse
Affiliation(s)
- Federico Maria Rubino
- Laboratory for Analytical Toxicology and Metabonomics, Department of Medicine, Surgery and Odontology, Università degli Studi di Milano at Ospedale San Paolo, v. Antonio di Rudinì 8, Milano I-20142, Italy.
| | | | | | | |
Collapse
|
69
|
Chen Y, Zhang R, Song Y, He J, Sun J, Bai J, An Z, Dong L, Zhan Q, Abliz Z. RRLC-MS/MS-based metabonomics combined with in-depth analysis of metabolic correlation network: finding potential biomarkers for breast cancer. Analyst 2009; 134:2003-11. [PMID: 19768207 DOI: 10.1039/b907243h] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A metabonomics strategy based on rapid resolution liquid chromatography/tandem mass spectrometry (RRLC-MS/MS), multivariate statistics and metabolic correlation networks has been implemented to find biologically significant metabolite biomarkers in breast cancer. RRLC-MS/MS analysis by electrospray ionization (ESI) in both positive and negative ion modes was employed to investigate human urine samples. The resulting data matrices were analyzed using multivariate analysis. Application of orthogonal projections to latent structures discriminate analysis (OPLS-DA) allowed us to extract several discriminated metabolites reflecting metabolic characteristics between healthy volunteers and breast cancer patients. Correlation network analysis between these metabolites has been further applied to select more reliable biomarkers. Finally, high resolution MS and MS/MS analyses were performed for the identification of the metabolites of interest. We identified 12 metabolites as potential biomarkers including amino acids, organic acids, and nucleosides. They revealed elevated tryptophan and nucleoside metabolism as well as protein degradation in breast cancer patients. These studies demonstrate the advantages of integrating metabolic correlation networks with metabonomics for finding significant potential biomarkers: this strategy not only helps identify potential biomarkers, it also further confirms these biomarkers and can even provide biochemical insights into changes in breast cancer.
Collapse
Affiliation(s)
- Yanhua Chen
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
70
|
Zhang H, Zhang D, Ray K, Zhu M. Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:999-1016. [PMID: 19598168 DOI: 10.1002/jms.1610] [Citation(s) in RCA: 197] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Identification of drug metabolites by liquid chromatography/mass spectrometry (LC/MS) involves metabolite detection in biological matrixes and structural characterization based on product ion spectra. Traditionally, metabolite detection is accomplished primarily on the basis of predicted molecular masses or fragmentation patterns of metabolites using triple-quadrupole and ion trap mass spectrometers. Recently, a novel mass defect filter (MDF) technique has been developed, which enables high-resolution mass spectrometers to be utilized for detecting both predicted and unexpected drug metabolites based on narrow, well-defined mass defect ranges for these metabolites. This is a new approach that is completely different from, but complementary to, traditional molecular mass- or MS/MS fragmentation-based LC/MS approaches. This article reviews the mass defect patterns of various classes of drug metabolites and the basic principles of the MDF approach. Examples are given on the applications of the MDF technique to the detection of stable and chemically reactive metabolites in vitro and in vivo. Advantages, limitations, and future applications are also discussed on MDF and its combinations with other data mining techniques for the detection and identification of drug metabolites.
Collapse
Affiliation(s)
- Haiying Zhang
- Department of Biotransformation, Bristol-Myers Squibb Research and Development, Princeton, NJ 08543, USA.
