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Sidhu KS, Amiel E, Budd RC, Matthews DE. Determination of cell volume as part of metabolomics experiments. Am J Physiol Cell Physiol 2021; 321:C947-C953. [PMID: 34613842 PMCID: PMC8714993 DOI: 10.1152/ajpcell.00613.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 09/15/2021] [Accepted: 10/06/2021] [Indexed: 11/22/2022]
Abstract
Cells regulate their cell volume, but cell volumes may change in response to metabolic and other perturbations. Many metabolomics experiments use cultured cells to measure changes in metabolites in response to physiological and other experimental perturbations, but the metabolomics workflow by mass spectrometry only determines total metabolite amounts in cell culture extracts. To convert metabolite amount to metabolite concentration requires knowledge of the number and volume of the cells. Measuring only metabolite amount can lead to incorrect or skewed results in cell culture experiments because cell size may change due to experimental conditions independent of change in metabolite concentration. We have developed a novel method to determine cell volume in cell culture experiments using a pair of stable isotopically labeled phenylalanine internal standards incorporated within the normal liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics workflow. This method relies on the flooding-dose technique where the intracellular concentration of a particular compound (in this case phenylalanine) is forced to equal its extracellular concentration. We illustrate the LC-MS/MS technique for two different mammalian cell lines. Although the method is applicable in general for determining cell volume, the major advantage of the method is its seamless incorporation within the normal metabolomics workflow.
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Affiliation(s)
| | - Eyal Amiel
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, The University of Vermont, Burlington, Vermont
| | - Ralph C Budd
- Department of Medicine, The University of Vermont, Burlington, Vermont
| | - Dwight E Matthews
- Department of Chemistry, The University of Vermont, Burlington, Vermont
- Department of Medicine, The University of Vermont, Burlington, Vermont
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2
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Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella AD, Shen Y, Cowan A, McReynolds MR, Kennedy BJ, Lato AM, Campagna SR, Singh M, Rabinowitz JD. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods 2021; 18:1377-1385. [PMID: 34711973 PMCID: PMC8733904 DOI: 10.1038/s41592-021-01303-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/16/2021] [Indexed: 11/08/2022]
Abstract
Liquid chromatography-high-resolution mass spectrometry (LC-MS)-based metabolomics aims to identify and quantify all metabolites, but most LC-MS peaks remain unidentified. Here we present a global network optimization approach, NetID, to annotate untargeted LC-MS metabolomics data. The approach aims to generate, for all experimentally observed ion peaks, annotations that match the measured masses, retention times and (when available) tandem mass spectrometry fragmentation patterns. Peaks are connected based on mass differences reflecting adduction, fragmentation, isotopes, or feasible biochemical transformations. Global optimization generates a single network linking most observed ion peaks, enhances peak assignment accuracy, and produces chemically informative peak-peak relationships, including for peaks lacking tandem mass spectrometry spectra. Applying this approach to yeast and mouse data, we identified five previously unrecognized metabolites (thiamine derivatives and N-glucosyl-taurine). Isotope tracer studies indicate active flux through these metabolites. Thus, NetID applies existing metabolomic knowledge and global optimization to substantially improve annotation coverage and accuracy in untargeted metabolomics datasets, facilitating metabolite discovery.
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Affiliation(s)
- Li Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Lin Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Xi Xing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ziyang Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Xin Teng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xianfeng Zeng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Antonio D Muscarella
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yihui Shen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexis Cowan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Melanie R McReynolds
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Brandon J Kennedy
- Lotus Separations, LLC, Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ashley M Lato
- Department of Chemistry, The University of Tennessee at Knoxville, Knoxville, TN, USA
| | - Shawn R Campagna
- Department of Chemistry, The University of Tennessee at Knoxville, Knoxville, TN, USA
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA.
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3
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Brunmair J, Gotsmy M, Niederstaetter L, Neuditschko B, Bileck A, Slany A, Feuerstein ML, Langbauer C, Janker L, Zanghellini J, Meier-Menches SM, Gerner C. Finger sweat analysis enables short interval metabolic biomonitoring in humans. Nat Commun 2021; 12:5993. [PMID: 34645808 PMCID: PMC8514494 DOI: 10.1038/s41467-021-26245-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 09/22/2021] [Indexed: 01/28/2023] Open
Abstract
Metabolic biomonitoring in humans is typically based on the sampling of blood, plasma or urine. Although established in the clinical routine, these sampling procedures are often associated with a variety of compliance issues, which are impeding time-course studies. Here, we show that the metabolic profiling of the minute amounts of sweat sampled from fingertips addresses this challenge. Sweat sampling from fingertips is non-invasive, robust and can be accomplished repeatedly by untrained personnel. The sweat matrix represents a rich source for metabolic phenotyping. We confirm the feasibility of short interval sampling of sweat from the fingertips in time-course studies involving the consumption of coffee or the ingestion of a caffeine capsule after a fasting interval, in which we successfully monitor all known caffeine metabolites as well as endogenous metabolic responses. Fluctuations in the rate of sweat production are accounted for by mathematical modelling to reveal individual rates of caffeine uptake, metabolism and clearance. To conclude, metabotyping using sweat from fingertips combined with mathematical network modelling shows promise for broad applications in precision medicine by enabling the assessment of dynamic metabolic patterns, which may overcome the limitations of purely compositional biomarkers.
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Affiliation(s)
- Julia Brunmair
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Mathias Gotsmy
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Laura Niederstaetter
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Benjamin Neuditschko
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria
| | - Astrid Slany
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Max Lennart Feuerstein
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Clemens Langbauer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lukas Janker
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Samuel M Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria.
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4
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Tsochatzis ED, Nebel C, Danielsen M, Sundekilde UK, Kastrup Dalsgaard T. Thermal degradation of metabolites in urine using multiple isotope-labelled internal standards for off-line GC metabolomics - effects of injector and oven temperatures. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1181:122902. [PMID: 34530307 DOI: 10.1016/j.jchromb.2021.122902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022]
Abstract
Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). An optimized derivatization protocol has been successfully applied using multiple isotope labelled analytical internal standards of selected deuterated and 13C selected compounds, covering a range of different groups of metabolites for non-automated GC metabolomics (off-line). Moreover, the study was also realized in a pooled urine sample, following metabolic profiling. A study of thermal degradation of metabolites due to GC inlet and oven programs (fast, slow) was performed, where the results indicated that both GC oven programs (fast and slow) negatively affected the thermal stability of the metabolites, while the fast-ramp GC program also suppressed MS signals. However, the use of multiple internal standards can overcome this drawback. The application of extended temperature ramp GC program presented identical behaviour on metabolite stability and better chromatographic separation combined with much lower signal suppression, compared to a short temperature ramp program. No effects were observed for organic acids, fatty acids, sugars and sugar alcohols, while significant differences were observed for amino acids. GC metabolomics is a strong tool that can facilitate analysis, but special attention is required for sampling handling and heating, before and during the GC analysis. The use and application of multiple multi-group internal standards is highly recommended.
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Affiliation(s)
- Emmanouil D Tsochatzis
- Department of Food Science, Agro Food Park 48, Aarhus N 8200, Denmark; CiFOOD, Centre for Innovative Research, Aarhus University. Agro Food Park 48, 8200 Aarhus N, Denmark
| | - Caroline Nebel
- Department of Food Science, Agro Food Park 48, Aarhus N 8200, Denmark
| | - Marianne Danielsen
- Department of Food Science, Agro Food Park 48, Aarhus N 8200, Denmark; CiFOOD, Centre for Innovative Research, Aarhus University. Agro Food Park 48, 8200 Aarhus N, Denmark; CBIO, Centre of Circular Bioeconomy, Blichers Allé 20, Tjele 8830, Denmark
| | - Ulrik K Sundekilde
- Department of Food Science, Agro Food Park 48, Aarhus N 8200, Denmark; CiFOOD, Centre for Innovative Research, Aarhus University. Agro Food Park 48, 8200 Aarhus N, Denmark
| | - Trine Kastrup Dalsgaard
- Department of Food Science, Agro Food Park 48, Aarhus N 8200, Denmark; CiFOOD, Centre for Innovative Research, Aarhus University. Agro Food Park 48, 8200 Aarhus N, Denmark; CBIO, Centre of Circular Bioeconomy, Blichers Allé 20, Tjele 8830, Denmark.
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5
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Alseekh S, Aharoni A, Brotman Y, Contrepois K, D'Auria J, Ewald J, C Ewald J, Fraser PD, Giavalisco P, Hall RD, Heinemann M, Link H, Luo J, Neumann S, Nielsen J, Perez de Souza L, Saito K, Sauer U, Schroeder FC, Schuster S, Siuzdak G, Skirycz A, Sumner LW, Snyder MP, Tang H, Tohge T, Wang Y, Wen W, Wu S, Xu G, Zamboni N, Fernie AR. Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nat Methods 2021; 18:747-756. [PMID: 34239102 PMCID: PMC8592384 DOI: 10.1038/s41592-021-01197-1] [Citation(s) in RCA: 322] [Impact Index Per Article: 107.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
- Institute of Plants Systems Biology and Biotechnology, Plovdiv, Bulgaria.
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - John D'Auria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jan Ewald
- Department of Bioinformatics, University of Jena, Jena, Germany
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Paul D Fraser
- Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Robert D Hall
- BU Bioscience, Wageningen Research, Wageningen, the Netherlands
- Laboratory of Plant Physiology, Wageningen University, Wageningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
| | - Steffen Neumann
- Bioinformatics and Scientific Data, Leibniz Institute for Plant Biochemistry, Halle, Germany
| | - Jens Nielsen
- BioInnovation Institute, Copenhagen, Denmark
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Kazuki Saito
- Plant Molecular Science Center, Chiba University, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Uwe Sauer
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Stefan Schuster
- Department of Bioinformatics, University of Jena, Jena, Germany
| | - Gary Siuzdak
- Center for Metabolomics and Mass Spectrometry, Scripps Research Institute, La Jolla, CA, USA
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Lloyd W Sumner
- Department of Biochemistry and MU Metabolomics Center, University of Missouri, Columbia, MO, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai, China
| | - Takayuki Tohge
- Department of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, School of Biological Sciences, Nanyang Technological University, Nanyang, Singapore
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Nicola Zamboni
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
- Institute of Plants Systems Biology and Biotechnology, Plovdiv, Bulgaria.
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6
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Akyol O, Tessier K, Akyol S. Accuracy and uniformity of the nomenclature of biogenic amines and polyamines in metabolomics studies: A preliminary study. Biochem Mol Biol Educ 2021; 49:441-445. [PMID: 33682332 DOI: 10.1002/bmb.21497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/09/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Metabolomics is one of the newest areas in biochemistry dedicated to investigating small biomolecules in biofluids, tissues, and cells. Cutting edge instruments used in metabolomics studies make it possible to identify thousands of biomolecules and determine their interactions with biological networks. This tremendous area has increased the significance of accurate chemical nomenclature of compounds. Therefore, the classification of the organic molecules has become one of the most important issues in the field. Biogenic amines are nitrogenous compounds of low molecular weight formed by the decarboxylation of amino acids or by the amination and the transamination of aldehydes and ketones during normal metabolic processes. This letter covers the topic of nomenclature with respect to the current usage of biogenic amines in scientific literature. We use metabolomics as an example of field reporting data on trace levels of molecules that may be miscategorized in primary literature. We suggest that the incorrect classification of molecules will influence science education adversely because resources used for teaching are drawn from primary literature references that may contain errors.
