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Mazur DM, Artaev VB, Lebedev AT. GC × GC-HRMS with complementary ionization methods in the suspect screening analysis of fragrance allergens: overwhelming or justified? Anal Bioanal Chem 2024; 416:4987-4997. [PMID: 39001903 DOI: 10.1007/s00216-024-05436-0] [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: 05/07/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
Modern gas chromatography-mass spectrometry (GC-MS) allows for the analysis of complex samples, such as fragrances. However, identifying all the constituents in natural fragrance mixtures, especially allergens that need to be listed on product labels, is a significant challenge. This is primarily due to the high complexity of the sample and the fact that electron ionization, the most commonly used ionization method in GC-MS, produces numerous nonspecific fragment ions, often resulting in the absence or very low abundance of the molecular ion. These factors affect confidence in assigning the analyte. In this study, we demonstrate that the combination of GC × GC separation, with high mass resolution and accurate mass measurements, as well as chemical ionization in addition to traditional electron ionization, becomes an efficient tool for reliable qualitative analysis of a mixture containing 100 fragrance allergens, even when many of them are closely related species or isomers. The proposed approach expands the applicability of the comprehensive GC × GC-HRMS method, which includes complementary ionization techniques, from studies on anthropogenic priority pollutants and emerging contaminants to the analysis of natural products. Although targeted qualitative and quantitative analysis of allergens in the modern laboratories is well organized, GC × GC-HRMS, being a useful complement to routine quality control of volatile allergens in fragrances, definitely gives an additional contribution to the analytical cases when conventional 1D-GC-MS faces some problems or uncertainties.
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Affiliation(s)
- Dmitrii M Mazur
- Department of Materials Science, MSU-BIT University, Shenzhen, 517182, China
| | | | - Albert T Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen, 517182, China.
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2
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Siddiqui MU, Sibtain M, Ahmad F, Zushi Y, Nabi D. Screening Disinfection Byproducts in Arid-Coastal Wastewater: A Workflow Using GC×GC-TOFMS, Passive Sampling, and NMF Deconvolution Algorithm. J Xenobiot 2024; 14:554-574. [PMID: 38804286 PMCID: PMC11130967 DOI: 10.3390/jox14020033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024] Open
Abstract
Disinfection during tertiary municipal wastewater treatment is a necessary step to control the spread of pathogens; unfortunately, it also gives rise to numerous disinfection byproducts (DBPs), only a few of which are regulated because of the analytical challenges associated with the vast number of potential DBPs. This study utilized polydimethylsiloxane (PDMS) passive samplers, comprehensive two-dimensional gas chromatography (GC×GC) coupled with time-of-flight mass spectrometry (TOFMS), and non-negative matrix factorization (NMF) spectral deconvolution for suspect screening of DBPs in treated wastewater. PDMS samplers were deployed upstream and downstream of the chlorination unit in a municipal wastewater treatment plant located in Abu Dhabi, and their extracts were analyzed using GC×GC-TOFMS. A workflow incorporating a multi-tiered, eight-filter screening process was developed, which successfully enabled the reliable isolation of 22 candidate DBPs from thousands of peaks. The NMF spectral deconvolution improved the match factor score of unknown mass spectra to the reference mass spectra available in the NIST library by 17% and facilitated the identification of seven additional DBPs. The close match of the first-dimension retention index data and the GC×GC elution patterns of DBPs, both predicted using the Abraham solvation model, with their respective experimental counterparts-with the measured data available in the NIST WebBook and the GC×GC elution patterns being those observed for the candidate peaks-significantly enhanced the accuracy of peak assignment. Isotopic pattern analysis revealed a close correspondence for 11 DBPs with clearly visible isotopologues in reference spectra, thereby further strengthening the confidence in the peak assignment of these DBPs. Brominated analogues were prevalent among the detected DBPs, possibly due to seawater intrusion. The fate, behavior, persistence, and toxicity of tentatively identified DBPs were assessed using EPI Suite™ and the CompTox Chemicals Dashboard. This revealed their significant toxicity to aquatic organisms, including developmental, mutagenic, and endocrine-disrupting effects in certain DBPs. Some DBPs also showed activity in various CompTox bioassays, implicating them in adverse molecular pathways. Additionally, 11 DBPs demonstrated high environmental persistence and resistance to biodegradation. This combined approach offers a powerful tool for future research and environmental monitoring, enabling accurate identification and assessment of DBPs and their potential risks.
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Affiliation(s)
- Muhammad Usman Siddiqui
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad 48000, Pakistan
| | - Muhammad Sibtain
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad 48000, Pakistan
| | - Farrukh Ahmad
- BioEnergy & Environmental Laboratory (BEEL), Masdar Institute Campus, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- California Environmental Protection Agency, Cypress, CA 90630, USA
| | - Yasuyuki Zushi
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8569, Ibaraki, Japan
| | - Deedar Nabi
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad 48000, Pakistan
- BioEnergy & Environmental Laboratory (BEEL), Masdar Institute Campus, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148 Kiel, Germany
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3
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Lang G, Henao C, Almstetter M, Arndt D, Goujon C, Maeder S. Non-targeted analytical comparison of a heated tobacco product aerosol against mainstream cigarette smoke: does heating tobacco produce an inherently different set of aerosol constituents? Anal Bioanal Chem 2024; 416:1349-1361. [PMID: 38217698 PMCID: PMC10861380 DOI: 10.1007/s00216-024-05126-x] [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: 11/08/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Smoking-related diseases remain a significant public health concern, and heated tobacco products (HTPs) have emerged as a potential alternative to cigarettes. While several studies have confirmed that HTP aerosols contain lower levels of harmful and potentially harmful constituents (HPHCs) than cigarette smoke, less is known about constituents that are intrinsically higher in HTP aerosols. This study provides a comprehensive comparative assessment of an HTP aerosol produced with Tobacco Heating System 2.2 (THS) and comparator cigarette (CC) smoke aiming at identifying all unique or increased compounds in THS aerosol by applying a broad set of LC-MS and GC × GC-MS methods. To focus on differences due to heating versus burning tobacco, confounding factors were minimized by using the same tobacco in both test items and not adding flavorants. Of all analytical features, only 3.5%-corresponding to 31 distinctive compounds-were significantly more abundant in THS aerosol than in CC smoke. A notable subset of these compounds was identified as reaction products of glycerol. The only compound unique to THS aerosol was traced back to its presence in a non-tobacco material in the test item and not a direct product of heating tobacco. Our results demonstrate that heating a glycerol-containing tobacco substrate to the temperatures applied in THS does not introduce new compounds in the resulting aerosol compared to CC smoke which are detectable with the method portfolio applied in this study. Overall, this study contributes to a better understanding of the chemical composition of HTP aerosols and their potential impact on human health.
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Affiliation(s)
- Gerhard Lang
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Carlos Henao
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Martin Almstetter
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Daniel Arndt
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Catherine Goujon
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Serge Maeder
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
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4
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Demicheva E, Dordiuk V, Polanco Espino F, Ushenin K, Aboushanab S, Shevyrin V, Buhler A, Mukhlynina E, Solovyova O, Danilova I, Kovaleva E. Advances in Mass Spectrometry-Based Blood Metabolomics Profiling for Non-Cancer Diseases: A Comprehensive Review. Metabolites 2024; 14:54. [PMID: 38248857 PMCID: PMC10820779 DOI: 10.3390/metabo14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Blood metabolomics profiling using mass spectrometry has emerged as a powerful approach for investigating non-cancer diseases and understanding their underlying metabolic alterations. Blood, as a readily accessible physiological fluid, contains a diverse repertoire of metabolites derived from various physiological systems. Mass spectrometry offers a universal and precise analytical platform for the comprehensive analysis of blood metabolites, encompassing proteins, lipids, peptides, glycans, and immunoglobulins. In this comprehensive review, we present an overview of the research landscape in mass spectrometry-based blood metabolomics profiling. While the field of metabolomics research is primarily focused on cancer, this review specifically highlights studies related to non-cancer diseases, aiming to bring attention to valuable research that often remains overshadowed. Employing natural language processing methods, we processed 507 articles to provide insights into the application of metabolomic studies for specific diseases and physiological systems. The review encompasses a wide range of non-cancer diseases, with emphasis on cardiovascular disease, reproductive disease, diabetes, inflammation, and immunodeficiency states. By analyzing blood samples, researchers gain valuable insights into the metabolic perturbations associated with these diseases, potentially leading to the identification of novel biomarkers and the development of personalized therapeutic approaches. Furthermore, we provide a comprehensive overview of various mass spectrometry approaches utilized in blood metabolomics research, including GC-MS, LC-MS, and others discussing their advantages and limitations. To enhance the scope, we propose including recent review articles supporting the applicability of GC×GC-MS for metabolomics-based studies. This addition will contribute to a more exhaustive understanding of the available analytical techniques. The Integration of mass spectrometry-based blood profiling into clinical practice holds promise for improving disease diagnosis, treatment monitoring, and patient outcomes. By unraveling the complex metabolic alterations associated with non-cancer diseases, researchers and healthcare professionals can pave the way for precision medicine and personalized therapeutic interventions. Continuous advancements in mass spectrometry technology and data analysis methods will further enhance the potential of blood metabolomics profiling in non-cancer diseases, facilitating its translation from the laboratory to routine clinical application.