| | | | | | | |
Collapse
|
71
|
Jian W, Yao M, Zhang D, Zhu M. Rapid Detection and Characterization of in Vitro and Urinary N-Acetyl-l-cysteine Conjugates Using Quadrupole-Linear Ion Trap Mass Spectrometry and Polarity Switching. Chem Res Toxicol 2009; 22:1246-55. [DOI: 10.1021/tx900035j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenying Jian
- Bioanalysis and Discovery Analytical Research and Biotransforamtion, Pharmaceutical Research and Development, Bristol-Myers Squibb, Princeton, New Jersey 08543
| | - Ming Yao
- Bioanalysis and Discovery Analytical Research and Biotransforamtion, Pharmaceutical Research and Development, Bristol-Myers Squibb, Princeton, New Jersey 08543
| | - Duxi Zhang
- Bioanalysis and Discovery Analytical Research and Biotransforamtion, Pharmaceutical Research and Development, Bristol-Myers Squibb, Princeton, New Jersey 08543
| | - Mingshe Zhu
- Bioanalysis and Discovery Analytical Research and Biotransforamtion, Pharmaceutical Research and Development, Bristol-Myers Squibb, Princeton, New Jersey 08543
| |
Collapse
|
72
|
Metabonomics study of liver cancer based on ultra performance liquid chromatography coupled to mass spectrometry with HILIC and RPLC separations. Anal Chim Acta 2009; 650:3-9. [PMID: 19720165 DOI: 10.1016/j.aca.2009.03.039] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Revised: 02/28/2009] [Accepted: 03/20/2009] [Indexed: 01/28/2023]
Abstract
In this study, urinary metabolites from liver cancer patients and healthy volunteers were studied by a metabonomic method based on ultra performance liquid chromatography coupled to mass spectrometry. Both hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) were used to separate the urinary metabolites. Principle component analysis (PCA) and partial least squares to latent structure-discriminant analysis (PLS-DA) models were built to separate the healthy volunteers from the liver cancer patients and to find compounds that are expressed in significantly different amounts between the two populations. 21 metabolite ions were considered as potential biomarkers according to the Variable importance in the Project (VIP) value and S-plot. Compared with RPLC, a more sensitive and stable response can be recorded in HILIC mode due to the high content of organic solvent used. Moreover, the liver cancer group and the healthy volunteers can be better separated based on the data from the HILIC separation, which indicates that HILIC is suitable for urinary metabonomic analysis. In HILIC mode, several polar compounds related to arginine and proline metabolism, alanine and aspartate metabolism, lysine degradation, nicotinate and nicotinamide metabolism were found to be significantly changed in the concentrations of the two different populations: healthy and cancer. In contrast, in RPLC mode, these changed compounds are related to fatty acids oxidation.
Collapse
|
73
|
Recent advances in applications of liquid chromatography–tandem mass spectrometry to the analysis of reactive drug metabolites. Chem Biol Interact 2009; 179:25-37. [DOI: 10.1016/j.cbi.2008.09.014] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 01/09/2023]
|
74
|
Chapter 3 Applications of Quadrupole-Linear Ion Trap Mass Spectrometry to the Analysis of Reactive Metabolites in Drug Discovery and Development. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1872-0854(09)00003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
75
|
Xiayan L, Legido-Quigley C. Advances in separation science applied to metabonomics. Electrophoresis 2008; 29:3724-36. [PMID: 18850642 DOI: 10.1002/elps.200700851] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Metabonomics focuses on metabolite profile changes in diverse living systems caused by a biological perturbation. These metabolite signatures can be achieved with techniques such as gas chromatography, high-performance liquid chromatography (ultra-high-performance/pressure liquid chromatography and capHPLC), capillary electrophoresis, and capillary electrochromatography normally hyphenated with MS. In this review we present the latest developments of the abovementioned techniques applied in the field of metabonomics, with applications covering phytochemistry, toxicology and clinical research.