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Affiliation(s)
- Omer Akyol
- Department of Anatomy and Molecular Medicine, Alabama College of Osteopathic Medicine, Dothan, Alabama, USA
| | - Kylie Tessier
- Michigan Math and Science Academy, Warren, Michigan, USA
| | - Sumeyya Akyol
- Beaumont Health System-Beaumont Research Institute, Royal Oak, Michigan, USA
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7
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Clark TN, Houriet J, Vidar WS, Kellogg JJ, Todd DA, Cech NB, Linington RG. Interlaboratory Comparison of Untargeted Mass Spectrometry Data Uncovers Underlying Causes for Variability. J Nat Prod 2021; 84:824-835. [PMID: 33666420 PMCID: PMC8326878 DOI: 10.1021/acs.jnatprod.0c01376] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite the value of mass spectrometry in modern natural products discovery workflows, it remains very difficult to compare data sets between laboratories. In this study we compared mass spectrometry data for the same sample set from two different laboratories (quadrupole time-of-flight and quadrupole-Orbitrap) and evaluated the similarity between these two data sets in terms of both mass spectrometry features and their ability to describe the chemical composition of the sample set. Somewhat surprisingly, the two data sets, collected with appropriate controls and replication, had very low feature overlap (25.7% of Laboratory A features overlapping 21.8% of Laboratory B features). Our data clearly demonstrate that differences in fragmentation, charge state, and adduct formation in the ionization source are a major underlying cause for these differences. Consistent with other recent literature, these findings challenge the conventional wisdom that electrospray ionization mass spectrometry (ESI-MS) yields a simple one-to-one correspondence between analytes in solution and features in the data set. Importantly, despite low overlap in feature lists, principal component analysis (PCA) generated qualitatively similar PCA plots. Overall, our findings demonstrate that comparing untargeted metabolomics data between laboratories is challenging, but that data sets with low feature overlap can yield the same qualitative description of a sample set using PCA.
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Affiliation(s)
- Trevor N. Clark
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Joëlle Houriet
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Warren S. Vidar
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Joshua J. Kellogg
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Daniel A. Todd
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Nadja B. Cech
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
- Corresponding Author Nadja B. Cech; Tel: 336-324-5011. Fax: 336-334-5402. . Roger G. Linington; Tel 778-7823517. Fax: 778-782-3765.
| | - Roger G. Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Corresponding Author Nadja B. Cech; Tel: 336-324-5011. Fax: 336-334-5402. . Roger G. Linington; Tel 778-7823517. Fax: 778-782-3765.
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McClain KM, Moore SC, Sampson JN, Henderson TR, Gebauer SK, Newman JW, Ross S, Pedersen TL, Baer DJ, Zanetti KA. Preanalytical Sample Handling Conditions and Their Effects on the Human Serum Metabolome in Epidemiologic Studies. Am J Epidemiol 2021; 190:459-467. [PMID: 32959873 DOI: 10.1093/aje/kwaa202] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
Many epidemiologic studies use metabolomics for discovery-based research. The degree to which sample handling may influence findings, however, is poorly understood. In 2016, serum samples from 13 volunteers from the US Department of Agriculture's Beltsville Human Nutrition Research Center were subjected to different clotting (30 minutes/120 minutes) and refrigeration (0 minutes/24 hours) conditions, as well as different numbers (0/1/4) and temperatures (ice/refrigerator/room temperature) of thaws. The median absolute percent difference (APD) between metabolite levels and correlations between levels across conditions were estimated for 628 metabolites. The potential for handling artifacts to induce false-positive associations was estimated using variable hypothetical scenarios in which 1%-100% of case samples had different handling than control samples. All handling conditions influenced metabolite levels. Across metabolites, the median APD when extending clotting time was 9.08%. When increasing the number of thaws from 0 to 4, the median APD was 10.05% for ice and 5.54% for room temperature. Metabolite levels were correlated highly across conditions (all r's ≥ 0.84), indicating that relative ranks were preserved. However, if handling varied even modestly by case status, our hypotheticals showed that results can be biased and can result in false-positive findings. Sample handling affects levels of metabolites, and special care should be taken to minimize effects. Shorter room-temperature thaws should be preferred over longer ice thaws, and handling should be meticulously matched by case status.
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Nagy T, Róth G, Kuki Á, Zsuga M, Kéki S. Mass Spectral Filtering by Mass-Remainder Analysis (MARA) at High Resolution and Its Application to Metabolite Profiling of Flavonoids. Int J Mol Sci 2021; 22:ijms22020864. [PMID: 33467107 PMCID: PMC7830504 DOI: 10.3390/ijms22020864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
Flavonoids represent an important class of secondary metabolites because of their potential health benefits and functions in plants. We propose a novel method for the comprehensive flavonoid filtering and screening based on direct infusion mass spectrometry (DIMS) analysis. The recently invented data mining procedure, the multi-step mass-remainder analysis (M-MARA) technique is applied for the effective mass spectral filtering of the peak rich spectra of natural herb extracts. In addition, our flavonoid-filtering algorithm facilitates the determination of the elemental composition. M-MARA flavonoid-filtering uses simple mathematical and logical operations and thus, it can easily be implemented in a regular spreadsheet software. A huge benefit of our method is the high speed and the low demand for computing power and memory that enables the real time application even for tandem mass spectrometric analysis. Our novel method was applied for the electrospray ionization (ESI) DIMS spectra of various herb extract, and the filtered mass spectral data were subjected to chemometrics analysis using principal component analysis (PCA).
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Affiliation(s)
- Tibor Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (G.R.); (Á.K.); (M.Z.)
| | - Gergő Róth
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (G.R.); (Á.K.); (M.Z.)
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Ákos Kuki
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (G.R.); (Á.K.); (M.Z.)
| | - Miklós Zsuga
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (G.R.); (Á.K.); (M.Z.)
| | - Sándor Kéki
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (G.R.); (Á.K.); (M.Z.)
- Correspondence: ; Fax: +36-52-518662
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Mervant L, Tremblay-Franco M, Jamin EL, Kesse-Guyot E, Galan P, Martin JF, Guéraud F, Debrauwer L. Osmolality-based normalization enhances statistical discrimination of untargeted metabolomic urine analysis: results from a comparative study. Metabolomics 2021; 17:2. [PMID: 33389209 DOI: 10.1007/s11306-020-01758-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Because of its ease of collection, urine is one of the most commonly used matrices for metabolomics studies. However, unlike other biofluids, urine exhibits tremendous variability that can introduce confounding inconsistency during result interpretation. Despite many existing techniques to normalize urine samples, there is still no consensus on either which method is most appropriate or how to evaluate these methods. OBJECTIVES To investigate the impact of several methods and combinations of methods conventionally used in urine metabolomics on the statistical discrimination of two groups in a simple metabolomics study. METHODS We applied 14 different strategies of normalization to forty urine samples analysed by liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). To evaluate the impact of these different strategies, we relied on the ability of each method to reduce confounding variability while retaining variability of interest, as well as the predictability of statistical models. RESULTS Among all tested normalization methods, osmolality-based normalization gave the best results. Moreover, we demonstrated that normalization using a specific dilution prior to the analysis outperformed post-acquisition normalization. We also demonstrated that the combination of various normalization methods does not necessarily improve statistical discrimination. CONCLUSIONS This study re-emphasized the importance of normalizing urine samples for metabolomics studies. In addition, it appeared that the choice of method had a significant impact on result quality. Consequently, we suggest osmolality-based normalization as the best method for normalizing urine samples. TRIAL REGISTRATION NUMBER NCT03335644.
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Affiliation(s)
- Loïc Mervant
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Marie Tremblay-Franco
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France.
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.
| | - Emilien L Jamin
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Emmanuelle Kesse-Guyot
- Sorbonne Paris Nord University, Inserm, INRAE, Cnam, Nutritional Epidemiology, Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 93017, Bobigny, France
| | - Pilar Galan
- Sorbonne Paris Nord University, Inserm, INRAE, Cnam, Nutritional Epidemiology, Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 93017, Bobigny, France
| | - Jean-François Martin
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Françoise Guéraud
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Debrauwer
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
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11
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Baima G, Iaderosa G, Citterio F, Grossi S, Romano F, Berta GN, Buduneli N, Aimetti M. Salivary metabolomics for the diagnosis of periodontal diseases: a systematic review with methodological quality assessment. Metabolomics 2021; 17:1. [PMID: 33387070 DOI: 10.1007/s11306-020-01754-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/30/2020] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Early diagnosis of periodontitis by means of a rapid, accurate and non-invasive method is highly desirable to reduce the individual and epidemiological burden of this largely prevalent disease. OBJECTIVES The aims of the present systematic review were to examine potential salivary metabolic biomarkers and pathways associated to periodontitis, and to assess the accuracy of salivary untargeted metabolomics for the diagnosis of periodontal diseases. METHODS Relevant studies identified from MEDLINE (PubMed), Embase and Scopus databases were systematically examined for analytical protocols, metabolic biomarkers and results from the multivariate analysis (MVA). Pathway analysis was performed using the MetaboAnalyst online software and quality assessment by means of a modified version of the QUADOMICS tool. RESULTS Twelve studies met the inclusion criteria, with sample sizes ranging from 19 to 130 subjects. Compared to periodontally healthy individuals, valine, phenylalanine, isoleucine, tyrosine and butyrate were found upregulated in periodontitis patients in most studies; while lactate, pyruvate and N-acetyl groups were the most significantly expressed in healthy individuals. Metabolic pathways that resulted dysregulated are mainly implicated in inflammation, oxidative stress, immune activation and bacterial energetic metabolism. The findings from MVA revealed that periodontitis is characterized by a specific metabolic signature in saliva, with coefficients of determination ranging from 0.52 to 0.99. CONCLUSIONS This systematic review summarizes candidate metabolic biomarkers and pathways related to periodontitis, which may provide opportunities for the validation of diagnostic or predictive models and the discovery of novel targets for monitoring and treating such a disease (PROSPERO CRD42020188482).