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Affiliation(s)
- Ekaterina Demicheva
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Vladislav Dordiuk
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Fernando Polanco Espino
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Konstantin Ushenin
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Autonomous Non-Profit Organization Artificial Intelligence Research Institute (AIRI), Moscow 105064, Russia
| | - Saied Aboushanab
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
| | - Vadim Shevyrin
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
| | - Aleksey Buhler
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Elena Mukhlynina
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Olga Solovyova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Irina Danilova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Elena Kovaleva
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
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Ray R, Rakesh A, Singh S, Madhyastha H, Mani NK. Hair and Nail-On-Chip for Bioinspired Microfluidic Device Fabrication and Biomarker Detection. Crit Rev Anal Chem 2023:1-27. [PMID: 38133962 DOI: 10.1080/10408347.2023.2291825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The advent of biosensors has tremendously increased our potential of identifying and solving important problems in various domains, ranging from food safety and environmental analysis, to healthcare and medicine. However, one of the most prominent drawbacks of these technologies, especially in the biomedical field, is to employ conventional samples, such as blood, urine, tissue extracts and other body fluids for analysis, which suffer from the drawbacks of invasiveness, discomfort, and high costs encountered in transportation and storage, thereby hindering these products to be applied for point-of-care testing that has garnered substantial attention in recent years. Therefore, through this review, we emphasize for the first time, the applications of switching over to noninvasive sampling techniques involving hair and nails that not only circumvent most of the aforementioned limitations, but also serve as interesting alternatives in understanding the human physiology involving minimal costs, equipment and human interference when combined with rapidly advancing technologies, such as microfluidics and organ-on-a-chip to achieve miniaturization on an unprecedented scale. The coalescence between these two fields has not only led to the fabrication of novel microdevices involving hair and nails, but also function as robust biosensors for the detection of biomarkers, chemicals, metabolites and nucleic acids through noninvasive sampling. Finally, we have also elucidated a plethora of futuristic innovations that could be incorporated in such devices, such as expanding their applications in nail and hair-based drug delivery, their potential in serving as next-generation wearable sensors and integrating these devices with machine-learning for enhanced automation and decentralization.
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Affiliation(s)
- Rohitraj Ray
- Department of Bioengineering (BE), Indian Institute of Science Bangalore, Bengaluru, Karnataka, India
| | - Amith Rakesh
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India
| | - Sheetal Singh
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Naresh Kumar Mani
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India
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6
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Chien HJ, Zheng YF, Wang WC, Kuo CY, Hsu YM, Lai CC. Determination of adulteration, geographical origins, and species of food by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2273-2323. [PMID: 35652168 DOI: 10.1002/mas.21780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Food adulteration, mislabeling, and fraud, are rising global issues. Therefore, a number of precise and reliable analytical instruments and approaches have been proposed to ensure the authenticity and accurate labeling of food and food products by confirming that the constituents of foodstuffs are of the kind and quality claimed by the seller and manufacturer. Traditional techniques (e.g., genomics-based methods) are still in use; however, emerging approaches like mass spectrometry (MS)-based technologies are being actively developed to supplement or supersede current methods for authentication of a variety of food commodities and products. This review provides a critical assessment of recent advances in food authentication, including MS-based metabolomics, proteomics and other approaches.
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Affiliation(s)
- Han-Ju Chien
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Feng Zheng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ming Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center For Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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7
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An H, Liu J, Chen Y, Huang Y, Chen J, Liu Z, Li S, Huang J. Characterization of key volatile compounds in jasmine tea infusion with different amount of flowers. Food Chem X 2023; 19:100750. [PMID: 37780321 PMCID: PMC10534111 DOI: 10.1016/j.fochx.2023.100750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 10/03/2023] Open
Abstract
The quality of jasmine tea is related to the volatiles of its infusion. In this study, the volatiles of jasmine tea infusion were extracted under the optimal conditions with a 50/30 μm DVB/CAR/PDMS fiber, tea/water ratio of 1:25 and extraction time of 5 min. A total of 204 volatiles were analyzed by comprehensive two-dimensional gas chromatography-quadrupole time-of-flight mass spectrometry (GC × GC-Q-TOF-MS). Twenty-five compounds were identified as the key volatile compounds by fold change (FC), orthogonal partial least squares discriminant analysis (OPLS-DA), and two-way orthogonal partial least squares analysis (O2PLS). Then optimal amount of flowers (80%-120%) was obtained by the equation describing key volatiles and quality of jasmine tea infusion. And 80% amount of flowers was more appropriate considering the production cost and more pleasant taste. This study laid a foundation for the extraction and research of volatiles of tea infusion and guided the reasonable amount of flowers to produce jasmine tea.
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Affiliation(s)
- Huimin An
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
| | - Jiashun Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
| | - Yuan Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
| | - Yiwen Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
| | - Jinhua Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Hunan Co - Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Zhonghua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Hunan Co - Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Shi Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Hunan Co - Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Jianan Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Hunan Co - Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
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Haertl T, Owsienko D, Schwinn L, Hirsch C, Eskofier BM, Lang R, Wirtz S, Loos HM. Exploring the interrelationship between the skin microbiome and skin volatiles: A pilot study. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1107463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Unravelling the interplay between a human’s microbiome and physiology is a relevant task for understanding the principles underlying human health and disease. With regard to human chemical communication, it is of interest to elucidate the role of the microbiome in shaping or generating volatiles emitted from the human body. In this study, we characterized the microbiome and volatile organic compounds (VOCs) sampled from the neck and axilla of ten participants (five male, five female) on two sampling days, by applying different methodological approaches. Volatiles emitted from the respective skin site were collected for 20 min using textile sampling material and analyzed on two analytical columns with varying polarity of the stationary phase. Microbiome samples were analyzed by a culture approach coupled with MALDI-TOF-MS analysis and a 16S ribosomal RNA gene (16S RNA) sequencing approach. Statistical and advanced data analysis methods revealed that classification of body sites was possible by using VOC and microbiome data sets. Higher classification accuracy was achieved by combination of both data pools. Cutibacterium, Staphylococcus, Micrococcus, Streptococcus, Lawsonella, Anaerococcus, and Corynebacterium species were found to contribute to classification of the body sites by the microbiome. Alkanes, esters, ethers, ketones, aldehydes and cyclic structures were used by the classifier when VOC data were considered. The interdisciplinary methodological platform developed here will enable further investigations of skin microbiome and skin VOCs alterations in physiological and pathological conditions.
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Duangkumpha K, Jariyasopit N, Wanichthanarak K, Dhakal E, Wisanpitayakorn P, Thotsiri S, Sirivatanauksorn Y, Kitiyakara C, Sathirapongsasuti N, Khoomrung S. GC × GC-TOFMS metabolomics analysis identifies elevated levels of plasma sugars and sugar alcohols in diabetic mellitus patients with kidney failure. J Biol Chem 2022; 298:102445. [PMID: 36055403 PMCID: PMC9531178 DOI: 10.1016/j.jbc.2022.102445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/12/2022] Open
Abstract
Two dimensional GC (GC × GC)-time-of-flight mass spectrometry (TOFMS) has been used to improve accurate metabolite identification in the chemical industry, but this method has not been applied as readily in biomedical research. Here, we evaluated and validated the performance of high resolution GC × GC-TOFMS against that of GC-TOFMS for metabolomics analysis of two different plasma matrices, from healthy controls (CON) and diabetes mellitus (DM) patients with kidney failure (DM with KF). We found GC × GC-TOFMS outperformed traditional GC-TOFMS in terms of separation performance and metabolite coverage. Several metabolites from both the CON and DM with KF matrices, such as carbohydrates and carbohydrate-conjugate metabolites, were exclusively detected using GC × GC-TOFMS. Additionally, we applied this method to characterize significant metabolites in the DM with KF group, with focused analysis of four metabolite groups: sugars, sugar alcohols, amino acids, and free fatty acids. Our plasma metabolomics results revealed 35 significant metabolites (12 unique and 23 concentration-dependent metabolites) in the DM with KF group, as compared with those in the CON and DM groups (N = 20 for each group). Interestingly, we determined 17 of the 35 (14/17 verified with reference standards) significant metabolites identified from both the analyses were metabolites from the sugar and sugar alcohol groups, with significantly higher concentrations in the DM with KF group than in the CON and DM groups. Enrichment analysis of these 14 metabolites also revealed that alterations in galactose metabolism and the polyol pathway are related to DM with KF. Overall, our application of GC × GC-TOFMS identified key metabolites in complex plasma matrices.
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Affiliation(s)
- Kassaporn Duangkumpha
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Narumol Jariyasopit
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kwanjeera Wanichthanarak
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Esha Dhakal
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pattipong Wisanpitayakorn
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sansanee Thotsiri
- Somdech Phra Debaratana Medical Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chagriya Kitiyakara
- Department of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Research Network of NANOTEC - MU Ramathibodi on Nanomedicine, Bangkok, Thailand
| | - Nuankanya Sathirapongsasuti
- Research Network of NANOTEC - MU Ramathibodi on Nanomedicine, Bangkok, Thailand; Section of Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand.