Collapse
Affiliation(s)
- Li Xiayan
- Pharmaceutical Sciences Research Division, King's College London, 150 Stamford Street, London, UK
| | | |
Collapse
|
76
|
Fowler BA, Conner EA, Yamauchi H. Proteomic and metabolomic biomarkers for III–V semiconductors: And prospects for application to nano-materials. Toxicol Appl Pharmacol 2008; 233:110-5. [DOI: 10.1016/j.taap.2008.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 11/27/2007] [Indexed: 10/22/2022]
|
77
|
Yao M, Ma L, Humphreys WG, Zhu M. Rapid screening and characterization of drug metabolites using a multiple ion monitoring-dependent MS/MS acquisition method on a hybrid triple quadrupole-linear ion trap mass spectrometer. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1364-1375. [PMID: 18416441 DOI: 10.1002/jms.1412] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A novel LC/MS/MS method that uses multiple ion monitoring (MIM) as a survey scan to trigger the acquisition of enhanced product ions (EPI) on a hybrid quadrupole-linear ion trap mass spectrometer (Q TRAP) was developed for drug metabolite identification. In the MIM experiment, multiple predicted metabolite ions were monitored in both Q1 and Q3. The collision energy in Q2 was set to a low value to minimize fragmentation. Results from analyzing ritonavir metabolites in rat hepatocytes demonstrate that MIM-EPI was capable of targeting a larger number of metabolites regardless of their fragmentation and retained sensitivity and duty cycle similar to multiple reaction monitoring (MRM)-EPI. MIM-based scanning methods were shown to be particularly useful in several applications. First, MIM-EPI enabled the sensitive detection and MS/MS acquisition of up to 100 predicted metabolites. Second, MIM-MRM-EPI was better than MRM-EPI in the analysis of metabolites that undergo either predictable or unpredictable fragmentation pathways. Finally, a combination of MIM-EPI and full-scan MS (EMS), as an alternative to EMS-EPI, was well suited for routine in vitro metabolite profiling. Overall, MIM-EPI significantly enhanced the metabolite identification capability of the hybrid triple quadrupole-linear ion trap LC/MS.
Collapse
Affiliation(s)
- Ming Yao
- Department of Biotransformation, Bristol-Myers Squibb Pharmaceutical Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | | | | | | |
Collapse
|
78
|
Werner E, Heilier JF, Ducruix C, Ezan E, Junot C, Tabet JC. Mass spectrometry for the identification of the discriminating signals from metabolomics: Current status and future trends. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:143-63. [DOI: 10.1016/j.jchromb.2008.07.004] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 06/20/2008] [Accepted: 07/01/2008] [Indexed: 01/18/2023]
|
79
|
Application of ultra-performance LC-TOF MS metabolite profiling techniques to the analysis of medicinal Panax herbs. Metabolomics 2008. [DOI: 10.1007/s11306-008-0115-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
80
|
Huang X, Shao L, Gong Y, Mao Y, Liu C, Qu H, Cheng Y. A metabonomic characterization of CCl4-induced acute liver failure using partial least square regression based on the GC/MS metabolic profiles of plasma in mice. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 870:178-85. [PMID: 18602877 DOI: 10.1016/j.jchromb.2008.05.049] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 04/22/2008] [Accepted: 05/05/2008] [Indexed: 12/19/2022]
Abstract
This work characterized the metabolism disorders of acute liver failure (ALF) induced by carbon tetrachloride (CCl(4)) in a mouse model with different dosage of intoxication (100, 500 and 1000 mg/kg). Metabolic profiles of mice plasma were detected by gas chromatography/mass spectrometry (GC/MS) after chemical derivatization. Here an effective information-extracting approach was implemented on the basis of partial least square regression analysis (PLS-RA). PLS modeling was achieved with two kinds of Y-vectors for the acquired metabonomics data and eight metabolites with different changing behaviors were selected. ALF of mice induced by CCl(4) was characterized by the elevation of glutamate, citrate, serine and threonine, as well as the decrease of alpha-glycerophosphate, docosahexaenoic acid, palmitic acid and oleic acid in plasma. The difference in the concentrations of serine, threonine, palmitic acid and oleic acid remained insignificant between the control and 100mg/kg groups, while significant distinction appeared when comparing the control and two higher dosed groups. The underlying regulation of CCl(4)-perturbed metabolic pathways was discussed according to the selected metabolites. The present study demonstrated a great potential of PLS-RA in exploiting a comprehensive metabolic effects of CCl(4) intoxication and its efficient capability to reveal the hepatotoxic mechanism of ALF induced by reactive oxygen species (ROS).