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Affiliation(s)
- Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy.
| | - Giovanni Iaderosa
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Filippo Citterio
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Silvia Grossi
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Federica Romano
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giovanni N Berta
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Nurcan Buduneli
- Department of Periodontology, School of Dentistry, Ege University, İzmir, Turkey
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
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12
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Creydt M, Fischer M. Mass-Spectrometry-Based Food Metabolomics in Routine Applications: A Basic Standardization Approach Using Housekeeping Metabolites for the Authentication of Asparagus. J Agric Food Chem 2020; 68:14343-14352. [PMID: 32249560 DOI: 10.1021/acs.jafc.0c01204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The low reproducibility of non-targeted liquid chromatography-mass spectrometry-based metabolomics approaches represents a major challenge for their implementation in routine analyses, because it is impossible to compare individual measurements directly with each other, if they were not analyzed in the same batch. This study describes a normalization process based on housekeeping metabolites in plant-based raw materials, which are present in comparatively constant concentrations and are subject to no or only minor deviations as a result of exogenous influences. As a model, an authenticity study was selected to determine the origin of white asparagus (Asparagus officinalis). Using three model data sets and one test data set, we were able to show that samples that have been measured independently of one another can be correctly assigned in terms of origin after the normalization with housekeeping metabolites. The procedure does not require internal standards or the measurements of further reference samples and can also be applied to other matrices and scientific issues.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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13
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Troisi J, Raffone A, Travaglino A, Belli G, Belli C, Anand S, Giugliano L, Cavallo P, Scala G, Symes S, Richards S, Adair D, Fasano A, Bottigliero V, Guida M. Development and Validation of a Serum Metabolomic Signature for Endometrial Cancer Screening in Postmenopausal Women. JAMA Netw Open 2020; 3:e2018327. [PMID: 32986110 PMCID: PMC7522698 DOI: 10.1001/jamanetworkopen.2020.18327] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IMPORTANCE Endometrial carcinoma (EC) is the most commonly diagnosed gynecologic cancer. Its early detection is advisable because 20% of women have advanced disease at the time of diagnosis. OBJECTIVE To clinically validate a metabolomics-based classification algorithm as a screening test for EC. DESIGN, SETTING, AND PARTICIPANTS This diagnostic study enrolled 2 cohorts. A multicenter prospective cohort, with 50 cases (postmenopausal women with EC; International Federation of Gynecology and Obstetrics stage I-III and grade G1-G3) and 70 controls (no EC but matched on age, years from menopause, tobacco use, and comorbidities), was used to train multiple classification models. The accuracy of each trained model was then used as a statistical weight to produce an ensemble machine learning algorithm for testing, which was validated with a subsequent prospective cohort of 1430 postmenopausal women. The study was conducted at the San Giovanni di Dio e Ruggi d'Aragona University Hospital of Salerno (Italy) and Lega Italiana per la Lotta contro i Tumori clinic in Avellino (Italy). Data collection was conducted from January 2018 to February 2019, and analysis was conducted from January to March 2019. MAIN OUTCOMES AND MEASURES The presence or absence of EC based on evaluation of the blood metabolome. Metabolites were extracted from dried blood samples from all participants and analyzed by gas chromatography-mass spectrometry. A confusion matrix was used to summarize test results. Performance indices included sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, and accuracy. Confirmation or exclusion of EC in women with a positive test result was by means of hysteroscopy. Participants with negative results were followed up 1 year after enrollment to investigate the appearance of EC signs. RESULTS The study population consisted of 1550 postmenopausal women. The mean (SD) age was 68.2 (11.7) years for participants with no EC in the training cohort, 69.4 (13.8) years for women with EC in the training cohort, and 59.7 (7.7) years for women in the validation cohort. Application of the ensemble machine learning to the validation cohort resulted in 16 true-positives, 2 false-positives, and 0 false-negatives, and it correctly classified more than 99% of samples. Disease prevalence was 1.12% (16 of 1430). CONCLUSIONS AND RELEVANCE In this study, dried blood metabolomic profile was used to assess the presence or absence of EC in postmenopausal women not receiving hormonal therapy with greater than 99% accuracy.
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Affiliation(s)
- Jacopo Troisi
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
- Theoreo, Montecorvino Pugliano, Salerno, Italy
- European Biomedical Research Institute of Salerno, Salerno, Italy
| | - Antonio Raffone
- Department of Neurosciences and Reproductive and Dentistry Sciences, University of Naples Federico II, Naples, Italy
| | - Antonio Travaglino
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Gaetano Belli
- Lega Italiana per la Lotta contro i Tumori, Avellino Section, Avellino, Italy
| | - Carmen Belli
- Lega Italiana per la Lotta contro i Tumori, Avellino Section, Avellino, Italy
| | - Santosh Anand
- Università degli Studi di Milano–Bicocca, Milano, Italy
- Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Luigi Giugliano
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Pierpaolo Cavallo
- Department of Physics, University of Salerno, Fisciano, Salerno, Italy
- Istituto Sistemi Complessi–Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Steven Symes
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga
- Department of Obstetrics and Gynecology, College of Medicine, University of Tennessee College of Medicine at Chattanooga
| | - Sean Richards
- Department of Obstetrics and Gynecology, College of Medicine, University of Tennessee College of Medicine at Chattanooga
- Department of Biology, Geology and Environmental Sciences, The University of Tennessee at Chattanooga
| | - David Adair
- Department of Obstetrics and Gynecology, College of Medicine, University of Tennessee College of Medicine at Chattanooga
| | - Alessio Fasano
- European Biomedical Research Institute of Salerno, Salerno, Italy
| | - Vincenzo Bottigliero
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Maurizio Guida
- Theoreo, Montecorvino Pugliano, Salerno, Italy
- Department of Neurosciences and Reproductive and Dentistry Sciences, University of Naples Federico II, Naples, Italy
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14
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Liu KH, Nellis M, Uppal K, Ma C, Tran V, Liang Y, Walker DI, Jones DP. Reference Standardization for Quantification and Harmonization of Large-Scale Metabolomics. Anal Chem 2020; 92:8836-8844. [PMID: 32490663 PMCID: PMC7887762 DOI: 10.1021/acs.analchem.0c00338] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reference standardization was developed to address quantification and harmonization challenges for high-resolution metabolomics (HRM) data collected across different studies or analytical methods. Reference standardization relies on the concurrent analysis of calibrated pooled reference samples at predefined intervals and enables a single-step batch correction and quantification for high-throughput metabolomics. Here, we provide quantitative measures of approximately 200 metabolites for each of three pooled reference materials (220 metabolites for Qstd3, 211 metabolites for CHEAR, 204 metabolites for NIST1950) and show application of this approach for quantification supports harmonization of metabolomics data collected from 3677 human samples in 17 separate studies analyzed by two complementary HRM methods over a 17-month period. The results establish reference standardization as a method suitable for harmonizing large-scale metabolomics data and extending capabilities to quantify large numbers of known and unidentified metabolites detected by high-resolution mass spectrometry methods.
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Affiliation(s)
- Ken H Liu
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Mary Nellis
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Karan Uppal
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Chunyu Ma
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - ViLinh Tran
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Yongliang Liang
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia 30322, United States
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15
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Sarvin B, Lagziel S, Sarvin N, Mukha D, Kumar P, Aizenshtein E, Shlomi T. Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample-specific ion distributions. Nat Commun 2020; 11:3186. [PMID: 32581242 PMCID: PMC7314751 DOI: 10.1038/s41467-020-17026-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 06/02/2020] [Indexed: 11/29/2022] Open
Abstract
Mass spectrometry based metabolomics is a widely used approach in biomedical research. However, current methods coupling mass spectrometry with chromatography are time-consuming and not suitable for high-throughput analysis of thousands of samples. An alternative approach is flow-injection mass spectrometry (FI-MS) in which samples are directly injected to the ionization source. Here, we show that the sensitivity of Orbitrap FI-MS metabolomics methods is limited by ion competition effect. We describe an approach for overcoming this effect by analyzing the distribution of ion m/z values and computationally determining a series of optimal scan ranges. This enables reproducible detection of ~9,000 and ~10,000 m/z features in metabolomics and lipidomics analysis of serum samples, respectively, with a sample scan time of ~15 s and duty time of ~30 s; a ~50% increase versus current spectral-stitching FI-MS. This approach facilitates high-throughput metabolomics for a variety of applications, including biomarker discovery and functional genomics screens.
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Affiliation(s)
- Boris Sarvin
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Shoval Lagziel
- Faculty of Computer Science, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Nikita Sarvin
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Dzmitry Mukha
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Praveen Kumar
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Elina Aizenshtein
- Lokey Center for Life Science and Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Tomer Shlomi
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
- Faculty of Computer Science, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
- Lokey Center for Life Science and Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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16
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Abstract
Data normalization is a big challenge in quantitative metabolomics approaches, whether targeted or untargeted. Without proper normalization, the mass-spectrometry and spectroscopy data can provide erroneous, sub-optimal data, which can lead to misleading and confusing biological results and thereby result in failed application to human healthcare, clinical, and other research avenues. To address this issue, a number of statistical approaches and software tools have been proposed in the literature and implemented over the years, thereby providing a multitude of approaches to choose from - either sample-based or data-based normalization strategies. In recent years, new dedicated software tools for metabolomics data normalization have surfaced as well. In this account article, I summarize the existing approaches and the new discoveries and research findings in this area of metabolomics data normalization, and I introduce some recent tools that aid in data normalization.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Section of Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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17
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Stotland AB, Spivia W, Orosco A, Andres AM, Gottlieb RA, Van Eyk JE, Parker SJ. MitoPlex: A targeted multiple reaction monitoring assay for quantification of a curated set of mitochondrial proteins. J Mol Cell Cardiol 2020; 142:1-13. [PMID: 32234390 PMCID: PMC7347090 DOI: 10.1016/j.yjmcc.2020.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
Mitochondria are the major source of cellular energy (ATP), as well as critical mediators of widespread functions such as cellular redox balance, apoptosis, and metabolic flux. The organelles play an especially important role in the maintenance of cardiac homeostasis; their inability to generate ATP following impairment due to ischemic damage has been directly linked to organ failure. Methods to quantify mitochondrial content are limited to low throughput immunoassays, measurement of mitochondrial DNA, or relative quantification by untargeted mass spectrometry. Here, we present a high throughput, reproducible and quantitative mass spectrometry multiple reaction monitoring based assay of 37 proteins critical to central carbon chain metabolism and overall mitochondrial function termed 'MitoPlex'. We coupled this protein multiplex with a parallel analysis of the central carbon chain metabolites (219 metabolite assay) extracted in tandem from the same sample, be it cells or tissue. In tests of its biological applicability in cells and tissues, "MitoPlex plus metabolites" indicated profound effects of HMG-CoA Reductase inhibition (e.g., statin treatment) on mitochondria of i) differentiating C2C12 skeletal myoblasts, as well as a clear opposite trend of statins to promote mitochondrial protein expression and metabolism in heart and liver, while suppressing mitochondrial protein and ii) aspects of metabolism in the skeletal muscle obtained from C57Bl6 mice. Our results not only reveal new insights into the metabolic effect of statins in skeletal muscle, but present a new high throughput, reliable MS-based tool to study mitochondrial dynamics in both cell culture and in vivo models.
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Affiliation(s)
- Aleksandr B Stotland
- Molecular Cardiobiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Weston Spivia
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Amanda Orosco
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Allen M Andres
- Molecular Cardiobiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Roberta A Gottlieb
- Molecular Cardiobiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America.
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Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech 2020; 31:11-26. [PMID: 31969795 PMCID: PMC6959150 DOI: 10.7171/jbt.20-3101-003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and they have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications.