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10
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Parastar H, Tauler R. Big (Bio)Chemical Data Mining Using Chemometric Methods: A Need for Chemists. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.201801134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hadi Parastar
- Department of Chemistry Sharif University of Technology Tehran Iran
| | - Roma Tauler
- Department of Environmental Chemistry IDAEA-CSIC 08034 Barcelona Spain
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11
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Perić I, Lješević M, Beškoski V, Nikolić M, Filipović D. Metabolomic profiling relates tianeptine effectiveness with hippocampal GABA, myo-inositol, cholesterol, and fatty acid metabolism restoration in socially isolated rats. Psychopharmacology (Berl) 2022; 239:2955-2974. [PMID: 35776189 DOI: 10.1007/s00213-022-06180-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/16/2022] [Indexed: 12/28/2022]
Abstract
RATIONALE Discovering biomarkers of major depressive disorder (MDD) can give a deeper understanding of this mood disorder and improve the ability to screen for, diagnose, and treat MDD. OBJECTIVES In this study, metabolomics was used in unraveling metabolite fluctuations of MDD and drug outcome by creating specific metabolomic fingerprints. We report metabolomic patterns of change of the hippocampus of adult male Wistar rats following chronic social isolation (CSIS) (6 weeks), an animal model of depression, and/or chronic tianeptine (Tian) treatment (10 mg kg-1 per day) (lasting 3 weeks of 6-week CSIS), monitored by using comprehensive GC × GC-MS. RESULTS The comparative metabolomic analysis highlighted the role of gamma aminobutyric acid (GABA), iso-allocholate, and unsaturated fatty acid metabolism alterations following the CSIS, which was corroborated with moderate to strong negative Pearson's correlation of GABA, docosahexaenoic, 9-hexadecenoic acid, 5,8,11,14-eicosatetraynoic, and arachidonic acids with immobility behavior in the forced swim test. The antidepressant effect of Tian restored GABA levels, which was absent in Tian resilient rats. Tian decreased myo-inositol and increased TCA cycle intermediates, amino acids, and cholesterol and its metabolite. As key molecules of divergence between Tian effectiveness and resilience, metabolomics revealed myo-inositol, GABA, cholesterol, and its metabolite. A significant moderate positive correlation between myo-inositol and immobility was revealed. Tian probably acted by upregulating NMDAR's and α2 adrenergic receptors (AR) or norepinephrine transporter in both control and stressed animals. CONCLUSION Metabolomics revealed several dysregulations underlying CSIS-induced depressive-like behavior and responsiveness to Tian, predominantly converging into NMDAR-mediated glutamate and myo-inositol signalization and GABA inhibitory pathways.
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Affiliation(s)
- Ivana Perić
- Department of Molecular Biology and Endocrinology, "VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovića Alasa 12-14, 11351, Vinča, Belgrade, Serbia
| | - Marija Lješević
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000, Belgrade, Serbia
| | - Vladimir Beškoski
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Milan Nikolić
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Dragana Filipović
- Department of Molecular Biology and Endocrinology, "VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovića Alasa 12-14, 11351, Vinča, Belgrade, Serbia.
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12
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Matuszczak M, Kiljańczyk A, Salagierski M. A Liquid Biopsy in Bladder Cancer—The Current Landscape in Urinary Biomarkers. Int J Mol Sci 2022; 23:ijms23158597. [PMID: 35955727 PMCID: PMC9369188 DOI: 10.3390/ijms23158597] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 02/06/2023] Open
Abstract
The non-muscle invasive bladder cancer tends to recur and progress. Therefore, it requires frequent follow-ups, generating costs and making it one of the most expensive neoplasms. Considering the expensive and invasive character of the current gold-standard diagnostic procedure, white-light cystoscopy, efforts to find an alternative method are ongoing. Although the last decade has seen significant advancements in urinary biomarker tests (UBTs) for bladder cancer, international guidelines have not recommended them. Currently, the paramount urgency is to find and validate the test with the best specificity and sensitivity, which would allow for the optimizing of diagnosis, prognosis, and a treatment plan. This review aims to summarise the up-to-date state of knowledge relating to UBTs and new developments in the detection, prognosis, and surveillance of bladder cancer and their potential applications in clinical practice.
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13
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Nam SL, Tarazona Carrillo K, de la Mata AP, de Bruin OM, Doukhanine E, Harynuk J. Evaluation of fresh, frozen, and lyophilized fecal samples by SPME and derivatization methods using GC×GC-TOFMS. Metabolomics 2022; 18:25. [PMID: 35426515 DOI: 10.1007/s11306-022-01881-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Feces is a highly complex matrix containing thousands of metabolites. It also contains live bacteria and enzymes, and does not have a static chemistry. Consequently, proper control of pre-analytical parameters is critical to minimize unwanted variations in the samples. However, no consensus currently exists on how fecal samples should be stored/processed prior to analysis. OBJECTIVE The effects of sample handling conditions on fecal metabolite profiles and abundances were examined using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS). METHODS Solid-phase microextraction (SPME) and derivatization via trimethylsilylation (TMS) were employed as complementary techniques to evaluate fresh, frozen, and lyophilized fecal samples with expanded coverage of the fecal metabolome. The total number of detected peaks and the signal intensities were compared among the different handling conditions. RESULTS Our analysis revealed that the metabolic profiles of fecal samples depend greatly on sample handling and processing conditions, which had a more pronounced effect on results obtained by SPME than by TMS derivatization. Overall, lyophilization resulted in a greater amount of total and class-specific metabolites, which may be attributed to cell lysis and/or membrane disintegration. CONCLUSIONS A comprehensive comparison of the sample handling conditions provides a deeper understanding of the physicochemical changes that occur within the samples during freezing and lyophilization. Based on our results, snap-freezing at -80 °C would be preferred over lyophilization for handling samples in the field of fecal metabolomics as this imparts the least change from the fresh condition.
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Affiliation(s)
- Seo Lin Nam
- Department of Chemistry, University of Alberta, T6G 2G2, Edmonton, Alberta, Canada
| | | | - A Paulina de la Mata
- Department of Chemistry, University of Alberta, T6G 2G2, Edmonton, Alberta, Canada
| | | | | | - James Harynuk
- Department of Chemistry, University of Alberta, T6G 2G2, Edmonton, Alberta, Canada.
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Mathema VB, Duangkumpha K, Wanichthanarak K, Jariyasopit N, Dhakal E, Sathirapongsasuti N, Kitiyakara C, Sirivatanauksorn Y, Khoomrung S. CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics. Brief Bioinform 2022; 23:bbab550. [PMID: 35022651 PMCID: PMC8921635 DOI: 10.1093/bib/bbab550] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/19/2021] [Accepted: 11/29/2021] [Indexed: 01/16/2023] Open
Abstract
Two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) provides a large amount of molecular information from biological samples. However, the lack of a comprehensive compound library or customizable bioinformatics tool is currently a challenge in GC × GC-TOFMS data analysis. We present an open-source deep learning (DL) software called contour regions of interest (ROI) identification, simulation and untargeted metabolomics profiler (CRISP). CRISP integrates multiple customizable deep neural network architectures for assisting the semi-automated identification of ROIs, contour synthesis, resolution enhancement and classification of GC × GC-TOFMS-based contour images. The approach includes the novel aggregate feature representative contour (AFRC) construction and stacked ROIs. This generates an unbiased contour image dataset that enhances the contrasting characteristics between different test groups and can be suitable for small sample sizes. The utility of the generative models and the accuracy and efficacy of the platform were demonstrated using a dataset of GC × GC-TOFMS contour images from patients with late-stage diabetic nephropathy and healthy control groups. CRISP successfully constructed AFRC images and identified over five ROIs to create a deepstacked dataset. The high fidelity, 512 × 512-pixels generative model was trained as a generator with a Fréchet inception distance of <47.00. The trained classifier achieved an AUROC of >0.96 and a classification accuracy of >95.00% for datasets with and without column bleed. Overall, CRISP demonstrates good potential as a DL-based approach for the rapid analysis of 4-D GC × GC-TOFMS untargeted metabolite profiles by directly implementing contour images. CRISP is available at https://github.com/vivekmathema/GCxGC-CRISP.
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Affiliation(s)
- Vivek Bhakta Mathema
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kassaporn Duangkumpha
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kwanjeera Wanichthanarak
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Narumol Jariyasopit
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Esha Dhakal
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nuankanya Sathirapongsasuti
- Section of Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Research Network of NANOTEC – MU Ramathibodi on Nanomedicine, Bangkok, Thailand
| | - Chagriya Kitiyakara
- Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Rama VI Rd., Ratchathewi, Bangkok 10400, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
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Zaid A, Khan MS, Yan D, Marriott PJ, Wong YF. Comprehensive two-dimensional gas chromatography with mass spectrometry: an advanced bioanalytical technique for clinical metabolomics studies. Analyst 2022; 147:3974-3992. [DOI: 10.1039/d2an00584k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review highlights the current state of knowledge in the development of GC × GC-MS for the analysis of clinical metabolites. Selected applications are described as well as our perspectives on current challenges and potential future directions.