Collapse
Affiliation(s)
- Xin Huang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | | | | | | | | | | |
Collapse
|
81
|
Wang Y, Wang J, Yao M, Zhao X, Fritsche J, Schmitt-Kopplin P, Cai Z, Wan D, Lu X, Yang S, Gu J, Häring HU, Schleicher ED, Lehmann R, Xu G. Metabonomics Study on the Effects of the Ginsenoside Rg3 in a β-Cyclodextrin-Based Formulation on Tumor-Bearing Rats by a Fully Automatic Hydrophilic Interaction/Reversed-Phase Column-Switching HPLC−ESI-MS Approach. Anal Chem 2008; 80:4680-8. [DOI: 10.1021/ac8002402] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yuan Wang
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Jiangshan Wang
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Ming Yao
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Xinjie Zhao
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Jens Fritsche
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Philippe Schmitt-Kopplin
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Zongwei Cai
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Dafang Wan
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Xin Lu
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Shengli Yang
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Jianren Gu
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Hans Ulrich Häring
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Erwin D. Schleicher
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Rainer Lehmann
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| | - Guowang Xu
- National Chromatography Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 16023 Dalian, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, 200032 Shanghai, China, Immatics Biotechnologies GmbH, 72076 Tuebingen, Germany, Helmholtz-Zentrum Muenchen—German Research Center for Environmental Health, Institute for Ecological Chemistry, Ingoldstaedter Landstrasse 1 D-85764 Neuherberg, Germany,
| |
Collapse
|
82
|
Madalinski G, Godat E, Alves S, Lesage D, Genin E, Levi P, Labarre J, Tabet JC, Ezan E, Junot C. Direct Introduction of Biological Samples into a LTQ-Orbitrap Hybrid Mass Spectrometer as a Tool for Fast Metabolome Analysis. Anal Chem 2008; 80:3291-303. [DOI: 10.1021/ac7024915] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
83
|
Guy PA, Tavazzi I, Bruce SJ, Ramadan Z, Kochhar S. Global metabolic profiling analysis on human urine by UPLC-TOFMS: issues and method validation in nutritional metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:253-60. [PMID: 18490203 DOI: 10.1016/j.jchromb.2008.04.034] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 04/07/2008] [Accepted: 04/13/2008] [Indexed: 11/26/2022]
Abstract
Optimisation and method validation was assessed here for metabolic profiling analysis of urine samples using UPLC-TOFMS. A longer run time of 31 min revealed greater reproducibility, and the higher number of variables was identified as compared to shortened run times (10 and 26 min). We have also implemented two QC urine samples enabling the assessment of the quality and reproducibility of the data generated during the whole analytical workflow (retention time drift, mass precision and fluctuation of the ion responses over time). Based on the QC data, suitable standards for ensuring consistent analytical results for metabolomics applications using the UPLC-MS techniques are recommended.
Collapse
Affiliation(s)
- Philippe A Guy
- BioAnalytical Science Department, Nestlé Research Center, P.O. Box 44, Vers-chez-les Blanc, 1000 Lausanne 26, Switzerland.
| | | | | | | | | |
Collapse
|
84
|
Sun J, Schnackenberg LK, Holland RD, Schmitt TC, Cantor GH, Dragan YP, Beger RD. Metabonomics evaluation of urine from rats given acute and chronic doses of acetaminophen using NMR and UPLC/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:328-40. [PMID: 18472313 DOI: 10.1016/j.jchromb.2008.04.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 04/08/2008] [Accepted: 04/09/2008] [Indexed: 01/26/2023]
Abstract
Urinary metabolic perturbations associated with acute and chronic acetaminophen-induced hepatotoxicity were investigated using nuclear magnetic resonance (NMR) spectroscopy and ultra performance liquid chromatography/mass spectrometry (UPLC/MS) metabonomics approaches to determine biomarkers of hepatotoxicity. Acute and chronic doses of acetaminophen (APAP) were administered to male Sprague-Dawley rats. NMR and UPLC/MS were able to detect both drug metabolites and endogenous metabolites simultaneously. The principal component analysis (PCA) of NMR or UPLC/MS spectra showed that metabolic changes observed in both acute and chronic dosing of acetaminophen were similar. Histopathology and clinical chemistry studies were performed and correlated well with the PCA analysis and magnitude of metabolite changes. Depletion of antioxidants (e.g. ferulic acid), trigonelline, S-adenosyl-L-methionine, and energy-related metabolites indicated that oxidative stress was caused by acute and chronic acetaminophen administration. Similar patterns of metabolic changes in response to acute or chronic dosing suggest similar detoxification and recovery mechanisms following APAP administration.