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Affiliation(s)
- Sheenah M. Mische
- New York University (NYU) Langone Medical Center, New
York, New York 10016, USA
| | - Nancy C. Fisher
- University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599, USA
| | - Susan M. Meyn
- Vanderbilt University Medical Center, Nashville,
Tennessee 37212, USA
| | - Katia Sol-Church
- University of Virginia School of Medicine,
Charlottesville, Virginia 22908, USA
| | | | | | - Marie Adams
- Van Andel Institute, Grand Rapids, Michigan 49503,
USA
| | - John M. Ashton
- University of Rochester Medical Center, West
Henrietta, New York 14642, USA
| | - Kym M. Delventhal
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | | | - Laura Holmes
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | - Pratik Jagtap
- University of Minnesota, Minneapolis, Minnesota
55455, USA
| | | | | | - Magnus Palmblad
- Leiden University Medical Center, Leiden 2333, The
Netherlands
| | - Brian C. Searle
- Institute for Systems Biology, Seattle, Washington
98109, USA
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19
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Albóniga OE, González O, Alonso RM, Xu Y, Goodacre R. Optimization of XCMS parameters for LC-MS metabolomics: an assessment of automated versus manual tuning and its effect on the final results. Metabolomics 2020; 16:14. [PMID: 31925557 DOI: 10.1007/s11306-020-1636-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/04/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Several software packages containing diverse algorithms are available for processing Liquid Chromatography-Mass Spectrometry (LC-MS) chromatographic data and within these deconvolution packages different parameters settings can lead to different outcomes. XCMS is the most widely used peak picking and deconvolution software for metabolomics, but the parameter selection can be hard for inexpert users. To solve this issue, the automatic optimization tools such as Isotopologue Parameters Optimization (IPO) can be extremely helpful. OBJECTIVES To evaluate the suitability of IPO as a tool for XCMS parameters optimization and compare the results with those manually obtained by an exhaustive examination of the LC-MS characteristics and performance. METHODS Raw HPLC-TOF-MS data from two types of biological samples (liver and plasma) analysed in both positive and negative electrospray ionization modes from three groups of piglets were processed with XCMS using parameters optimized following two different approaches: IPO and Manual. The outcomes were compared to determine the advantages and disadvantages of using each method. RESULTS IPO processing produced the higher number of repeatable (%RSD < 20) and significant features for all data sets and allowed the different piglet groups to be distinguished. Nevertheless, on multivariate level, similar clustering results were obtained by Principal Component Analysis (PCA) when applied to IPO and manual matrices. CONCLUSION IPO is a useful optimization tool that helps in choosing the appropriate parameters. It works well on data with a good LC-MS performance but the lack of such adequate data can result in unrealistic parameter settings, which might require further investigation and manual tuning. On the contrary, manual selection criteria requires deeper knowledge on LC-MS, programming language and XCMS parameter interpretation, but allows a better fine-tuning of the parameters, and thus more robust deconvolution.
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Affiliation(s)
- Oihane E Albóniga
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, Spain.
| | - Oskar González
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, Spain
| | - Rosa M Alonso
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, Spain
| | - Yun Xu
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Royston Goodacre
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
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Pittard WS, Villaveces CK, Li S. A Bioinformatics Primer to Data Science, with Examples for Metabolomics. Methods Mol Biol 2020; 2104:245-263. [PMID: 31953822 DOI: 10.1007/978-1-0716-0239-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
With the increasing importance of big data in biomedicine, skills in data science are a foundation for the individual career development and for the progress of science. This chapter is a practical guide to working with high-throughput biomedical data. It covers how to understand and set up the computing environment, to start a research project with proper and effective data management, and to perform common bioinformatics tasks such as data wrangling, quality control, statistical analysis, and visualization, with examples on metabolomics data. Concepts and tools related to coding and scripting are discussed. Version control, knitr and Jupyter notebooks are important to project management, collaboration, and research reproducibility. Overall, this chapter describes a core set of skills to work in bioinformatics, and can serve as a reference text at the level of a graduate course and interfacing with data science.
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Affiliation(s)
- W Stephen Pittard
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Shuzhao Li
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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Abstract
In this chapter, we summarize data preprocessing and data analysis strategies used for analysis of NMR data for metabolomics studies. Metabolomics consists of the analysis of the low molecular weight compounds in cells, tissues, or biological fluids, and has been used to reveal biomarkers for early disease detection and diagnosis, to monitor interventions, and to provide information on pathway perturbations to inform mechanisms and identifying targets. Metabolic profiling (also termed metabotyping) involves the analysis of hundreds to thousands of molecules using mainly state-of-the-art mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy technologies. While NMR is less sensitive than mass spectrometry, NMR does provide a wealth of complex and information rich metabolite data. NMR data together with the use of conventional statistics, modeling methods, and bioinformatics tools reveals biomarker and mechanistic information. A typical NMR spectrum, with up to 64k data points, of a complex biological fluid or an extract of cells and tissues consists of thousands of sharp signals that are mainly derived from small molecules. In addition, a number of advanced NMR spectroscopic methods are available for extracting information on high molecular weight compounds such as lipids or lipoproteins. There are numerous data preprocessing, data reduction, and analysis methods developed and evolving in the field of NMR metabolomics. Our goal is to provide an extensive summary of NMR data preprocessing and analysis strategies by providing examples and open source and commercially available analysis software and bioinformatics tools.
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Affiliation(s)
- Wimal Pathmasiri
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
| | - Kristine Kay
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan McRitchie
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan Sumner
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
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Baker ES, Patti GJ. Perspectives on Data Analysis in Metabolomics: Points of Agreement and Disagreement from the 2018 ASMS Fall Workshop. J Am Soc Mass Spectrom 2019; 30:2031-2036. [PMID: 31440979 PMCID: PMC7310669 DOI: 10.1007/s13361-019-02295-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 05/04/2023]
Abstract
In November 2018, the American Society for Mass Spectrometry hosted the Annual Fall Workshop on informatic methods in metabolomics. The Workshop included sixteen lectures presented by twelve invited speakers. The focus of the talks was untargeted metabolomics performed with liquid chromatography/mass spectrometry. In this review, we highlight five recurring topics that were covered by multiple presenters: (i) data sharing, (ii) artifacts and contaminants, (iii) feature degeneracy, (iv) database organization, and (v) requirements for metabolite identification. Our objective here is to present viewpoints that were widely shared among participants, as well as those in which varying opinions were articulated. We note that most of the presenting speakers employed different data processing software, which underscores the diversity of informatic programs currently being used in metabolomics. We conclude with our thoughts on the potential role of reference datasets as a step towards standardizing data processing methods in metabolomics.
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Affiliation(s)
- Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA.
| | - Gary J Patti
- Departments of Chemistry and Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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Lorkiewicz PK, Gibb AA, Rood BR, He L, Zheng Y, Clem BF, Zhang X, Hill BG. Integration of flux measurements and pharmacological controls to optimize stable isotope-resolved metabolomics workflows and interpretation. Sci Rep 2019; 9:13705. [PMID: 31548575 PMCID: PMC6757038 DOI: 10.1038/s41598-019-50183-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Stable isotope-resolved metabolomics (SIRM) provides information regarding the relative activity of numerous metabolic pathways and the contribution of nutrients to specific metabolite pools; however, SIRM experiments can be difficult to execute, and data interpretation is challenging. Furthermore, standardization of analytical procedures and workflows remain significant obstacles for widespread reproducibility. Here, we demonstrate the workflow of a typical SIRM experiment and suggest experimental controls and measures of cross-validation that improve data interpretation. Inhibitors of glycolysis and oxidative phosphorylation as well as mitochondrial uncouplers serve as pharmacological controls, which help define metabolic flux configurations that occur under well-controlled metabolic states. We demonstrate how such controls and time course labeling experiments improve confidence in metabolite assignments as well as delineate metabolic pathway relationships. Moreover, we demonstrate how radiolabeled tracers and extracellular flux analyses integrate with SIRM to improve data interpretation. Collectively, these results show how integration of flux methodologies and use of pharmacological controls increase confidence in SIRM data and provide new biological insights.
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Affiliation(s)
- Pawel K Lorkiewicz
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, USA
- Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, USA
| | - Andrew A Gibb
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, USA
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Benjamin R Rood
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, USA
| | - Liqing He
- Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, USA
| | - Yuting Zheng
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, USA
| | - Brian F Clem
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Xiang Zhang
- Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, USA
| | - Bradford G Hill
- Department of Medicine, Division of Environmental Medicine, Christina Lee Brown Envirome Institute, Diabetes and Obesity Center, University of Louisville, Louisville, USA.
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Li Y, Li L. Mass Accuracy Check Using Common Background Peaks for Improving Metabolome Data Quality in Chemical Isotope Labeling LC-MS. J Am Soc Mass Spectrom 2019; 30:1733-1741. [PMID: 31140076 DOI: 10.1007/s13361-019-02248-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/24/2019] [Accepted: 05/05/2019] [Indexed: 06/09/2023]
Abstract
Chemical isotope labeling (CIL) LC-MS is a highly sensitive and quantitative method for metabolome analysis. Because of a large number of peaks detectable in a sample and the need of running many samples in a metabolomics project, any significant change in mass measurement accuracy during the whole period of running samples can adversely affect the downstream peak alignment and quantitative analysis. Herein, we report a rapid method to check the mass accuracy of individual spectra in each CIL LC-MS run in order to flag up any run containing spectra with accuracy drift that falls outside the expected error. The flagged run may be re-run or discarded before merging with other runs for peak alignment and analysis. This method is based on the observation that some background signals are commonly detected in almost all spectra collected in CIL LC-MS runs. A mass accuracy check (MAC) software program has been developed to first find the common background mass peaks and then use them as mass references to calculate any mass shifts over the course of multiple sample runs. Using a metabolome dataset of 324 human cerebrospinal fluid (CSF) samples and 35 quality control (QC) samples produced by CIL LC-MS, we show that this accuracy check method can streamline the initial raw data processing for downstream analysis in metabolomics.
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Affiliation(s)
- Yunong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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Freiburghaus K, Largiadèr CR, Stettler C, Fiedler GM, Bally L, Bovet C. Metabolomics by UHPLC-MS: benefits provided by complementary use of Q-TOF and QQQ for pathway profiling. Metabolomics 2019; 15:120. [PMID: 31463683 DOI: 10.1007/s11306-019-1585-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/22/2019] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Non-targeted metabolic profiling using high-resolution mass spectrometry (HRMS) is a standard approach for pathway identification despite technical limitations. OBJECTIVES To assess the performance of combining targeted quadrupole (QQQ) analysis with HRMS for in-depth pathway profiling. METHODS Serum of exercising patients with type 1 diabetes (T1D) was profiled using targeted and non-targeted assays. RESULTS Non-targeted analysis yielded a broad unbiased metabolic profile, targeted analysis increased coverage of purine metabolism (twofold) and TCA cycle (three metabolites). CONCLUSION Our screening strategy combined the benefits of the unbiased full-scan HRMS acquisition with the deeper insight into specific pathways by large-scale QQQ analysis.
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MESH Headings
- Citric Acid Cycle
- Diabetes Mellitus, Type 1/blood
- Diabetes Mellitus, Type 1/metabolism
- Humans
- Limit of Detection
- Male
- Metabolome
- Metabolomics/methods
- Metabolomics/standards
- Physical Conditioning, Human
- Purines/metabolism
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Electrospray Ionization/standards
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/standards
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Affiliation(s)
- Katrin Freiburghaus
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Carlo Rodolfo Largiadèr
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christoph Stettler
- Department of Diabetes, Endocrinology, Clinical Nutrition & Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Georg Martin Fiedler
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Lia Bally
- Department of Diabetes, Endocrinology, Clinical Nutrition & Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cédric Bovet
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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Rahman S, Ul Haq F, Ali A, Khan MN, Shah SMZ, Adhikhari A, El-Seedi HR, Musharraf SG. Combining untargeted and targeted metabolomics approaches for the standardization of polyherbal formulations through UPLC-MS/MS. Metabolomics 2019; 15:116. [PMID: 31440842 DOI: 10.1007/s11306-019-1582-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/17/2019] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Polyherbal formulations are an integral part of various indigenous medicinal systems such as Traditional Chinese Medicine (TCM) and Ayurveda. The presence of a very large number of compounds makes the quality control of polyherbal formulations very difficult. OBJECTIVES To overcome this problem, we have developed a comprehensive strategy for the dereplication of natural products in polyherbal formulations by using Adhatoda vasica as a case study. METHODS The strategy is based on five major steps: the collection of plant samples from different locations to observe the effects of environmental variables; LC-ESI-MS/MS-based untargeted metabolite profiling of the plant samples to identify marker compounds using extensive chemometric analysis of the obtained data; the identification of marker compounds in polyherbal products; the isolation, purification and characterization of the marker compounds; and MRM-based quantitative analysis of the isolated marker compounds using LC-ESI-MS/MS. RESULTS Using this strategy, we identified a total of 51 compounds in the methanolic extract of A. vasica plants from 14 accessions. Chemical fingerprinting of the plant led to the identification of characteristic peaks that were used to confirm the presence of A. vasica in complex polyherbal formulations. Four quinazoline alkaloids (marker compounds) were isolated, purified and quantified in various herbal formulations containing A. vasica. CONCLUSION This method demonstrates a comprehensive strategy based on untargeted and targeted metabolite analysis that can be used for the standardization of complex polyherbal formulations.