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Affiliation(s)
- Atiqah Zaid
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Mohammad Sharif Khan
- Cargill Research and Development Center, Cargill, 14800 28th Ave N, Plymouth, MN 55447, USA
| | - Dandan Yan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Yong Foo Wong
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
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16
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Ye D, Li X, Shen J, Xia X. Microbial metabolomics: From novel technologies to diversified applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Defining Blood Plasma and Serum Metabolome by GC-MS. Metabolites 2021; 12:metabo12010015. [PMID: 35050137 PMCID: PMC8779220 DOI: 10.3390/metabo12010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.
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18
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Cox LA, Chan J, Rao P, Hamid Z, Glenn JP, Jadhav A, Das V, Karere GM, Quillen E, Kavanagh K, Olivier M. Integrated omics analysis reveals sirtuin signaling is central to hepatic response to a high fructose diet. BMC Genomics 2021; 22:870. [PMID: 34861817 PMCID: PMC8641221 DOI: 10.1186/s12864-021-08166-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Dietary high fructose (HFr) is a known metabolic disruptor contributing to development of obesity and diabetes in Western societies. Initial molecular changes from exposure to HFr on liver metabolism may be essential to understand the perturbations leading to insulin resistance and abnormalities in lipid and carbohydrate metabolism. We studied vervet monkeys (Clorocebus aethiops sabaeus) fed a HFr (n=5) or chow diet (n=5) for 6 weeks, and obtained clinical measures of liver function, blood insulin, cholesterol and triglycerides. In addition, we performed untargeted global transcriptomics, proteomics, and metabolomics analyses on liver biopsies to determine the molecular impact of a HFr diet on coordinated pathways and networks that differed by diet. RESULTS We show that integration of omics data sets improved statistical significance for some pathways and networks, and decreased significance for others, suggesting that multiple omics datasets enhance confidence in relevant pathway and network identification. Specifically, we found that sirtuin signaling and a peroxisome proliferator activated receptor alpha (PPARA) regulatory network were significantly altered in hepatic response to HFr. Integration of metabolomics and miRNAs data further strengthened our findings. CONCLUSIONS Our integrated analysis of three types of omics data with pathway and regulatory network analysis demonstrates the usefulness of this approach for discovery of molecular networks central to a biological response. In addition, metabolites aspartic acid and docosahexaenoic acid (DHA), protein ATG3, and genes ATG7, and HMGCS2 link sirtuin signaling and the PPARA network suggesting molecular mechanisms for altered hepatic gluconeogenesis from consumption of a HFr diet.
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Affiliation(s)
- Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA.
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA.
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA.
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, 27157, Winston-Salem, NC, USA.
| | - Jeannie Chan
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Prahlad Rao
- University of Tennessee Health Science Center, TN, Memphis, USA
| | - Zeeshan Hamid
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
| | - Jeremy P Glenn
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Avinash Jadhav
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Vivek Das
- Novo Nordisk Research Center, Seattle, WA, USA
| | - Genesio M Karere
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Ellen Quillen
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Kylie Kavanagh
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, 27157, Winston-Salem, NC, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
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Mass spectrometry based metabolomics of volume-restricted in-vivo brain samples: Actual status and the way forward. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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DeBastiani A, Majuta SN, Sharif D, Attanayake K, Li C, Li P, Valentine SJ. Characterizing Multidevice Capillary Vibrating Sharp-Edge Spray Ionization for In-Droplet Hydrogen/Deuterium Exchange to Enhance Compound Identification. ACS OMEGA 2021; 6:18370-18382. [PMID: 34308068 PMCID: PMC8296548 DOI: 10.1021/acsomega.1c02362] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/23/2021] [Indexed: 05/10/2023]
Abstract
Multidevice capillary vibrating sharp-edge spray ionization (cVSSI) source parameters have been examined to determine their effects on conducting in-droplet hydrogen/deuterium exchange (HDX) experiments. Control experiments using select compounds indicate that the observed differences in mass spectral isotopic distributions obtained upon initiation of HDX result primarily from solution-phase reactions as opposed to gas-phase exchange. Preliminary studies have determined that robust HDX can only be achieved with the application of same-polarity voltage to both the analyte and the deuterium oxide reagent (D2O) cVSSI devices. Additionally, a similar HDX reactivity dependence on the voltage applied to the D2O device for various analytes is observed. Analyte and reagent flow experiments show that, for the multidevice cVSSI setup employed, there is a nonlinear dependence on the D2O reagent flow rate; increasing the D2O reagent flow by 100% results in only an ∼10-20% increase in deuterium incorporation for this setup. Instantaneous (subsecond) response times have been demonstrated in the initiation or termination of HDX, which is achieved by turning on or off the reagent cVSSI device piezoelectric transducer. The ability to distinguish isomeric species by in-droplet HDX is presented. Finally, a demonstration of a three-component cVSSI device setup to perform multiple (successive or in combination) in-droplet chemistries to enhance compound ionization and identification is presented and a hypothetical metabolomics workflow consisting of successive multidevice activation is briefly discussed.
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21
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Abstract
Comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) is a powerful tool for the analysis of complex mixtures, and it is ideally suited to discovery studies where the entire sample is potentially of interest. Unfortunately, when unit mass resolution mass spectrometers are used, many detected compounds have spectra that do not match well with libraries. This could be due to the compound not being in the library, or the compound having a weak/nonexistent molecular ion cluster. While high-speed, high-resolution mass spectrometers, or ion sources with softer ionization than 70 eV electron impact (EI) may help with some of this, many GC×GC systems presently in use employ low-resolution mass spectrometers and 70 eV EI ionization. Scripting tools that apply filters to GC×GC-TOFMS data based on logical operations applied to spectral and/or retention data have been used previously for environmental and petroleum samples. This approach rapidly filters GC×GC-TOFMS peak tables (or raw data) and is available in software from multiple vendors. In this work, we present a series of scripts that have been developed to rapidly classify major groups of compounds that are of relevance to metabolomics studies including: fatty acid methyl esters, free fatty acids, aldehydes, alcohols, ketones, amino acids, and carbohydrates.
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Lin JY, Juo BR, Yeh YH, Fu SH, Chen YT, Chen CL, Wu KP. Putative markers for the detection of early-stage bladder cancer selected by urine metabolomics. BMC Bioinformatics 2021; 22:305. [PMID: 34090341 PMCID: PMC8180080 DOI: 10.1186/s12859-021-04235-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early detection of bladder cancer remains challenging because patients with early-stage bladder cancer usually have no incentive to take cytology or cystoscopy tests if they are asymptomatic. Our goal is to find non-invasive marker candidates that may help us gain insight into the metabolism of early-stage bladder cancer and be examined in routine health checks. RESULTS We acquired urine samples from 124 patients diagnosed with early-stage bladder cancer or hernia (63 cancer patients and 61 controls). In which 100 samples were included in our marker discovery cohort, and the remaining 24 samples were included in our independent test cohort. We obtained metabolic profiles of 922 compounds of the samples by gas chromatography-mass spectrometry. Based on the metabolic profiles of the marker discovery cohort, we selected marker candidates using Wilcoxon rank-sum test with Bonferroni correction and leave-one-out cross-validation; we further excluded compounds detected in less than 60% of the bladder cancer samples. We finally selected eight putative markers. The abundance of all the eight markers in bladder cancer samples was high but extremely low in hernia samples. Moreover, the up-regulation of these markers might be in association with sugars and polyols metabolism. CONCLUSIONS In the present study, comparative urine metabolomics selected putative metabolite markers for the detection of early-stage bladder cancer. The suggested relations between early-stage bladder cancer and sugars and polyols metabolism may create opportunities for improving the detection of bladder cancer.
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Affiliation(s)
- Jia-You Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Bao-Rong Juo
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, 33302, Taiwan
| | - Yu-Hsuan Yeh
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shu-Hsuan Fu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, 33302, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, 33302, Taiwan
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan
| | - Chien-Lun Chen
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan.
| | - Kun-Pin Wu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
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Adutwum LA, Kwao JK, Harynuk JJ. Unique ion filter-A data reduction tool for chemometric analysis of raw comprehensive two-dimensional gas chromatography-mass spectrometry data. J Sep Sci 2021; 44:2773-2784. [PMID: 33932270 DOI: 10.1002/jssc.202001127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/17/2021] [Accepted: 04/27/2021] [Indexed: 11/07/2022]
Abstract
Comprehensive gas chromatography with time of flight mass spectrometry is a powerful tool in the analysis of complex samples. Chemometric analysis of raw chromatographic data is more useful in one- and two-dimensional separations relative to peak tables. The data volume from such experiments generally necessitates the use of data reduction tools. Such tools often sacrifice some of the multivariate information in the mass to charge ratio dimension. The unique ion filter reduces the over-redundancy in two-dimensional gas chromatography-mass spectrometry data by limiting the data to a few unique/pseudo-unique ions, sub-peaks/slices in the first dimension, and spectra in the second dimension. We explore the performance of this algorithm through careful inspection of two-dimensional gas chromatography-mass spectrometry data before and after application of the filter. A reduction (99%) in the number of variables in a two-dimensional gas chromatography-mass spectrometry chromatogram passed on to subsequent analysis was observed. Feature selection times for model optimization reduced from 229 (±13) to 6.8 (±0.5) min when the filter was applied. An estimate of two unique/pseudo-unique ions, one sub-peak in the first dimension and five spectra in the second dimension were considered to provide a true representation of each chromatogram and provided enough information to achieve 100% model prediction accuracy.