Collapse
Affiliation(s)
- Jinchun Sun
- Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
| | | | | | | | | | | | | |
Collapse
|
85
|
Theodoridis G, Gika HG, Wilson ID. LC-MS-based methodology for global metabolite profiling in metabonomics/metabolomics. Trends Analyt Chem 2008. [DOI: 10.1016/j.trac.2008.01.008] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
86
|
Aristolochic acid induced changes in the metabolic profile of rat urine. J Pharm Biomed Anal 2008; 46:757-62. [DOI: 10.1016/j.jpba.2007.11.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 11/27/2007] [Accepted: 11/27/2007] [Indexed: 11/18/2022]
|
87
|
Kellert M, Wagner S, Lutz U, Lutz WK. Biomarkers of Furan Exposure by Metabolic Profiling of Rat Urine with Liquid Chromatography-Tandem Mass Spectrometry and Principal Component Analysis. Chem Res Toxicol 2008; 21:761-8. [DOI: 10.1021/tx7004212] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Kellert
- Department of Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
| | - Silvia Wagner
- Department of Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
| | - Ursula Lutz
- Department of Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
| | - Werner K. Lutz
- Department of Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
| |
Collapse
|
88
|
Chen J, Zhao X, Fritsche J, Yin P, Schmitt-Kopplin P, Wang W, Lu X, Häring HU, Schleicher ED, Lehmann R, Xu G. Practical Approach for the Identification and Isomer Elucidation of Biomarkers Detected in a Metabonomic Study for the Discovery of Individuals at Risk for Diabetes by Integrating the Chromatographic and Mass Spectrometric Information. Anal Chem 2008; 80:1280-9. [DOI: 10.1021/ac702089h] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jing Chen
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Xinjie Zhao
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Jens Fritsche
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Peiyuan Yin
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Philippe Schmitt-Kopplin
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Wenzhao Wang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Xin Lu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Hans Ulrich Häring
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Erwin D. Schleicher
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Rainer Lehmann
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| | - Guowang Xu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China, Division of Clinical Chemistry and Pathobiochemistry, Central Laboratory, University Hospital Tuebingen, D-72076 Tuebingen, Germany, GSF-National Research Center for Environment and Health, Institute for Ecological Chemistry, Ingoldstädter Landstrasse 1, D-85764 Neuherberg, Germany, and Department of Internal Medicine 4, University Hospital Tubingen, D-72076 Tubingen, Germany
| |
Collapse
|
89
|
Lu X, Xu G. LC-MS Metabonomics Methodology in Biomarker Discovery. BIOMARKER METHODS IN DRUG DISCOVERY AND DEVELOPMENT 2008. [DOI: 10.1007/978-1-59745-463-6_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
90
|
Chan W, Lee KC, Liu N, Wong RNS, Liu H, Cai Z. Liquid chromatography/mass spectrometry for metabonomics investigation of the biochemical effects induced by aristolochic acid in rats: the use of information-dependent acquisition for biomarker identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:873-880. [PMID: 18288688 DOI: 10.1002/rcm.3438] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The toxic effects of oral administrations of nephrotoxic and carcinogenic aristolochic acid (AA) to male Sprague-Dawley rats were investigated by using high-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometer. Analysis of the urine and plasma samples revealed distinct changes in the biochemical patterns in the AA-dosed rats. After peak finding and alignment, principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) were used for multivariate data analysis. Potential biomarkers were studied by high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses. The MS/MS spectra of all endogenous metabolites satisfying the pre-defined criteria were acquired in a single information-dependent acquisition (IDA) analysis, demonstrating that IDA was an efficient approach for structural elucidation in metabonomic studies. Citric acid and a glucuronide-containing metabolite were observed as potential biomarkers in rat urine. A significant increase in plasma creatinine concentration was also observed in the AA-dosed rats, which indicated that AA induced an adverse effect on the renal clearance function.