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Affiliation(s)
- Saeedur Rahman
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Faraz Ul Haq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Noman Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Syed Muhammad Zaki Shah
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Achyut Adhikhari
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Hesham R El-Seedi
- Pharmacognosoy Group, Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Box 574, 75 123, Uppsala, Sweden
- Alrayan Medical College, Medina, 42541, Kingdom of Saudi Arabia
| | - Syed Ghulam Musharraf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Castaño-Cerezo S, Kulyk-Barbier H, Millard P, Portais JC, Heux S, Truan G, Bellvert F. Functional analysis of isoprenoid precursors biosynthesis by quantitative metabolomics and isotopologue profiling. Metabolomics 2019; 15:115. [PMID: 31435826 PMCID: PMC6704079 DOI: 10.1007/s11306-019-1580-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/13/2019] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Isoprenoids are amongst the most abundant and diverse biological molecules and are involved in a broad range of biological functions. Functional understanding of their biosynthesis is thus key in many fundamental and applicative fields, including systems biology, medicine and biotechnology. However, available methods do not yet allow accurate quantification and tracing of stable isotopes incorporation for all the isoprenoids precursors. OBJECTIVES We developed and validated a complete methodology for quantitative metabolomics and isotopologue profiling of isoprenoid precursors in the yeast Saccharomyces cerevisiae. METHODS This workflow covers all the experimental and computational steps from sample collection and preparation to data acquisition and processing. It also includes a novel quantification method based on liquid chromatography coupled to high-resolution mass spectrometry. Method validation followed the Metabolomics Standards Initiative guidelines. RESULTS This workflow ensures accurate absolute quantification (RSD < 20%) of all mevalonate and prenyl pyrophosphates intermediates with a high sensitivity over a large linear range (from 0.1 to 50 pmol). In addition, we demonstrate that this workflow brings crucial information to design more efficient phytoene producers. Results indicate stable turnover rates of prenyl pyrophosphate intermediates in the constructed strains and provide quantitative information on the change of the biosynthetic flux of phytoene precursors. CONCLUSION This methodology fills one of the last technical gaps for functional studies of isoprenoids biosynthesis and should be applicable to other eukaryotic and prokaryotic (micro)organisms after adaptation of some organism-dependent steps. This methodology also opens the way to 13C-metabolic flux analysis of isoprenoid biosynthesis.
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Affiliation(s)
| | - Hanna Kulyk-Barbier
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean-Charles Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Stéphanie Heux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Gilles Truan
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Floriant Bellvert
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.
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Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM. Use cases, best practice and reporting standards for metabolomics in regulatory toxicology. Nat Commun 2019; 10:3041. [PMID: 31292445 PMCID: PMC6620295 DOI: 10.1038/s41467-019-10900-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/07/2019] [Indexed: 12/23/2022] Open
Abstract
Metabolomics is a widely used technology in academic research, yet its application to regulatory science has been limited. The most commonly cited barrier to its translation is lack of performance and reporting standards. The MEtabolomics standaRds Initiative in Toxicology (MERIT) project brings together international experts from multiple sectors to address this need. Here, we identify the most relevant applications for metabolomics in regulatory toxicology and develop best practice guidelines, performance and reporting standards for acquiring and analysing untargeted metabolomics and targeted metabolite data. We recommend that these guidelines are evaluated and implemented for several regulatory use cases.
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Affiliation(s)
- Mark R Viant
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | | | | | | | - David J T Epps
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | | | | | | | | | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
| | - Reza M Salek
- International Agency for Research on Cancer, Lyon, France
| | - Tilmann Walk
- BASF Metabolome Solutions, 10589, Berlin, Germany
| | - Ralf J M Weber
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Li-Gao R, Hughes DA, le Cessie S, de Mutsert R, den Heijer M, Rosendaal FR, Willems van Dijk K, Timpson NJ, Mook-Kanamori DO. Assessment of reproducibility and biological variability of fasting and postprandial plasma metabolite concentrations using 1H NMR spectroscopy. PLoS One 2019; 14:e0218549. [PMID: 31220183 PMCID: PMC6586348 DOI: 10.1371/journal.pone.0218549] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022] Open
Abstract
Introduction It is crucial to understand the factors that introduce variability before applying metabolomics to clinical and biomarker research. Objectives We quantified technical and biological variability of both fasting and postprandial metabolite concentrations measured using 1H NMR spectroscopy in plasma samples. Methods In the Netherlands Epidemiology of Obesity study (n = 6,671), 148 metabolite concentrations (101 metabolites belonging to lipoprotein subclasses) were measured under fasting and postprandial states (150 minutes after a mixed liquid meal). Technical variability was evaluated among 265 fasting and 851 postprandial samples, with the identical blood plasma sample being measured twice by the same laboratory protocol. Biological reproducibility was assessed by measuring 165 individuals twice across time for evaluation of short- (<6 months) and long-term (>3 years) biological variability. Intra-class coefficients (ICCs) were used to assess variability. The ICCs of the fasting metabolites were compared with the postprandial metabolites using two-sided paired Wilcoxon test separately for short- and long-term measurements. Results Both fasting and postprandial metabolite concentrations showed high technical reproducibility using 1H NMR spectroscopy (median ICC = 0.99). Postprandial metabolite concentrations revealed slightly higher ICC scores than fasting ones in short-term repeat measures (median ICC in postprandial and fasting metabolite concentrations 0.72 versus 0.67, Wilcoxon p-value = 8.0×10−14). Variability did not increase further in a long-term repeat measure, with median ICC in postprandial of 0.64 and in fasting metabolite concentrations 0.66. Conclusion Technical reproducibility is excellent. Biological reproducibility of postprandial metabolite concentrations showed a less or equal variability than fasting metabolite concentrations over time.
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Affiliation(s)
- Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- * E-mail:
| | - David A. Hughes
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Saskia le Cessie
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martin den Heijer
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Internal Medicine, VU Medical Center, Amsterdam, The Netherlands
| | - Frits R. Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ko Willems van Dijk
- Department of Internal Medicine, division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
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30
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Ackermann D, Groessl M, Pruijm M, Ponte B, Escher G, d’Uscio CH, Guessous I, Ehret G, Pechère-Bertschi A, Martin PY, Burnier M, Dick B, Vogt B, Bochud M, Rousson V, Dhayat NA. Reference intervals for the urinary steroid metabolome: The impact of sex, age, day and night time on human adult steroidogenesis. PLoS One 2019; 14:e0214549. [PMID: 30925175 PMCID: PMC6440635 DOI: 10.1371/journal.pone.0214549] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/14/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Urinary steroid metabolomics by GC-MS is an established method in both clinical and research settings to describe steroidogenic disorders. However, population-based reference intervals for adults do not exist. METHODS We measured daytime and night time urinary excretion of 40 steroid metabolites by GC-MS in 1128 adult participants of European ancestry, aged 18 to 90 years, within a large population-based, multicentric, cross-sectional study. Age and sex-related patterns in adjacent daytime and night time urine collections over 24 hours were modelled for each steroid metabolite by multivariable linear mixed regression. We compared our results with those obtained through a systematic literature review on reference intervals of urinary steroid excretion. RESULTS Flexible models were created for all urinary steroid metabolites thereby estimating sex- and age-related changes of the urinary steroid metabolome. Most urinary steroid metabolites showed an age-dependence with the exception of 6β-OH-cortisol, 18-OH-cortisol, and β-cortol. Reference intervals for all metabolites excreted during 24 hours were derived from the 2.5th and 97.5th percentile of modelled reference curves. The excretion rate per period of metabolites predominantly derived from the adrenals was mainly higher during the day than at night and the correlation between day and night time metabolite excretion was highly positive for most androgens and moderately positive for glucocorticoids. CONCLUSIONS This study gives unprecedented new insights into sex- and age-specificity of the human adult steroid metabolome and provides further information on the day/night variation of urinary steroid hormone excretion. The population-based reference ranges for 40 GC-MS-measured metabolites will facilitate the interpretation of steroid profiles in clinical practice.
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Affiliation(s)
- Daniel Ackermann
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Michael Groessl
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Menno Pruijm
- Nephrology Service, University Hospital of Lausanne, Lausanne, Switzerland
| | - Belen Ponte
- Nephrology Service, Department of Specialties of Internal Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Geneviève Escher
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Claudia H. d’Uscio
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Idris Guessous
- Department of Community Medicine, Primary Care and Emergency Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Georg Ehret
- Cardiology Service, Department of Specialties of Internal Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Antoinette Pechère-Bertschi
- Endocrinology Service, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
| | - Pierre-Yves Martin
- Nephrology Service, Department of Specialties of Internal Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Michel Burnier
- Nephrology Service, University Hospital of Lausanne, Lausanne, Switzerland
| | - Bernhard Dick
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Bruno Vogt
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Murielle Bochud
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland
| | - Valentin Rousson
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland
| | - Nasser A. Dhayat
- Department of Nephrology and Hypertension and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O'Donovan C, Playdon M, Raftery D, Shaughnessy D, Souza A, Spaeder T, Spalholz B, Tayyari F, Ubhi B, Verma M, Walk T, Wilson I, Witkin K, Bearden DW, Zanetti KA. Towards quality assurance and quality control in untargeted metabolomics studies. Metabolomics 2019; 15:4. [PMID: 30830465 PMCID: PMC6443086 DOI: 10.1007/s11306-018-1460-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
We describe here the agreed upon first development steps and priority objectives of a community engagement effort to address current challenges in quality assurance (QA) and quality control (QC) in untargeted metabolomic studies. This has included (1) a QA and QC questionnaire responded to by the metabolomics community in 2015 which recommended education of the metabolomics community, development of appropriate standard reference materials and providing incentives for laboratories to apply QA and QC; (2) a 2-day 'Think Tank on Quality Assurance and Quality Control for Untargeted Metabolomic Studies' held at the National Cancer Institute's Shady Grove Campus and (3) establishment of the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) to drive forward developments in a coordinated manner.