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Affiliation(s)
- Lawrence A Adutwum
- Department of Pharmaceutical Chemistry, University of Ghana, Accra, Ghana.,Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joanna Koryo Kwao
- Department of Pharmaceutical Chemistry, University of Ghana, Accra, Ghana
| | - James J Harynuk
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Patel D, Taudte RV, Nizio K, Herok G, Cranfield C, Shimmon R. Headspace analysis of E-cigarette fluids using comprehensive two dimensional GC×GC-TOF-MS reveals the presence of volatile and toxic compounds. J Pharm Biomed Anal 2021; 196:113930. [PMID: 33581591 DOI: 10.1016/j.jpba.2021.113930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 11/30/2022]
Abstract
The analysis of electronic cigarrete (E-cigarette) fluids by high performance liquid chromatography or gas chromatography (GC) coupled to mass spectrometry (MS), GC hyphenated to flame-ionisation detection, or nuclear magnetic resonance spectroscopy poses many challenges due to the complex matrix and extremely high number of compounds present. In order to overcome these challenges, this study focused on the detection of the multiple complex compounds classes produced by the pyrolysis of E-cigarette liquids using comprehensive two dimensional gas chromatography (GCxGC) coupled to time of flight (TOF)-MS. Gas samples were prepared by heating E-liquids inside aluminium tins for 5 min. The tins were placed in a sand bath, which was temperature controlled at 200 °C. The samples were collected using thermal desorption tubes connected to volatile organic compound (VOC) sampling pump attached and subsequently analysed using GCxGC-TOF-MS. The greater peak resolution obtained when using GCxGC-TOF-MS allowed to distinguish many toxic compounds and VOCs that could not be detected by the other methods mentioned above. As a result, a comprehensive list of volatile compounds emitted from E-cigarette fluids when heated was established, which might allow a better understanding of potential health effects of vaping. Heating E-liquids to moderate temperature results in the emission of over 1000 volatile compounds of which over 150 are toxic. These compounds are either present in the liquid or can be formed during storage or heating leading to a more complex volatile profile of E-cigarette liquids than previously assumed. The application of GCxGC-TOF-MS allows the elucidation of this profile and therefore a better understanding of possible health implications.
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Affiliation(s)
- Darshil Patel
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW, Australia; Department of Chimie-Biochimie-Physique, University du Quebec a Trois Rivieres, Trois Rivieres, Canada
| | - R Verena Taudte
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW, Australia; Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-University, Erlangen, Nuremberg, Germany.
| | - Katie Nizio
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW, Australia
| | - George Herok
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Charles Cranfield
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Ronald Shimmon
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW, Australia
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Sun W, Braatz RD. Opportunities in tensorial data analytics for chemical and biological manufacturing processes. Comput Chem Eng 2020. [DOI: 10.1016/j.compchemeng.2020.107099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Román-Kustas J, Hoffman JB, Alonso D, Reed JH, Gonsalves AE, Oh J, Hong S, Jo KD, Dana CE, Alleyne M, Miljkovic N, Cropek DM. Analysis of cicada wing surface constituents by comprehensive multidimensional gas chromatography for species differentiation. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Specificity of metabolic colorectal cancer biomarkers in serum through effect size. Metabolomics 2020; 16:88. [PMID: 32789702 DOI: 10.1007/s11306-020-01707-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/30/2020] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Colorectal cancer is one of the most diagnosed cancers, leading to numerous deaths. In addition to existing screening methods, metabolic profiling could help both to diagnose and to understand the various states of the disease. OBJECTIVES Find specific candidate biomarkers (CB) in serum of patients with colorectal cancer (CRC), in comparison to the situation after remission (R-CRC), evaluated on distinct patients. METHODS All serum samples were analyzed using comprehensive two-dimensional gas chromatography (GC × GC) coupled to high resolution time of flight mass spectrometry (TOF-MS) through an optimized and validated untargeted analytical method regulated by a quality control (QC) system. First, we used a specific multi-approaches data (pre)processing workflow to highlight, annotate and assess the performances of the most altered metabolites between CRC patients (n = 18) and healthy control samples (HC, n = 19) specifically matched for age and gender, two of the most influential confounding factors. On the contrary, due to the difficulty to control for all clinical and demographic traits when sampling small cohorts, the samples from patients in remission (n = 17) were not matched. Because of the consequent risk of bias, the usual null hypothesis significance tests (NHST) could not be applied reliably. Therefore, we compared the R-CRC samples to another specifically matched group of healthy controls (R-HC, n = 17), and used this comparison to indirectly address the difference between patients with colorectal cancer and patients in remission through a measure called effect size (ES) whose methodological aspects were investigated. RESULTS 24 candidate biomarkers were found significantly altered and able to discriminate the CRC and HC samples efficiently (Receiver Operating Characteristic (ROC) area under the curve (AUC) of 0.86, sensitivity and specificity of 0.72 and 0.78). 10 of those were found to have signals close to healthy levels in the R-CRC samples and were therefore specific to colorectal cancer. In the point-biserial case studied here, r-like (strength of association) and d-like (standardized mean difference) ES were directly convertible and only linear and rank-based ES were different. We therefore used and recommend Hedges' g, Spearman's rho and Kendall's tau, along with an unstandardized ES. The confidence intervals, that quantify the uncertainty of the measure, were well represented through scatterplots and distribution curves. CONCLUSION The candidate biomarkers found, along with their specificity, could help for the detection of colorectal cancer, the diagnosis of remission, and for the understanding of its pathophysiology, after proper validation on independent cohorts. The effect size, here applied on a MS global profiling data set, is an ideal complement to NHST and a useful tool to compare and combine distinct cohorts, within a study as well as between studies (meta-analysis).
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Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic & Biological Analytical Chemistry Group, University of Liège, Allée du 6 août, B6c, B-4000, Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA Institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, University of Liège, Quartier Hôpital, Avenue de l'hôpital 13, B34-35, B-4000, Liège, Belgium
| | - Edouard Louis
- GIGA Institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, University of Liège, Quartier Hôpital, Avenue de l'hôpital 13, B34-35, B-4000, Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic & Biological Analytical Chemistry Group, University of Liège, Allée du 6 août, B6c, B-4000, Liège (Sart Tilman), Belgium.
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Bridge C, Giardina M. Stronger associations of oil-based sexual lubricants and hygiene products using GC×GC–MS. Forensic Chem 2020. [DOI: 10.1016/j.forc.2019.100207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Chen Z, Gao Y, Zhong D. Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies. Biomed Chromatogr 2020; 34:e4798. [PMID: 31994210 DOI: 10.1002/bmc.4798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
Abstract
Chromatographic method has long been recognized as the most widely used separation method in bioanalytical research. However, the relatively low sensitivity of existing chromatographic methods remains a significant challenge, as the requirements for experimental procedures become more demanding. This review discusses the main causes for the low sensitivity of chromatographic methods and aims to introduce different technologies for enhancing their sensitivity in the following aspects: (i) different pretreatment methods for improving clean-up efficiency and recovery; (ii) derivatization step for altering the chromatographic behavior of analytes and enhancing MS ionization efficiency; (iii) optimal LC-MS conditions and appropriate separation mechanism; and (iv) applications of other chromatographic methods, including miniaturized LC, 2D-LC, 2D-GC, and supercritical fluid chromatography. Altogether, this review is devoted to summarizing the recent technologies reported in the literature and providing new strategies for the detection of bioanalytes.
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Affiliation(s)
- Zhendong Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuxiong Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dafang Zhong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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An R, Lu J, Chen W, Zhou B, Chen Y, Wang X, Yang M. Distinguishing the rhizomes of Atractylodes japonica, Atractylodes chinensis, and Atractylodes lancea by comprehensive two-dimensional gas chromatography coupled with mass spectrometry combined with multivariate data analysis. Pharmacogn Mag 2020. [DOI: 10.4103/pm.pm_33_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Using Multiple Analytical Platforms to Investigate the Androgen Depletion Effects on Fecal Metabolites in a Mouse Model of Systemic Lupus Erythematosus. J Proteome Res 2019; 19:667-676. [PMID: 31820642 DOI: 10.1021/acs.jproteome.9b00558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by circulating autoantibodies that deposit in target organs (e.g., kidneys), resulting in chronic inflammation and eventual destruction of the organ. SLE is much more prevalent in females than males in both humans and spontaneous mouse models of lupus, such as NZBxNZW F1 (BWF1) mice. Depleting androgens by castration dramatically increases the susceptibility of BWF1 male to lupus. We compared fecal metabolite profiles of castrated BWF1 (androgen-depleted) male, intact (androgen-replete) male, and female mice. Four analytical platforms were employed to study the profiles of polar metabolites in mouse feces collected from adult BWF1 mice, and a total of 435 metabolites was identified. Of these, the abundance levels of 72 metabolites were significantly different between castrated and intact male groups, and 63 metabolites were different between female and male groups. Pathway analysis indicated that the pathway differences between castrated and intact male mice closely resembled the pathway differences between female and intact male mice, suggesting that low levels of androgens, whether due to depletion (castrated male) or endogenous (female), are associated with multiple fecal metabolomic alterations, which could potentially affect SLE progression. Our findings demonstrate that analyzing fecal metabolites using multiple analytical platforms holds great promise for detecting metabolomic alterations in complex disease model systems.