Collapse
Affiliation(s)
- Wan Chan
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | | | | | | | | | | |
Collapse
|
91
|
LC-MS-based metabonomics analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 866:64-76. [PMID: 17983864 DOI: 10.1016/j.jchromb.2007.10.022] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/15/2007] [Accepted: 10/16/2007] [Indexed: 02/07/2023]
Abstract
Metabonomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. It has shown particular promise in the areas of toxicology and drug development, functional genomics, systems biology, and clinical diagnosis. Comprehensive metabonomics investigations are primarily a challenge for analytical chemistry. High-performance liquid chromatography-mass spectrometry (HPLC-MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its main advantages include wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing HPLC-MS for metabonomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, the strategy and application of HPLC-MS-based metabonomics are reviewed.
Collapse
|
92
|
Shanaiah N, Desilva MA, Nagana Gowda GA, Raftery MA, Hainline BE, Raftery D. Class selection of amino acid metabolites in body fluids using chemical derivatization and their enhanced 13C NMR. Proc Natl Acad Sci U S A 2007; 104:11540-4. [PMID: 17606902 PMCID: PMC1913896 DOI: 10.1073/pnas.0704449104] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report a chemical derivatization method that selects a class of metabolites from a complex mixture and enhances their detection by 13C NMR. Acetylation of amines directly in aqueous medium with 1,1'-13C(2) acetic anhydride is a simple method that creates a high sensitivity and quantitative label in complex biofluids with minimal sample pretreatment. Detection using either 1D or 2D 13C NMR experiments produces highly resolved spectra with improved sensitivity. Experiments to identify and compare amino acids and related metabolites in normal human urine and serum samples as well as in urine from patients with the inborn errors of metabolism tyrosinemia type II, argininosuccinic aciduria, homocystinuria, and phenylketonuria demonstrate the method. The use of metabolite derivatization and 13C NMR spectroscopy produces data suitable for metabolite profiling analysis of biofluids on a time scale that allows routine use. Extension of this approach to enhance the NMR detection of other classes of metabolites has also been accomplished. The improved detection of low-concentration metabolites shown here creates opportunities to improve the understanding of the biological processes and develop improved disease detection methodologies.
Collapse
Affiliation(s)
| | - M. Aruni Desilva
- *Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907; and
| | - G. A. Nagana Gowda
- *Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907; and
| | - Michael A. Raftery
- *Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907; and
| | - Bryan E. Hainline
- Department of Pediatrics, Section of Pediatric Metabolism and Genetics, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Daniel Raftery
- *Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907; and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
93
|
Orhan H. Analyses of representative biomarkers of exposure and effect by chromatographic, mass spectrometric, and nuclear magnetic resonance techniques: method development and application in life sciences. J Sep Sci 2007; 30:149-74. [PMID: 17390611 DOI: 10.1002/jssc.200600322] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Biomarkers are essential tools in monitoring studies, which include environmental monitoring, biological monitoring, biological effect monitoring, and health surveillance, as well as drug development processes. Their discovery, validation, and analysis require highly sensitive and selective analytical technologies. In this regard, gas and liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy have facilitated great achievements in all these areas. In addition and closely related to biomarkers, the ongoing developments in these techniques promise a better understanding of the nature and mechanisms of toxic effects originating from various chemical, biological, or physical sources. This Review compiles studies performed on selected biomarkers with respect to both method development and application. Section 1 summarizes the concept of biomarkers; their application in various industrial/occupational, agricultural, drug developmental, and medical/clinical platforms. This section also focuses on biotransformation studies in close relation to biomarker discovery and validation, and on major techniques utilized in this area. In Section 2, biotransformation of volatile anesthetics in humans with a focus on mercapturic acid derivatives as potential biomarkers of effect is reviewed. The use of GC-ECD, GC/MS, and 19F-NMR in these studies is described. Section 3 focuses on the analysis of aldehydic lipid peroxidation degradation products by GC-ECD in mammalian cells in which oxidative stress induced chemically, and in humans after various challenges; anesthetic exposure, ischemia-reperfusion, and controlled endurance exercise. In Section 4, method development for protein and DNA oxidation products by LC-tandem MS and its application in mammalian cells and in humans are summarized. Possibilities, limitations, and future perspectives are discussed in Section 5.