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Affiliation(s)
- Richard D Beger
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, USA.
| | - Warwick B Dunn
- School of Biosciences, Phenome Centre Birmingham and Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK.
| | | | | | | | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Leslie Derr
- Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Thomas Flynn
- Food and Drug Administration, Silver Spring, MD, USA
| | - Thomas Hartung
- Johns Hopkins School of Public Health, Baltimore, MD, USA
| | | | | | - Ping-Ching Hsu
- University of Arkansas Medical Sciences, Little Rock, AR, USA
| | - Christina Jones
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | | | - Katrice Lippa
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Padma Maruvada
- National Institute of Diabetes and Digestive and Kidney Disorders, Bethesda, MD, USA
| | - Jonathan Mosley
- National Exposure Research Laboratory, US Environmental Protection Agency, Athens, GA, USA
| | | | - Claire O'Donovan
- European Molecular Biology Laboratory -European Bioinformatics Institute, Hinxton, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | - Daniel W Bearden
- National Institute of Standards and Technology, Charleston, SC, USA
- Ichthus Unlimited, LLC, 109, S. 32nd Street, West Des Moines, IA, USA
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Abstract
"Omics" revolution during the last few decades has vastly increased the understanding of the biological processes that remained obscure in part due to the lack of quality data. Genomics, transcriptomics, epigenomics, proteomics, lipidomics, metabolomics, and microbiomics form an invaluable array of fields that contribute holistically to a global understanding of the intertwined roles of the basic constituents of life and how they comprehensively paint a picture of disease. Metabolomics, in particular, is the study of metabolites, which are the products of cellular metabolic processes (small molecules, i.e., fatty acids, amino acids, or carbohydrates, are part of metabolomics). In this chapter, it is explained how to achieve a metabolomics profiling of aqueous humor using a special isotopic carbon labeling, a novel technique that combines a tremendous effectiveness with simplicity. The very nature of this technique guarantees the exclusion of false positives, since the algorithms are based on the recognition of unique isotopic patterns.
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Affiliation(s)
| | - Ciara Myer
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anna Junk
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Miami Veterans Affairs Healthcare System, Miami, FL, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
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Beale DJ, Pinu FR, Kouremenos KA, Poojary MM, Narayana VK, Boughton BA, Kanojia K, Dayalan S, Jones OAH, Dias DA. Review of recent developments in GC-MS approaches to metabolomics-based research. Metabolomics 2018; 14:152. [PMID: 30830421 DOI: 10.1007/s11306-018-1449-2] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC-MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and 'in house' metabolite databases available. AIM OF REVIEW This review provides an overview of developments in GC-MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC-MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is to both highlight and provide an update on GC-MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC-MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.
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Affiliation(s)
- David J Beale
- Land and Water, Commonwealth Scientific & Industrial Research Organization (CSIRO), P.O. Box 2583, Brisbane, QLD, 4001, Australia.
| | - Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Trajan Scientific and Medical, 7 Argent Pl, Ringwood, 3134, Australia
| | - Mahesha M Poojary
- Chemistry Section, School of Science and Technology, University of Camerino, via S. Agostino 1, 62032, Camerino, Italy
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Vinod K Narayana
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | - Komal Kanojia
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, GPO Box 2476, Melbourne, 3001, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, 3083, Australia.
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La Frano MR, Carmichael SL, Ma C, Hardley M, Shen T, Wong R, Rosales L, Borkowski K, Pedersen TL, Shaw GM, Stevenson DK, Fiehn O, Newman JW. Impact of post-collection freezing delay on the reliability of serum metabolomics in samples reflecting the California mid-term pregnancy biobank. Metabolomics 2018; 14:151. [PMID: 30830400 DOI: 10.1007/s11306-018-1450-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Population-based biorepositories are important resources, but sample handling can affect data quality. OBJECTIVE Identify metabolites of value for clinical investigations despite extended postcollection freezing delays, using protocols representing a California mid-term pregnancy biobank. METHODS Blood collected from non-pregnant healthy female volunteers (n = 20) underwent three handling protocols after 30 min clotting at room temperature: (1) ideal-samples frozen (- 80 °C) within 2 h of collection; (2) delayed freezing-samples held at room temperature for 3 days, then 4 °C for 9 days, the median times for biobank samples, and then frozen; (3) delayed freezing with freeze-thaw-the delayed freezing protocol with a freeze-thaw cycle simulating retrieved sample sub-aliquoting. Mass spectrometry-based untargeted metabolomic analyses of primary metabolism and complex lipids and targeted profiling of oxylipins, endocannabinoids, ceramides/sphingoid-bases, and bile acids were performed. Metabolite concentrations and intraclass correlation coefficients (ICC) were compared, with the ideal protocol as the reference. RESULTS Sixty-two percent of 428 identified compounds had good to excellent ICCs, a metric of concordance between measurements of samples handled with the different protocols. Sphingomyelins, phosphatidylcholines, cholesteryl esters, triacylglycerols, bile acids and fatty acid diols were the least affected by non-ideal handling, while sugars, organic acids, amino acids, monoacylglycerols, lysophospholipids, N-acylethanolamides, polyunsaturated fatty acids, and numerous oxylipins were altered by delayed freezing. Freeze-thaw effects were assay-specific with lipids being most stable. CONCLUSIONS Despite extended post-collection freezing delays characteristic of some biobanks of opportunistically collected clinical samples, numerous metabolomic compounds had both stable levels and good concordance.
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Affiliation(s)
- Michael R La Frano
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
- Department of Nutrition, University of California Davis, Davis, CA, USA
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | | | - Chen Ma
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Macy Hardley
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Tong Shen
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
| | - Ron Wong
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Lorenzo Rosales
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Kamil Borkowski
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA
| | | | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John W Newman
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA.
- Department of Nutrition, University of California Davis, Davis, CA, USA.
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA.
- Obesity and Metabolism Research Unit, USDA-ARS-WHNRC, 430 West Health Sciences Drive, Davis, CA, 95616, USA.
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Kennedy AD, Wittmann BM, Evans AM, Miller LAD, Toal DR, Lonergan S, Elsea SH, Pappan KL. Metabolomics in the clinic: A review of the shared and unique features of untargeted metabolomics for clinical research and clinical testing. J Mass Spectrom 2018; 53:1143-1154. [PMID: 30242936 DOI: 10.1002/jms.4292] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Metabolomics is the untargeted measurement of the metabolome, which is composed of the complement of small molecules detected in a biological sample. As such, metabolomic analysis produces a global biochemical phenotype. It is a technology that has been utilized in the research setting for over a decade. The metabolome is directly linked to and is influenced by genetics, epigenetics, environmental factors, and the microbiome-all of which affect health. Metabolomics can be applied to human clinical diagnostics and to other fields such as veterinary medicine, nutrition, exercise, physiology, agriculture/plant biochemistry, and toxicology. Applications of metabolomics in clinical testing are emerging, but several aspects of its use as a clinical test differ from applications focused on research or biomarker discovery and need to be considered for metabolomics clinical test data to have optimum impact, be meaningful, and be used responsibly. In this review, we deconstruct aspects and challenges of metabolomics for clinical testing by illustrating the significance of test design, accurate and precise data acquisition, quality control, data processing, n-of-1 comparison to a reference population, and biochemical pathway analysis. We describe how metabolomics technology is integral to defining individual biochemical phenotypes, elaborates on human health and disease, and fits within the precision medicine landscape. Finally, we conclude by outlining some future steps needed to bring metabolomics into the clinical space and to be recognized by the broader medical and regulatory fields.
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Affiliation(s)
| | | | | | | | | | | | - Sarah H Elsea
- Department of Molecular and Human Genetics and Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
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36
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Ibarra-González I, Cruz-Bautista I, Bello-Chavolla OY, Vela-Amieva M, Pallares-Méndez R, Ruiz de Santiago Y Nevarez D, Salas-Tapia MF, Rosas-Flota X, González-Acevedo M, Palacios-Peñaloza A, Morales-Esponda M, Aguilar-Salinas CA, Del Bosque-Plata L. Optimization of kidney dysfunction prediction in diabetic kidney disease using targeted metabolomics. Acta Diabetol 2018; 55:1151-1161. [PMID: 30173364 DOI: 10.1007/s00592-018-1213-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/09/2018] [Indexed: 01/05/2023]
Abstract
AIMS Metabolomics have been used to evaluate the role of small molecules in human disease. However, the cost and complexity of the methodology and interpretation of findings have limited the transference of knowledge to clinical practice. Here, we apply a targeted metabolomics approach using samples blotted in filter paper to develop clinical-metabolomics models to detect kidney dysfunction in diabetic kidney disease (DKD). METHODS We included healthy controls and subjects with type 2 diabetes (T2D) with and without DKD and investigated the association between metabolite concentrations in blood and urine with eGFR and albuminuria. We also evaluated performance of clinical, biochemical and metabolomic models to improve kidney dysfunction prediction in DKD. RESULTS Using clinical-metabolomics models, we identified associations of decreased eGFR with body mass index (BMI), uric acid and C10:2 levels; albuminuria was associated to years of T2D duration, A1C, uric acid, creatinine, protein intake and serum C0, C10:2 and urinary C12:1 levels. DKD was associated with age, A1C, uric acid, BMI, serum C0, C10:2, C8:1 and urinary C12:1. Inclusion of metabolomics increased the predictive and informative capacity of models composed of clinical variables by decreasing Akaike's information criterion, and was replicated both in training and validation datasets. CONCLUSIONS Targeted metabolomics using blotted samples in filter paper is a simple, low-cost approach to identify outcomes associated with DKD; the inclusion of metabolomics improves predictive capacity of clinical models to identify kidney dysfunction and DKD-related outcomes.
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Affiliation(s)
- Isabel Ibarra-González
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, UNAM-Instituto Nacional de Pediatría, Mexico City, Mexico
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Ivette Cruz-Bautista
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
| | - Omar Yaxmehen Bello-Chavolla
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- MD/PhD (PECEM) Program, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Marcela Vela-Amieva
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Rigoberto Pallares-Méndez
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Diana Ruiz de Santiago Y Nevarez
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - María Fernanda Salas-Tapia
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Ximena Rosas-Flota
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Mayela González-Acevedo
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Adriana Palacios-Peñaloza
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Mario Morales-Esponda
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Carlos Alberto Aguilar-Salinas
- Unidad de Investigación en Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
| | - Laura Del Bosque-Plata
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610, Mexico City, Mexico.
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Abstract
Metabolomics is one of the newer omics fields, and has enabled researchers to complement genomic and protein level analysis of disease with both semi-quantitative and quantitative metabolite levels, which are the chemical mediators that constitute a given phenotype. Over more than a decade, methodologies have advanced for both targeted (quantification of specific analytes) as well as untargeted metabolomics (biomarker discovery and global metabolite profiling). Untargeted metabolomics is especially useful when there is no a priori metabolic hypothesis. Liquid chromatography coupled to mass spectrometry (LC-MS) has been the preferred choice for untargeted metabolomics, given the versatility in metabolite coverage and sensitivity of these instruments. Resolving and profiling many hundreds to thousands of metabolites with varying chemical properties in a biological sample presents unique challenges, or pitfalls. In this review, we address the various obstacles and corrective measures available in four major aspects associated with an untargeted metabolomics experiment: (1) experimental design, (2) pre-analytical (sample collection and preparation), (3) analytical (chromatography and detection), and (4) post-analytical (data processing).
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Affiliation(s)
- Ilya Gertsman
- Biochemical Genetics and Metabolomics Laboratory, Department of Pediatrics, University of California San Diego, 9500 Gilman Dr. La Jolla, CA, 92093-0830, USA
| | - Bruce A Barshop
- Biochemical Genetics and Metabolomics Laboratory, Department of Pediatrics, University of California San Diego, 9500 Gilman Dr. La Jolla, CA, 92093-0830, USA.