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Untargeted Serum Metabolic Profiling by Comprehensive Two-Dimensional Gas Chromatography–High-Resolution Time-of-Flight Mass Spectrometry. J Proteome Res 2019; 19:1013-1028. [DOI: 10.1021/acs.jproteome.9b00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Edouard Louis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
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Shi X, Wang S, Jasbi P, Turner C, Hrovat J, Wei Y, Liu J, Gu H. Database-Assisted Globally Optimized Targeted Mass Spectrometry (dGOT-MS): Broad and Reliable Metabolomics Analysis with Enhanced Identification. Anal Chem 2019; 91:13737-13745. [PMID: 31556994 DOI: 10.1021/acs.analchem.9b03107] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Xiaojian Shi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Shuai Wang
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
- Department of Vascular Surgery, The First Hospital of Jilin University, Jilin University, Changchun, Jilin Province 130021, People’s Republic of China
| | - Paniz Jasbi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Cassidy Turner
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Jonathan Hrovat
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Yiping Wei
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People’s Republic of China
| | - Jingping Liu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
- Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People’s Republic of China
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
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Prodhan MAI, Shi B, Song M, He L, Yuan F, Yin X, Bohman P, McClain CJ, Zhang X. Integrating comprehensive two-dimensional gas chromatography mass spectrometry and parallel two-dimensional liquid chromatography mass spectrometry for untargeted metabolomics. Analyst 2019; 144:4331-4341. [PMID: 31192319 PMCID: PMC6677244 DOI: 10.1039/c9an00560a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The diverse characteristics and large number of entities make metabolite separation challenging in metabolomics. To date, there is not a singular instrument capable of analyzing all types of metabolites. In order to achieve a better separation for higher peak capacity and accurate metabolite identification and quantification, we integrated GC × GC-MS and parallel 2DLC-MS for analysis of polar metabolites. To test the performance of the developed system, 13 rats were fed different diets to form two animal groups. Polar metabolites extracted from rat livers were analyzed by GC × GC-MS, parallel 2DLC-MS (-) and parallel 2DLC-MS (+), respectively. By integrating all data together, 58 metabolites were detected with significant change in their abundance levels between groups (p≤ 0.05). Of the 58 metabolites, three metabolites were detected in two platforms and two in all three platforms. Manual examination showed that discrepancy of metabolite regulation measured by different platforms was mainly caused by the poor shape of chromatographic peaks resulting from low instrument response. Pathway analysis demonstrated that integrating the results from multiple platforms increased the confidence of metabolic pathway assignment.
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Affiliation(s)
- Md Aminul Islam Prodhan
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA. and University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, USA and University of Louisville Hepatobiology & Toxicology Program, University of Louisville, Louisville, KY 40208, USA and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Biyun Shi
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA. and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Ming Song
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, USA and University of Louisville Hepatobiology & Toxicology Program, University of Louisville, Louisville, KY 40208, USA and Department of Medicine, University of Louisville, Louisville, KY 40208, USA
| | - Liqing He
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA. and University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, USA and University of Louisville Hepatobiology & Toxicology Program, University of Louisville, Louisville, KY 40208, USA and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Fang Yuan
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA. and University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, USA and University of Louisville Hepatobiology & Toxicology Program, University of Louisville, Louisville, KY 40208, USA and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA. and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Patrick Bohman
- Thermo Fisher Scientific International Inc., 3000 Lakeside Dr., Bannockburn, IL 60015, USA
| | - Craig J McClain
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, USA and University of Louisville Hepatobiology & Toxicology Program, University of Louisville, Louisville, KY 40208, USA and Department of Medicine, University of Louisville, Louisville, KY 40208, USA and Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY 40208, USA and Robley Rex Louisville VAMC, Louisville, Kentucky 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA. and University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, USA and University of Louisville Hepatobiology & Toxicology Program, University of Louisville, Louisville, KY 40208, USA and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA and Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY 40208, USA
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Kim S, Yin X, Prodhan MAI, Zhang X, Zhong Z, Kato I. Global Plasma Profiling for Colorectal Cancer-Associated Volatile Organic Compounds: a Proof-of-Principle Study. J Chromatogr Sci 2019; 57:385-396. [PMID: 30796770 PMCID: PMC6478127 DOI: 10.1093/chromsci/bmz011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/14/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022]
Abstract
Volatile organic compounds (VOCs) could reflect changes resulting from ongoing pathophysiological processes and altered body metabolisms, and thus have been studied for various types of cancers. We aimed to test an advanced global metabolomic technique to characterize circulating VOCs in patients diagnosed with colorectal cancer (CRC). We employed solid-phase microextraction (SPME) and comprehensive two-dimensional gas chromatography mass-spectrometry (GC × GC-MS). We analyzed 30 random plasma samples from incident cases of CRC. The 30 samples were from population controls enrolled in a large population-based case-control study. The number of metabolite peaks detected in the cases was significantly lower than that detected in the controls (median 1530 vs. 1694, P = 0.02). Partial least squares-discriminant analysis showed clear VOC profile differences between the CRC and the controls. After adjustment for multiple comparisons at the 5% false discovery rate level, five VOCs were differentially expressed between the cases and the controls. Among these five VOCs, 2,3,4-trimethyl-hexane (decreased) and 2,4-dimethylhept-1-ene (increased) were both lipid peroxidation products but not previously reported for CRC. In summary, this study pointed to an intriguing observation that the richness of volatile metabolites may be reduced in CRC cases and demonstrated the utility of SPME GC × GC-MS in discovery of candidate markers for further validation.
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Affiliation(s)
- Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit MI, USA
- Biostatistics Core, Karmanos Cancer Institute, Wayne State University, Detroit MI, USA
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, Louisville, Kentucky, USA
| | | | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky, USA
| | - Zichun Zhong
- Department of Computer Science, College of Engineering, Wayne State University, Detroit MI, USA
| | - Ikuko Kato
- Department of Oncology, Wayne State University School of Medicine, Detroit MI, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit MI, USA
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Metabolome-based signature of disease pathology in MS. Mult Scler Relat Disord 2019; 31:12-21. [PMID: 30877925 DOI: 10.1016/j.msard.2019.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/06/2019] [Accepted: 03/05/2019] [Indexed: 11/21/2022]
Abstract
BACKGROUND Diagnostic delays are common for multiple sclerosis (MS) since diagnosis typically depends on the presentation of nonspecific clinical symptoms together with radiologically-determined central nervous system (CNS) lesions. It is important to reduce diagnostic delays as earlier initiation of disease modifying therapies mitigates long-term disability. Developing a metabolomic blood-based MS biomarker is attractive, but prior efforts have largely focused on specific subsets of metabolite classes or analytical platforms. Thus, there are opportunities to interrogate metabolite profiles using more expansive and comprehensive approaches for developing MS biomarkers and for advancing our understanding of MS pathogenesis. METHODS To identify putative blood-based MS biomarkers, we comprehensively interrogated the metabolite profiles in 12 non-Hispanic white, non-smoking, male MS cases who were drug naïve for 3 months prior to biospecimen collection and 13 non-Hispanic white, non-smoking male controls who were frequency matched to cases by age and body mass index. We performed untargeted two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS) and targeted lipidomic and amino acid analysis on serum. 325 metabolites met quality control and supervised machine learning was used to identify metabolites most informative for MS status. The discrimination potential of these select metabolites were assessed using receiver operator characteristic curves based on logistic models; top candidate metabolites were defined as having area under the curves (AUC) >80%. The associations between whole-genome expression data and the top candidate metabolites were examined, followed by pathway enrichment analyses. Similar associations were examined for 175 putative MS risk variants and the top candidate metabolites. RESULTS 12 metabolites were determined to be informative for MS status, of which 6 had AUCs >80%: pyroglutamate, laurate, acylcarnitine C14:1, N-methylmaleimide, and 2 phosphatidylcholines (PC ae 40:5, PC ae 42:5). These metabolites participate in glutathione metabolism, fatty acid metabolism/oxidation, cellular membrane composition, and transient receptor potential channel signaling. Pathway analyses based on the gene expression association for each metabolite suggested enrichment for pathways associated with apoptosis and mitochondrial dysfunction. Interestingly, the predominant MS genetic risk allele HLA-DRB1×15:01 was associated with one of the 6 top metabolites. CONCLUSION Our analysis represents the most comprehensive description of metabolic changes associated with MS in serum, to date, with the inclusion of genomic and genetic information. We identified atypical metabolic processes that differed between MS patients and controls, which may enable the development of biological targets for diagnosis and treatment.