Collapse
Affiliation(s)
- Hilmi Orhan
- Department of Toxicology, Faculty of Pharmacy, Ege University, 35100 Bornova-Izmir, Turkey.
| |
Collapse
|
94
|
Abstract
We provide an overview of how the underlying philosophy of chemometrics is integrated throughout metabonomic studies. Four steps are demonstrated: (1) definition of the aim, (2) selection of objects, (3) sample preparation and characterization, and (4) evaluation of the collected data. This includes the tools applied for linear modeling, for example, Statistical Experimental Design (SED), Principal Component Analysis (PCA), Partial least-squares (PLS), Orthogonal-PLS (OPLS), and dynamic extensions thereof. This is illustrated by examples from the literature.
Collapse
Affiliation(s)
- Johan Trygg
- Research Group for Chemometrics, Institute of Chemistry, Umeå University, Sweden
| | | | | |
Collapse
|
95
|
Abstract
To perform metabonomics investigations, it is necessary to generate comprehensive metabolite profiles for complex samples such as biofluids and tissue/tissue extracts. Analytical technologies that can be used to achieve this aim are constantly evolving, and new developments are changing the way in which such profiles' metabolite profiles can be generated. Here, the utility of various analytical techniques for global metabolite profiling, such as, e.g., 1H NMR, MS, HPLC-MS, and GC-MS, are explored and compared.
Collapse
Affiliation(s)
- Eva Maria Lenz
- Department of Drug Metabolism and Pharmacokinetics, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | | |
Collapse
|
96
|
Wagner S, Scholz K, Sieber M, Kellert M, Voelkel W. Tools in Metabonomics: An Integrated Validation Approach for LC-MS Metabolic Profiling of Mercapturic Acids in Human Urine. Anal Chem 2007; 79:2918-26. [PMID: 17315979 DOI: 10.1021/ac062153w] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While for 1H NMR techniques there already exist common analytical and reporting standards, this does not apply to LC-MS metabolic profiling approaches. These standards are the more recommended when applying metabonomics to human biofluids, particularly urine samples, due to the high degree of biological variation compared to animals. A control study was performed, and urine samples of 30 healthy male and female human subjects were collected at intervals of 8 h twice a day for three consecutive days. Using selective multiple reaction monitoring in combination with a column-switching tool for the analysis of the mercapturate pattern, samples were screened for time and gender differences, the most common confounders. Data preprocessing parameters, alignment, scaling to internal standards, and normalization techniques were optimized by PCA, PLS-DA, and OPLS models. Great care was taken in the validation process of both analytical and chemometric protocols. Additionally, a problem of LC-MS, the combination of "different-batch" data to "one-batch" data could be solved by a batchwise scaling procedure. Based on these results, the use of metabolic profiling via mercapturates will be feasible for the detection of disease or toxicity markers in the future since mercapturates are important biomarkers of reactive metabolites known to be involved in many toxic processes.