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Waaijenborg S, Korobko O, Willems van Dijk K, Lips M, Hankemeier T, Wilderjans TF, Smilde AK, Westerhuis JA. Fusing metabolomics data sets with heterogeneous measurement errors. PLoS One 2018; 13:e0195939. [PMID: 29698490 PMCID: PMC5919515 DOI: 10.1371/journal.pone.0195939] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/03/2018] [Indexed: 11/18/2022] Open
Abstract
Combining different metabolomics platforms can contribute significantly to the discovery of complementary processes expressed under different conditions. However, analysing the fused data might be hampered by the difference in their quality. In metabolomics data, one often observes that measurement errors increase with increasing measurement level and that different platforms have different measurement error variance. In this paper we compare three different approaches to correct for the measurement error heterogeneity, by transformation of the raw data, by weighted filtering before modelling and by a modelling approach using a weighted sum of residuals. For an illustration of these different approaches we analyse data from healthy obese and diabetic obese individuals, obtained from two metabolomics platforms. Concluding, the filtering and modelling approaches that both estimate a model of the measurement error did not outperform the data transformation approaches for this application. This is probably due to the limited difference in measurement error and the fact that estimation of measurement error models is unstable due to the small number of repeats available. A transformation of the data improves the classification of the two groups.
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Affiliation(s)
- Sandra Waaijenborg
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Oksana Korobko
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mirjam Lips
- Department of Endocrinology and Metabolism, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Hankemeier
- Division Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands
| | - Tom F. Wilderjans
- Methodology & Statistics Unit, Institute of Psychology, Leiden University, Leiden, The Netherlands
- Research Group of Quantitative Psychology and Individual Differences, KU Leuven, Leuven, Belgium
| | - Age K. Smilde
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Johan A. Westerhuis
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Statistics, North-West University, Potchefstroom, South Africa
- * E-mail:
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De Livera AM, Olshansky G, Simpson JA, Creek DJ. NormalizeMets: assessing, selecting and implementing statistical methods for normalizing metabolomics data. Metabolomics 2018; 14:54. [PMID: 30830328 DOI: 10.1007/s11306-018-1347-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/03/2018] [Indexed: 02/02/2023]
Abstract
INTRODUCTION In metabolomics studies, unwanted variation inevitably arises from various sources. Normalization, that is the removal of unwanted variation, is an essential step in the statistical analysis of metabolomics data. However, metabolomics normalization is often considered an imprecise science due to the diverse sources of variation and the availability of a number of alternative strategies that may be implemented. OBJECTIVES We highlight the need for comparative evaluation of different normalization methods and present software strategies to help ease this task for both data-oriented and biological researchers. METHODS We present NormalizeMets-a joint graphical user interface within the familiar Microsoft Excel and freely-available R software for comparative evaluation of different normalization methods. The NormalizeMets R package along with the vignette describing the workflow can be downloaded from https://cran.r-project.org/web/packages/NormalizeMets/ . The Excel Interface and the Excel user guide are available on https://metabolomicstats.github.io/ExNormalizeMets . RESULTS NormalizeMets allows for comparative evaluation of normalization methods using criteria that depend on the given dataset and the ultimate research question. Hence it guides researchers to assess, select and implement a suitable normalization method using either the familiar Microsoft Excel and/or freely-available R software. In addition, the package can be used for visualisation of metabolomics data using interactive graphical displays and to obtain end statistical results for clustering, classification, biomarker identification adjusting for confounding variables, and correlation analysis. CONCLUSION NormalizeMets is designed for comparative evaluation of normalization methods, and can also be used to obtain end statistical results. The use of freely-available R software offers an attractive proposition for programming-oriented researchers, and the Excel interface offers a familiar alternative to most biological researchers. The package handles the data locally in the user's own computer allowing for reproducible code to be stored locally.
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Affiliation(s)
- Alysha M De Livera
- Biostatistics Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3800, Australia.
| | - Gavriel Olshansky
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3800, Australia
| | - Julie A Simpson
- Biostatistics Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3800, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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Cañueto D, Gómez J, Salek RM, Correig X, Cañellas N. rDolphin: a GUI R package for proficient automatic profiling of 1D 1H-NMR spectra of study datasets. Metabolomics 2018; 14:24. [PMID: 30830320 DOI: 10.1007/s11306-018-1319-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 01/03/2018] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Adoption of automatic profiling tools for 1H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices. OBJECTIVES To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process. METHODS rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality. RESULTS The information and quality achieved in two public datasets of complex matrices are maximized. CONCLUSION rDolphin is an open-source R package ( http://github.com/danielcanueto/rDolphin ) able to provide the best balance between accuracy, reproducibility and ease of use.
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Affiliation(s)
- Daniel Cañueto
- Metabolomics Platform, IISPV, DEEEA, Universitat Rovira i Virgili, Campus Sescelades, Carretera de Valls, s/n, 43007, Tarragona, Spain.
| | - Josep Gómez
- Intensive Care Unit, Joan XXIII University Hospital, IISPV, Carrer Dr. Mallafrè Guasch, 4, 43005, Tarragona, Spain
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Xavier Correig
- Metabolomics Platform, IISPV, DEEEA, Universitat Rovira i Virgili, Campus Sescelades, Carretera de Valls, s/n, 43007, Tarragona, Spain
- CIBERDEM, Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, 28029, Madrid, Spain
| | - Nicolau Cañellas
- Metabolomics Platform, IISPV, DEEEA, Universitat Rovira i Virgili, Campus Sescelades, Carretera de Valls, s/n, 43007, Tarragona, Spain.
- CIBERDEM, Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, 28029, Madrid, Spain.
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Harada S, Hirayama A, Chan Q, Kurihara A, Fukai K, Iida M, Kato S, Sugiyama D, Kuwabara K, Takeuchi A, Akiyama M, Okamura T, Ebbels TMD, Elliott P, Tomita M, Sato A, Suzuki C, Sugimoto M, Soga T, Takebayashi T. Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry. PLoS One 2018; 13:e0191230. [PMID: 29346414 PMCID: PMC5773198 DOI: 10.1371/journal.pone.0191230] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Background Cohort studies with metabolomics data are becoming more widespread, however, large-scale studies involving 10,000s of participants are still limited, especially in Asian populations. Therefore, we started the Tsuruoka Metabolomics Cohort Study enrolling 11,002 community-dwelling adults in Japan, and using capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography–mass spectrometry. The CE-MS method is highly amenable to absolute quantification of polar metabolites, however, its reliability for large-scale measurement is unclear. The aim of this study is to examine reproducibility and validity of large-scale CE-MS measurements. In addition, the study presents absolute concentrations of polar metabolites in human plasma, which can be used in future as reference ranges in a Japanese population. Methods Metabolomic profiling of 8,413 fasting plasma samples were completed using CE-MS, and 94 polar metabolites were structurally identified and quantified. Quality control (QC) samples were injected every ten samples and assessed throughout the analysis. Inter- and intra-batch coefficients of variation of QC and participant samples, and technical intraclass correlation coefficients were estimated. Passing-Bablok regression of plasma concentrations by CE-MS on serum concentrations by standard clinical chemistry assays was conducted for creatinine and uric acid. Results and conclusions In QC samples, coefficient of variation was less than 20% for 64 metabolites, and less than 30% for 80 metabolites out of the 94 metabolites. Inter-batch coefficient of variation was less than 20% for 81 metabolites. Estimated technical intraclass correlation coefficient was above 0.75 for 67 metabolites. The slope of Passing-Bablok regression was estimated as 0.97 (95% confidence interval: 0.95, 0.98) for creatinine and 0.95 (0.92, 0.96) for uric acid. Compared to published data from other large cohort measurement platforms, reproducibility of metabolites common to the platforms was similar to or better than in the other studies. These results show that our CE-MS platform is suitable for conducting large-scale epidemiological studies.
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Affiliation(s)
- Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
- MRC-PHE Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kota Fukai
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Ayano Takeuchi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Miki Akiyama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Timothy M. D. Ebbels
- MRC-PHE Centre for Environment and Health, Imperial College London, London, United Kingdom
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London, United Kingdom
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
- MRC-PHE Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Chizuru Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
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Rindlisbacher B, Schmid C, Geiser T, Bovet C, Funke-Chambour M. Serum metabolic profiling identified a distinct metabolic signature in patients with idiopathic pulmonary fibrosis - a potential biomarker role for LysoPC. Respir Res 2018; 19:7. [PMID: 29321022 PMCID: PMC5764001 DOI: 10.1186/s12931-018-0714-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/02/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a lethal lung disease of unknown etiology. Patients present loss of lung function, dyspnea and dry cough. Diagnosis requires compatible radiologic imaging and, in undetermined cases, invasive procedures such as bronchoscopy and surgical lung biopsy. The pathophysiological mechanisms of IPF are not completely understood. Lung injury with abnormal alveolar epithelial repair is thought to be a major cause for activation of profibrotic pathways in IPF. Metabolic signatures might indicate pathological pathways involved in disease development and progression. Reliable serum biomarker would help to improve both diagnostic approach and monitoring of drug effects. METHOD The global metabolic profiles measured by ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) of ten stable IPF patients were compared to the ones of ten healthy participants. The results were validated in an additional study of eleven IPF patients and ten healthy controls. RESULTS We discovered 10 discriminative metabolic features using multivariate and univariate statistical analysis. Among them, we identified one metabolite at a retention time of 9.59 min that was two times more abundant in the serum of IPF patients compared to healthy participants. Based on its ion pattern, a lysophosphatidylcholine (LysoPC) was proposed. LysoPC is a precursor of lysophosphatidic acid (LPA) - a known mediator for lung fibrosis with its pathway currently being evaluated as new therapeutic drug target for IPF and other fibrotic diseases. CONCLUSIONS We identified a LysoPC by UHPLC-HRMS as potential biomarker in serum of patients with IPF. Further validation studies in a larger cohort are necessary to determine its role in IPF. TRIAL REGISTRATION Serum samples from IPF patients have been obtained within the clinical trial NCT02173145 at baseline and from the idiopathic interstitial pneumonia (IIP) cohort study. The study was approved by the Swiss Ethics Committee, Bern (KEK 002/14 and 246/15 or PB_2016-01524).
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Affiliation(s)
- Barbara Rindlisbacher
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Cornelia Schmid
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Geiser
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cédric Bovet
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Manuela Funke-Chambour
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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Abstract
LC-MS/MS- and GC-MS-based targeted metabolomics is typically conducted by analyzing and quantifying a cascade of metabolites with methods specifically developed for the metabolite class. Here we describe an approach for the development of multi-residue analytical profiles, calibration standards, and internal standard solutions in support of a fast, simple, and low-cost plasma sample preparation that captures and quantitates a range of metabolite cascades.
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Affiliation(s)
| | - John W Newman
- Obesity and Metabolism Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Western Human Nutrition Research Center, University of California Davis, Davis, CA, USA.
- Department of Nutrition, University of California Davis, Davis, CA, USA.
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA, USA.