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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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Llorente C, Jimenez R, Brotman Y, Fernie AR, Sreenivasulu N. Rice Grain Quality Benchmarking Through Profiling of Volatiles and Metabolites in Grains Using Gas Chromatography Mass Spectrometry. Methods Mol Biol 2019; 1892:187-199. [PMID: 30397807 DOI: 10.1007/978-1-4939-8914-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Gas chromatograph coupled with mass spectrometer is widely used to profile volatiles and metabolites from the homogenized rice flour obtained from mature grains. Rice grains consist of central endosperm which stores majorly starch and, in addition, accumulate various storage proteins as storage reserves. The outer nutritious aleurone layer stores lipids, sugar alcohols, volatiles, antioxidants, vitamins, and various micronutrients. Once paddy sample is dehulled, milled, and ground cryogenically, the brown rice flour is subjected to extraction of primary metabolites and volatiles using an appropriate extraction method. In metabolite profiling of the liquid extract obtained from the rice sample, mixture is initially subjected to methoxyamination then silylation before being subjected to untargeted metabolite profiling. Peaks obtained are processed for noise reduction and specific signal selection. Volatile compounds are initially extracted using a solid phase adsorbent prior to analysis. All these compounds, metabolites, and volatiles are detected in the mass selective detector by fragmentation at 70 eV ionization energy and the resultant mass spectrum compared with a built-in library of compounds. Data mined from the gas chromatography mass spectrometry analysis are then subjected to post-processing statistical analysis.
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Affiliation(s)
- Cindy Llorente
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Rosario Jimenez
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Yariv Brotman
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Nese Sreenivasulu
- International Rice Research Institute, Los Baños, Laguna, Philippines.
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Keppler EAH, Jenkins CL, Davis TJ, Bean HD. Advances in the application of comprehensive two-dimensional gas chromatography in metabolomics. Trends Analyt Chem 2018; 109:275-286. [PMID: 30662103 PMCID: PMC6333419 DOI: 10.1016/j.trac.2018.10.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Due to excellent separation capacity for complex mixtures of chemicals, comprehensive two-dimensional gas chromatography (GC × GC) is being utilized with increasing frequency for metabolomics analyses. This review describes recent advances in GC × GC method development for metabolomics, organismal sampling techniques compatible with GC × GC, metabolomic discoveries made using GC × GC, and recommendations and best practices for collecting and reporting GC × GC metabolomics data.
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Affiliation(s)
| | - Carrie L Jenkins
- School of Life Sciences, Arizona State University, Tempe, AZ, 85283, USA
| | - Trenton J Davis
- School of Life Sciences, Arizona State University, Tempe, AZ, 85283, USA
| | - Heather D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, 85283, USA
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Xiang Z, Chen X, Zhao Z, Xiao X, Guo P, Song H, Yang X, Huang M. Analysis of volatile components in Dalbergia cochinchinensis Pierre by a comprehensive two-dimensional gas chromatography with mass spectrometry method using a solid-state modulator. J Sep Sci 2018; 41:4315-4322. [PMID: 30299576 DOI: 10.1002/jssc.201800636] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/10/2018] [Accepted: 09/22/2018] [Indexed: 11/07/2022]
Abstract
Volatile components in Dalbergia cochinchinensis Pierre were analysed using a comprehensive two-dimensional gas chromatography with mass spectrometry method featuring a new solid-state modulator. Compared to one-dimensional gas chromatography, the number of detected peaks were significantly increased. A total of 45 major compounds were identified in this study and the forward and reverse match factors of these compounds were both above 800. The results showed that the volatile components in Dalbergia cochinchinensis Pierre were primarily aldehyde and ketone compounds such as benzaldehyde, cinnamaldehyde, 4-chromanone, 1-(2-hydroxyphenyl)ethanone and acetophenone. In addition, a semi-quantitative analysis was conducted to determine the contents of the detected compounds based on peak area percentage. Moreover, the repeatability of the comprehensive two-dimensional gas chromatography-mass spectrometry analysis in this study was quite satisfactory with relative standard deviations less than 12.7% for intraday and 17.3% for interday measurements.
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Affiliation(s)
- Zhangmin Xiang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
| | - Xiaotian Chen
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
| | - Zhijun Zhao
- J&X Technologies (Shanghai) Co., Ltd., Shanghai, P. R. China
| | - Xue Xiao
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
| | - Pengran Guo
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
| | - Huacan Song
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
| | - Xi Yang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
| | - Minghua Huang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, P. R. China
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Misra BB, Bassey E, Bishop AC, Kusel DT, Cox LA, Olivier M. High-resolution gas chromatography/mass spectrometry metabolomics of non-human primate serum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1497-1506. [PMID: 29874398 PMCID: PMC6395519 DOI: 10.1002/rcm.8197] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Metabolomics analyses using gas chromatography/mass spectrometry (GC/MS)-based metabolomics are heavily impeded by the lack of high-resolution mass spectrometers and limited spectral libraries to complement the excellent chromatography that GC platforms offer, a challenge that is being addressed with the implementation of high-resolution (HR) platforms such as 1D-GC/Orbitrap-MS. METHODS We used serum samples from a non-human primate (NHP), a baboon (Papio hamadryas), with suitable quality controls to quantify the chemical space using an advanced HRMS platform for confident metabolite identification and robust quantification to assess the suitability of the platform for routine clinical metabolomics research. In a complementary approach, we also analyzed the same serum samples using two-dimensional gas chromatography/time-of-flight mass spectrometry (2D-GC/TOF-MS) for metabolite identification and quantification following established standard protocols. RESULTS Overall, the 2D-GC/TOF-MS (~5000 peaks per sample) and 1D-GC/Orbitrap-MS (~500 peaks per sample) analyses enabled identification and quantification of a total of 555 annotated metabolites from the NHP serum with a spectral similarity score Rsim ≥ 900 and signal-to-noise (S/N) ratio of >25. A common set of 30 metabolites with HMDB and KEGG IDs was quantified in the serum samples by both platforms where 2D-GC/TOF-MS enabled quantification of a total 384 metabolites (118 HMDB IDs) and 1D-GC/Orbitrap-MS analysis quantification of a total 200 metabolites (47 HMDB IDs). Thus, roughly 30-70% of the peaks remain unidentified or un-annotated across both platforms. CONCLUSIONS Our study provides insights into the benefits and limitations of the use of a higher mass resolution and mass accuracy instrument for untargeted GC/MS-based metabolomics with multi-dimensional chromatography in future studies addressing clinical conditions or exposome studies.
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Affiliation(s)
- Biswapriya B. Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
| | - Ekong Bassey
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose 95134, CA, USA
| | - Andrew C. Bishop
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
| | - David T. Kusel
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose 95134, CA, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio 78227, Texas USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio 78227, Texas USA
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Prodhan MAI, Sleman AA, Kim S, McClain C, Zhang X. Generalization of Reference System for Calculating the Second Dimension Retention Index in GC × GC–MS. JOURNAL OF ANALYSIS AND TESTING 2018. [DOI: 10.1007/s41664-018-0074-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Misra BB, Upadhayay RP, Cox LA, Olivier M. Optimized GC-MS metabolomics for the analysis of kidney tissue metabolites. Metabolomics 2018; 14:75. [PMID: 30830353 DOI: 10.1007/s11306-018-1373-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/15/2018] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Metabolomics is a promising approach for discovery of relevant biomarkers in cells, tissues, organs, and biofluids for disease identification and prediction. The field has mostly relied on blood-based biofluids (serum, plasma, urine) as non-invasive sources of samples as surrogates of tissue or organ-specific conditions. However, the tissue specificity of metabolites pose challenges in translating blood metabolic profiles to organ-specific pathophysiological changes, and require further downstream analysis of the metabolites. OBJECTIVES As part of this project, we aim to develop and optimize an efficient extraction protocol for the analysis of kidney tissue metabolites representative of key primate metabolic pathways. METHODS Kidney cortex and medulla tissues of a baboon were homogenized and extracted using eight different extraction protocols including methanol/water, dichloromethane/methanol, pure methanol, pure water, water/methanol/chloroform, methanol/chloroform, methanol/acetonitrile/water, and acetonitrile/isopropanol/water. The extracts were analyzed by a two-dimensional gas chromatography time-of-flight mass-spectrometer (2D GC-ToF-MS) platform after methoximation and silylation. RESULTS Our analysis quantified 110 shared metabolites in kidney cortex and medulla tissues from hundreds of metabolites found among the eight different solvent extractions spanning low to high polarities. The results revealed that medulla is metabolically richer compared to the cortex. Dichloromethane and methanol mixture (3:1) yielded highest number of metabolites across both the tissue types. Depending on the metabolites of interest, tissue type, and the biological question, different solvents can be used to extract specific groups of metabolites. CONCLUSION This investigation provides insights into selection of extraction solvents for detection of classes of metabolites in renal cortex and medulla, which is fundamentally important for identification of prognostic and diagnostic metabolic kidney biomarkers for future therapeutic applications.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
| | - Ram P Upadhayay
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
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Ahn YG, Jeon SH, Lim HB, Choi NR, Hwang GS, Kim YP, Lee JY. Analysis of Polycyclic Aromatic Hydrocarbons in Ambient Aerosols by Using One-Dimensional and Comprehensive Two-Dimensional Gas Chromatography Combined with Mass Spectrometric Method: A Comparative Study. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:8341630. [PMID: 29805841 PMCID: PMC5901813 DOI: 10.1155/2018/8341630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/06/2018] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Advanced separation technology paired with mass spectrometry is an ideal method for the analysis of atmospheric samples having complex chemical compositions. Due to the huge variety of both natural and anthropogenic sources of organic compounds, simultaneous quantification and identification of organic compounds in aerosol samples represents a demanding analytical challenge. In this regard, comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC×GC-TOFMS) has become an effective analytical method. However, verification and validation approaches to quantify these analytes have not been critically evaluated. We compared the performance of gas chromatography with quadrupole mass spectrometry (GC-qMS) and GC×GC-TOFMS for quantitative analysis of eighteen target polycyclic aromatic hydrocarbons (PAHs). The quantitative obtained results such as limits of detection (LODs), limits of quantification (LOQs), and recoveries of target PAHs were approximately equivalent based on both analytical methods. Furthermore, a larger number of analytes were consistently identified from the aerosol samples by GC×GC-TOFMS compared to GC-qMS. Our findings suggest that GC×GC-TOFMS would be widely applicable to the atmospheric and related sciences with simultaneous target and nontarget analysis in a single run.