Collapse
Affiliation(s)
- Silvia Wagner
- Department of Toxicology, University of Wuerzburg, Versbacher Strasse 9, Wuerzburg, Germany
| | | | | | | | | |
Collapse
|
97
|
Pan Z, Raftery D. Comparing and combining NMR spectroscopy and mass spectrometry in metabolomics. Anal Bioanal Chem 2007; 387:525-7. [PMID: 16955259 DOI: 10.1007/s00216-006-0687-8] [Citation(s) in RCA: 289] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhengzheng Pan
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | | |
Collapse
|
98
|
Gu H, Chen H, Pan Z, Jackson AU, Talaty N, Xi B, Kissinger C, Duda C, Mann D, Raftery D, Cooks RG. Monitoring Diet Effects via Biofluids and Their Implications for Metabolomics Studies. Anal Chem 2007; 79:89-97. [PMID: 17194125 DOI: 10.1021/ac060946c] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of diet on metabolites found in rat urine samples has been investigated using nuclear magnetic resonance (NMR) and a new ambient ionization mass spectrometry experiment, extractive electrospray ionization mass spectrometry (EESI-MS). Urine samples from rats with three different dietary regimens were readily distinguished using multivariate statistical analysis on metabolites detected by NMR and MS. To observe the effect of diet on metabolic pathways, metabolites related to specific pathways were also investigated using multivariate statistical analysis. Discrimination is increased by making observations on restricted compound sets. Changes in diet at 24-h intervals led to predictable changes in the spectral data. Principal component analysis was used to separate the rats into groups according to their different dietary regimens using the full NMR, EESI-MS data or restricted sets of peaks in the mass spectra corresponding only to metabolites found in the urea cycle and metabolism of amino groups pathway. By contrast, multivariate analysis of variance from the score plots showed that metabolites of purine metabolism obscure the classification relative to the full metabolite set. These results suggest that it may be possible to reduce the number of statistical variables used by monitoring the biochemical variability of particular pathways. It should also be possible by this procedure to reduce the effect of diet in the biofluid samples for such purposes as disease detection.
Collapse
Affiliation(s)
- Haiwei Gu
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
99
|
Sangster TP, Wingate JE, Burton L, Teichert F, Wilson ID. Investigation of analytical variation in metabonomic analysis using liquid chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:2965-70. [PMID: 17680628 DOI: 10.1002/rcm.3164] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Sources of analytical variation in high-performance liquid chromatography/mass spectrometry (HPLC/MS), such as changes in retention, mass accuracy or signal intensity, have been investigated to assess their importance as a variable in the metabonomic analysis of human urine. In this study chromatographic retention and mass accuracy were found to be quite reproducible with the most significant source of analytical variation in the data sets obtained being the result of changes in detector response. Depending on the signal intensity threshold used to define the presence of a peak a sample component could be present in some replicate injections and absent in others within the same run. The implementation of a more sophisticated data software analysis package was found to greatly reduce the impact of detector response variability resulting in improved data analysis.
Collapse
Affiliation(s)
- Tim P Sangster
- Huntingdon Life Science, East Millstone, NJ 08875-2360, USA.
| | | | | | | | | |
Collapse
|
100
|
Chan ECY, Yap SL, Lau AJ, Leow PC, Toh DF, Koh HL. Ultra-performance liquid chromatography/time-of-flight mass spectrometry based metabolomics of raw and steamed Panax notoginseng. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:519-28. [PMID: 17238214 DOI: 10.1002/rcm.2864] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
At present, metabolite profiling is of growing importance in herbal medicine fields such as breeding, formulation, quality control and clinical trials. This preliminary study indicated that ultra-performance liquid chromatography/time-of-flight mass spectrometry (UPLC/TOFMS)-based metabolomics allows direct detection of down-stream derivatives of metabolites, arising from the herbal formulation process. This analytical approach allows the discrimination and tentative authentication of unique biomarkers related to different herbal extracts using unsupervised multivariate principal component analysis (PCA). The tentative identification of biomarkers is complemented significantly by the accurate mass measurement of TOFMS and the high resolution and high retention time reproducibility rendered by UPLC. The application of this approach in herbal extract discrimination and ginsenoside biomarker discovery of raw and steamed Panax notoginseng (Burk.) F.H. Chen is demonstrated and discussed.
Collapse
Affiliation(s)
- Eric C Y Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore.
| | | | | | | | | | | |
Collapse
|