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CULP-HILL R, REISZ JA, HANSEN KC, D’ALESSANDRO A. Investigation of the effects of storage and freezing on mixes of heavy-labeled metabolite and amino acid standards. Rapid Commun Mass Spectrom 2017; 31:2030-2034. [PMID: 28910859 PMCID: PMC5673535 DOI: 10.1002/rcm.7989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE High-throughput metabolomics has now made it possible for small/medium-sized laboratories to analyze thousands of samples/year from the most diverse biological matrices including biofluids, cell and tissue extracts. In large-scale metabolomics studies, stable-isotope-labeled standards are increasingly used to normalize for matrix effects and control for technical reproducibility (e.g. extraction efficiency, chromatographic retention times and mass spectrometry signal stability). However, it is currently unknown how stable mixes of commercially available standards are following repeated freeze/thaw cycles or prolonged storage of aliquots. METHODS Standard mixes for 13 C, 15 N or deuterated isotopologues of amino acids and key metabolites from the central carbon and nitrogen pathways (e.g. glycolysis, Krebs cycle, redox homeostasis, purines) were either repeatedly frozen/thawed for up to 10 cycles or diluted into aliquots prior to frozen storage for up to 42 days. Samples were characterized by ultra-high-pressure liquid chromatography/mass spectrometry to determine the stability of the aliquoted standards upon freezing/thawing or prolonged storage. RESULTS Metabolite standards were stable over up to 10 freeze/thaw cycles, with the exception of adenosine and glutathione, showing technical variability across aliquots in a freeze/thaw-cycle-independent fashion. Storage for up to 42 days of mixes of commercially available standards did not significantly affect the stability of amino acid or metabolite standards for the first 2 weeks, while progressive degradation (statistically significant for fumarate) was observed after 3 weeks. CONCLUSIONS Refrigerated or frozen preservation for at least 2 weeks of aliquoted heavy-labeled standard mixes for metabolomics analysis is a feasible and time-/resource-saving strategy for standard metabolomics laboratories.
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Affiliation(s)
- Rachel CULP-HILL
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Julie A. REISZ
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Kirk C. HANSEN
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Angelo D’ALESSANDRO
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
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Okuma N, Saita M, Hoshi N, Soga T, Tomita M, Sugimoto M, Kimoto K. Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile. PLoS One 2017; 12:e0183109. [PMID: 28813487 PMCID: PMC5557591 DOI: 10.1371/journal.pone.0183109] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/28/2017] [Indexed: 11/18/2022] Open
Abstract
Background This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation. Methods Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry. Results In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors. Conclusions Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation.
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Affiliation(s)
- Nobuyuki Okuma
- Department of Oral Interdisciplinary Medicine, Graduate School of Dentistry, Kanagawa Dental University, Kanagawa, Japan
| | - Makiko Saita
- Department of Oral Interdisciplinary Medicine, Graduate School of Dentistry, Kanagawa Dental University, Kanagawa, Japan
- * E-mail:
| | - Noriyuki Hoshi
- Department of Oral Interdisciplinary Medicine, Graduate School of Dentistry, Kanagawa Dental University, Kanagawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Division of Environmental Pathology, Department of Oral Science, Graduate School of Dentistry, Kanagawa Dental University, Kanagawa, Japan
- Health Promotion and Preemptive Medicine, Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, Shinjuku, Tokyo, Japan
| | - Katsuhiko Kimoto
- Department of Oral Interdisciplinary Medicine, Graduate School of Dentistry, Kanagawa Dental University, Kanagawa, Japan
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Jaeger C, Méret M, Schmitt CA, Lisec J. Compound annotation in liquid chromatography/high-resolution mass spectrometry based metabolomics: robust adduct ion determination as a prerequisite to structure prediction in electrospray ionization mass spectra. Rapid Commun Mass Spectrom 2017; 31:1261-1266. [PMID: 28499062 DOI: 10.1002/rcm.7905] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE A bottleneck in metabolic profiling of complex biological extracts is confident, non-supervised annotation of ideally all contained, chemically highly diverse small molecules. Recent computational strategies combining sum formula prediction with in silico fragmentation achieve confident de novo annotation, once the correct neutral mass of a compound is known. Current software solutions for automated adduct ion assignment, however, are either publicly unavailable or have been validated against only few experimental electrospray ionization (ESI) mass spectra. METHODS We here present findMAIN (find Main Adduct IoN), a new heuristic approach for interpreting ESI mass spectra. findMAIN scores MS1 spectra based on explained intensity, mass accuracy and isotope charge agreement of adducts and related ionization products and annotates peaks of the (de)protonated molecule and adduct ions. The approach was validated against 1141 ESI positive mode spectra of chemically diverse standard compounds acquired on different high-resolution mass spectrometric instruments (Orbitrap and time-of-flight). Robustness against impure spectra was evaluated. RESULTS Correct adduct ion assignment was achieved for up to 83% of the spectra. Performance was independent of compound class and mass spectrometric platform. The algorithm proved highly tolerant against spectral contamination as demonstrated exemplarily for co-eluting compounds as well as systematically by pairwise mixing of spectra. When used in conjunction with MS-FINDER, a state-of-the-art sum formula tool, correct sum formulas were obtained for 77% of spectra. It outperformed both 'brute force' approaches and current state-of-the-art annotation packages tested as potential alternatives. Limitations of the heuristic pertained to poorly ionizing compounds and cationic compounds forming [M]+ ions. CONCLUSIONS A new, validated approach for interpreting ESI mass spectra is presented, filling a gap in the nontargeted metabolomics workflow. It is freely available in the latest version of R package InterpretMSSpectrum.
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Affiliation(s)
- Carsten Jaeger
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | | | - Clemens A Schmitt
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Jan Lisec
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Li B, Tang J, Yang Q, Li S, Cui X, Li Y, Chen Y, Xue W, Li X, Zhu F. NOREVA: normalization and evaluation of MS-based metabolomics data. Nucleic Acids Res 2017; 45:W162-W170. [PMID: 28525573 PMCID: PMC5570188 DOI: 10.1093/nar/gkx449] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/22/2017] [Accepted: 05/09/2017] [Indexed: 01/15/2023] Open
Abstract
Diverse forms of unwanted signal variations in mass spectrometry-based metabolomics data adversely affect the accuracies of metabolic profiling. A variety of normalization methods have been developed for addressing this problem. However, their performances vary greatly and depend heavily on the nature of the studied data. Moreover, given the complexity of the actual data, it is not feasible to assess the performance of methods by single criterion. We therefore developed NOREVA to enable performance evaluation of various normalization methods from multiple perspectives. NOREVA integrated five well-established criteria (each with a distinct underlying theory) to ensure more comprehensive evaluation than any single criterion. It provided the most complete set of the available normalization methods, with unique features of removing overall unwanted variations based on quality control metabolites and allowing quality control samples based correction sequentially followed by data normalization. The originality of NOREVA and the reliability of its algorithms were extensively validated by case studies on five benchmark datasets. In sum, NOREVA is distinguished for its capability of identifying the well performed normalization method by taking multiple criteria into consideration and can be an indispensable complement to other available tools. NOREVA can be freely accessed at http://server.idrb.cqu.edu.cn/noreva/.
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Affiliation(s)
- Bo Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Jing Tang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Qingxia Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xuejiao Cui
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Yinghong Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xiaofeng Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Perez de Souza L, Naake T, Tohge T, Fernie AR. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 2017; 6:1-20. [PMID: 28520864 PMCID: PMC5499862 DOI: 10.1093/gigascience/gix037] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/19/2023] Open
Abstract
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway toward improving our coverage of the plant metabolome.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Siskos AP, Jain P, Römisch-Margl W, Bennett M, Achaintre D, Asad Y, Marney L, Richardson L, Koulman A, Griffin JL, Raynaud F, Scalbert A, Adamski J, Prehn C, Keun HC. Interlaboratory Reproducibility of a Targeted Metabolomics Platform for Analysis of Human Serum and Plasma. Anal Chem 2017; 89:656-665. [PMID: 27959516 PMCID: PMC6317696 DOI: 10.1021/acs.analchem.6b02930] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A critical question facing the field of metabolomics is whether data obtained from different centers can be effectively compared and combined. An important aspect of this is the interlaboratory precision (reproducibility) of the analytical protocols used. We analyzed human samples in six laboratories using different instrumentation but a common protocol (the AbsoluteIDQ p180 kit) for the measurement of 189 metabolites via liquid chromatography (LC) or flow injection analysis (FIA) coupled to tandem mass spectrometry (MS/MS). In spiked quality control (QC) samples 82% of metabolite measurements had an interlaboratory precision of <20%, while 83% of averaged individual laboratory measurements were accurate to within 20%. For 20 typical biological samples (serum and plasma from healthy individuals) the median interlaboratory coefficient of variation (CV) was 7.6%, with 85% of metabolites exhibiting a median interlaboratory CV of <20%. Precision was largely independent of the type of sample (serum or plasma) or the anticoagulant used but was reduced in a sample from a patient with dyslipidaemia. The median interlaboratory accuracy and precision of the assay for standard reference plasma (NIST SRM 1950) were 107% and 6.7%, respectively. Likely sources of irreproducibility were the near limit of detection (LOD) typical abundance of some metabolites and the degree of manual review and optimization of peak integration in the LC-MS/MS data after acquisition. Normalization to a reference material was crucial for the semi-quantitative FIA measurements. This is the first interlaboratory assessment of a widely used, targeted metabolomics assay illustrating the reproducibility of the protocol and how data generated on different instruments could be directly integrated in large-scale epidemiological studies.
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Affiliation(s)
| | - Pooja Jain
- Department of Surgery and Cancer, Imperial College London, W12 0NN, UK
| | - Werner Römisch-Margl
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Mark Bennett
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - David Achaintre
- International Agency for Research on Cancer (IARC), Biomarkers Group, F-69372 Lyon, France
| | - Yasmin Asad
- The Institute of Cancer Research, ICR, Sutton, SM2 5NG, UK
| | - Luke Marney
- MRC Human Nutrition Research, Cambridge, CB1 9NL, UK
| | | | | | | | | | - Augustin Scalbert
- International Agency for Research on Cancer (IARC), Biomarkers Group, F-69372 Lyon, France
| | - Jerzy Adamski
- Genome Analysis Center, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Cornelia Prehn
- Genome Analysis Center, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Hector C. Keun
- Department of Surgery and Cancer, Imperial College London, W12 0NN, UK
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Assar S, Schoenmakers I, Koulman A, Prentice A, Jones KS. UPLC-MS/MS Determination of Deuterated 25-Hydroxyvitamin D (d 3-25OHD 3) and Other Vitamin D Metabolites for the Measurement of 25OHD Half-Life. Methods Mol Biol 2017; 1546:257-265. [PMID: 27896775 DOI: 10.1007/978-1-4939-6730-8_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plasma 25-hydroxyvitamin D (25OHD) half-life (25OHDt 1/2) is a dynamic marker of vitamin D metabolism that can be used to assess vitamin D expenditure and help inform vitamin D requirements. Our group recently established an approach to determine the 25OHDt 1/2 as an alternative biomarker of 25OHD expenditure in humans. The approach uses a small oral dose of stable isotope labeled 25OHD3 [3-2H-25OHD3 (6,19,19-d3)] (d3-25OHD3) (tracer), which is distinguishable from endogenous 25OHD by liquid chromatography tandem-mass spectrometry (LC-MS/MS). We report here the method, which relies on protein precipitation, purification with solid phase extraction, derivatization with 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), and determination of the compounds by isotope-dilution UPLC-MS/MS. The method proved to be rapid and sensitive (LOQ 0.2 nmol/L) for the quantification of this tracer as well as the other vitamin D metabolites: 25OHD3, 25OHD2, and 24,25(OH)2D3 in human plasma.
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Affiliation(s)
- Shima Assar
- MRC Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK.
| | - Inez Schoenmakers
- MRC Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK
| | - Albert Koulman
- MRC Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK
| | - Ann Prentice
- MRC Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK
| | - Kerry S Jones
- MRC Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK
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