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Affiliation(s)
- Yun Gyong Ahn
- Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea
| | - So Hyeon Jeon
- Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea
| | - Hyung Bae Lim
- Air Quality Research Division, National Institute of Environmental Research, Incheon 22689, Republic of Korea
| | - Na Rae Choi
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03759, Republic of Korea
| | - Geum-Sook Hwang
- Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea
| | - Yong Pyo Kim
- Department of Chemical Engineering and Material Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yi Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03759, Republic of Korea
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Parastar H, Garreta-Lara E, Campos B, Barata C, Lacorte S, Tauler R. Chemometrics comparison of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry Daphnia magna
metabolic profiles exposed to salinity. J Sep Sci 2018; 41:2368-2379. [DOI: 10.1002/jssc.201701336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/17/2018] [Accepted: 02/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Hadi Parastar
- Department of Chemistry; Sharif University of Technology; Tehran Iran
| | | | - Bruno Campos
- Department of Environmental Chemistry; IDAEA-CSIC; Barcelona Spain
| | - Carlos Barata
- Department of Environmental Chemistry; IDAEA-CSIC; Barcelona Spain
| | - Silvia Lacorte
- Department of Environmental Chemistry; IDAEA-CSIC; Barcelona Spain
| | - Roma Tauler
- Department of Environmental Chemistry; IDAEA-CSIC; Barcelona Spain
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Tauler R, Parastar H. Big (Bio)Chemical Data Mining Using Chemometric Methods: A Need for Chemists. Angew Chem Int Ed Engl 2018; 61:e201801134. [DOI: 10.1002/anie.201801134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Roma Tauler
- IDAEA-CSIC Environmental Chemistry Jordi Girona 18-26 08034 Barcelona SPAIN
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Prodhan MAI, Yin X, Kim S, McClain C, Zhang X. Surface fitting for calculating the second dimension retention index in comprehensive two-dimensional gas chromatography mass spectrometry. J Chromatogr A 2018; 1539:62-70. [PMID: 29395161 PMCID: PMC5826898 DOI: 10.1016/j.chroma.2018.01.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 11/21/2022]
Abstract
Comprehensive two-dimensional gas chromatography mass spectrometry (GC × GC-MS) has been widely used for analysis of volatile compounds. However, the second dimension retention index (I) of each compound is not widely used to aid compound identification owing to the limited accuracy of I calculation. We report a surface fitting approach to the calculation of I using n-alkanes (C7-C30) as references, where the second dimension retention time (2tR) and the second dimension column temperature (2Te) formed the X-Y plane and the I was the Z-axis to form the I surface. Compared to the conventional approach for calculating I using isovolatility curves, the surface fitting approach eliminated the construction of isovolatility curves for the reference compounds and gives better reproducibility. The goodness of the proposed surface fitting achieved R2 = 0.9999 and RMSE = 6.1 retention index units (iu). Ten-fold cross validation demonstrated the surface fitting approach had a good predictability with average R2 = 0.9999 and RMSE = 6.6 iu. The developed method was also applied to calculate the second dimension retention indices of compound standards in two commercial mixtures MegaMix A and MegaMix B. The mean standard deviation of the calculated I was only 1.6 iu for compounds in MegaMix A and 3.4 iu for compounds in MegaMix B. Compared with the literature results, the small value of standard deviation in the calculated retention index using surface fitting method shows that the surface fitting method has less measurement variability than the conventional isovolatility curve approach.
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Affiliation(s)
- Md Aminul Islam Prodhan
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA; University of Louisville Alcohol Research Center, Louisville, KY 40208, USA; University of Louisville Hepatobiology & Toxicology Program, Louisville, KY 40208, USA; Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA; University of Louisville Alcohol Research Center, Louisville, KY 40208, USA; University of Louisville Hepatobiology & Toxicology Program, Louisville, KY 40208, USA; Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA
| | - Seongho Kim
- Biostatistics Core, Karmanos Cancer Institute, Department of Oncology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Craig McClain
- University of Louisville Alcohol Research Center, Louisville, KY 40208, USA; University of Louisville Hepatobiology & Toxicology Program, Louisville, KY 40208, USA; Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY 40208, USA; Department of Medicine, University of Louisville, Louisville, KY 40208, USA; Robley Rex Louisville VAMC, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA; University of Louisville Alcohol Research Center, Louisville, KY 40208, USA; University of Louisville Hepatobiology & Toxicology Program, Louisville, KY 40208, USA; Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, USA; Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY 40208, USA.
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48
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Veenaas C, Haglund P. A retention index system for comprehensive two-dimensional gas chromatography using polyethylene glycols. J Chromatogr A 2018; 1536:67-74. [DOI: 10.1016/j.chroma.2017.08.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 08/15/2017] [Accepted: 08/20/2017] [Indexed: 10/19/2022]
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Miyazaki T, Okada K, Yamashita T, Miyazaki M. Two-dimensional gas chromatography time-of-flight mass spectrometry-based serum metabolic fingerprints of neonatal calves before and after first colostrum ingestion. J Dairy Sci 2017; 100:4354-4364. [DOI: 10.3168/jds.2017-12557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/29/2017] [Indexed: 12/26/2022]
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Yu Z, Huang H, Reim A, Charles PD, Northage A, Jackson D, Parry I, Kessler BM. Optimizing 2D gas chromatography mass spectrometry for robust tissue, serum and urine metabolite profiling. Talanta 2017; 165:685-691. [PMID: 28153317 PMCID: PMC5294743 DOI: 10.1016/j.talanta.2017.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 12/31/2022]
Abstract
Two-dimensional gas chromatography mass spectrometry (GCxGC-MS) is utilized to an increasing extent in biomedical metabolomics. Here, we established and adapted metabolite extraction and derivatization protocols for cell/tissue biopsy, serum and urine samples according to their individual properties. GCxGC-MS analysis revealed detection of ~600 molecular features from which 165 were characterized representing different classes such as amino acids, fatty acids, lipids, carbohydrates, nucleotides and small polar components of glycolysis and the Krebs cycle using electron impact (EI) spectrum matching and validation using external standard compounds. Advantages of two-dimensional gas chromatography based resolution were demonstrated by optimizing gradient length and separation through modulation between the first and second column, leading to a marked increase in metabolite identification due to improved separation as exemplified for lactate versus pyruvate, talopyranose versus methyl palmitate and inosine versus docosahexaenoic acid. Our results demonstrate that GCxGC-MS represents a robust metabolomics platform for discovery and targeted studies that can be used with samples derived from the clinic. GCxGC-MS detected ~600 features;165 represented metabolites of different classes. Optimizing gradient length and separation through modulation improved metabolite ID. improved separation of lactate/pyruvate, talopyranose/palmitate and inosine/docosahexaenoate.
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Affiliation(s)
- Zhanru Yu
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Honglei Huang
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Alexander Reim
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Alan Northage
- Shimadzu UK Limited, Mill Court, Featherstone Road Wolverton, Mill South, Milton Keynes MK12 5RD, UK
| | - Dianne Jackson
- Shimadzu UK Limited, Mill Court, Featherstone Road Wolverton, Mill South, Milton Keynes MK12 5RD, UK
| | - Ian Parry
- Shimadzu UK Limited, Mill Court, Featherstone Road Wolverton, Mill South, Milton Keynes MK12 5RD, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
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