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Yan Y, Hemmler D, Schmitt-Kopplin P. Discovery of Glycation Products: Unraveling the Unknown Glycation Space Using a Mass Spectral Library from In Vitro Model Systems. Anal Chem 2024; 96:3569-3577. [PMID: 38346319 PMCID: PMC10902809 DOI: 10.1021/acs.analchem.3c05540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The nonenzymatic reaction between amino acids (AAs) and reducing sugars, also known as the Maillard reaction, is the primary source of free glycation products (GPs) in vivo and in vitro. The limited number of MS/MS records for GPs in public libraries hinders the annotation and investigation of nonenzymatic glycation. To address this issue, we present a mass spectral library containing the experimental MS/MS spectra of diverse GPs from model systems. Based on the conceptional reaction processes and structural characteristics of products, we classified GPs into common GPs (CGPs) and modified AAs (MAAs). A workflow for annotating GPs was established based on the structural and fragmentation patterns of each GP type. The final spectral library contains 157 CGPs, 499 MAAs, and 2426 GP spectra with synthetic model system information, retention time, precursor m/z, MS/MS, and annotations. As a proof-of-concept, we demonstrated the use of the library for screening GPs in unidentified spectra of human plasma and urine. The AAs with the C6H10O5 modification, fructosylation from Amadori rearrangement, were the most found GPs. With the help of the model system, we confirmed the existence of C6H10O5-modified Valine in human plasma by matching both retention time, MS1, and MS/MS without reference standards. In summary, our GP library can serve as an online resource to quickly screen possible GPs in an untargeted metabolomics workflow, furthermore with the model system as a practical synthesis method to confirm their identity.
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Affiliation(s)
- Yingfei Yan
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Daniel Hemmler
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising 85354, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising 85354, Germany
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2
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Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM, Falcone EL. Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease. J Allergy Clin Immunol 2023; 152:1619-1633.e11. [PMID: 37659505 PMCID: PMC11279821 DOI: 10.1016/j.jaci.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND Chronic granulomatous disease (CGD) is caused by defects in any 1 of the 6 subunits forming the nicotinamide adenine dinucleotide phosphate oxidase complex 2 (NOX2), leading to severely reduced or absent phagocyte-derived reactive oxygen species production. Almost 50% of patients with CGD have inflammatory bowel disease (CGD-IBD). While conventional IBD therapies can treat CGD-IBD, their benefits must be weighed against the risk of infection. Understanding the impact of NOX2 defects on the intestinal microbiota may lead to the identification of novel CGD-IBD treatments. OBJECTIVE We sought to identify microbiome and metabolome signatures that can distinguish individuals with CGD and CGD-IBD. METHODS We conducted a cross-sectional observational study of 79 patients with CGD, 8 pathogenic variant carriers, and 19 healthy controls followed at the National Institutes of Health Clinical Center. We profiled the intestinal microbiome (amplicon sequencing) and stool metabolome, and validated our findings in a second cohort of 36 patients with CGD recruited through the Primary Immune Deficiency Treatment Consortium. RESULTS We identified distinct intestinal microbiome and metabolome profiles in patients with CGD compared to healthy individuals. We observed enrichment for Erysipelatoclostridium spp, Sellimonas spp, and Lachnoclostridium spp in CGD stool samples. Despite differences in bacterial alpha and beta diversity between the 2 cohorts, several taxa correlated significantly between both cohorts. We further demonstrated that patients with CGD-IBD have a distinct microbiome and metabolome profile compared to patients without CGD-IBD. CONCLUSION Intestinal microbiome and metabolome signatures distinguished patients with CGD and CGD-IBD, and identified potential biomarkers and therapeutic targets.
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Affiliation(s)
| | - Yu Han
- Division of Molecular Genetics and Pathology, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Md; Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Christa S Zerbe
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Theo Heller
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Md
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Samantha A Kreuzberg
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Beatriz E Marciano
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Yik Siu
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY
| | - Drew R Jones
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | | | - Amy M Tsou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, Mass; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Sean Conlan
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Md
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Md
| | - Mariam Quinones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Md
| | - Caroline Grou
- Bioinformatics Core, Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Virginie Calderon
- Bioinformatics Core, Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Clayton Deming
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Md
| | - Jennifer W Leiding
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Baltimore, Md
| | - Danielle E Arnold
- Immune Deficiency-Cellular Therapy Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Md
| | - Brent R Logan
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, Wis
| | - Linda M Griffith
- Division of Allergy, Immunology, and Transplantation, NIAID, NIH, Bethesda, Md
| | - Aleksandra Petrovic
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital and Research Center, Seattle, Wash
| | - Talal I Mousallem
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Neena Kapoor
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children's Hospital Los Angeles, Los Angeles, Calif
| | - Jennifer R Heimall
- Division of Allergy and Immunology, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Jessie L Barnum
- Division of Blood and Marrow Transplantation and Cellular Therapies, University of Pittsburgh Medical Center (UPMC) and Children's Hospital of Pittsburgh, Pittsburgh, Pa
| | - Malika Kapadia
- Department of Pediatrics, Harvard University Medical School, Boston, Mass
| | - Nicola Wright
- Section of Hematology/Immunology, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Ahmad Rayes
- Intermountain Primary Children's Hospital, University of Utah, Salt Lake City, Utah
| | - Sharat Chandra
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Larisa A Broglie
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wis
| | - Deepak Chellapandian
- Center for Cell and Gene Therapy for Non-Malignant Conditions, Johns Hopkins All Children's Hospital, St Petersburg, Fla
| | - Christin L Deal
- Division of Allergy and Immunology, UPMC, Children's Hospital of Pittsburgh, Pittsburgh, Pa
| | - Eyal Grunebaum
- Division of Immunology and Allergy, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada; Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Si Lim
- Department of Pediatrics, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, Hawaii; University of Hawai'i Cancer Center, University of Hawai'i at Mānoa, Honolulu, Hawaii
| | | | - Rebecca A Marsh
- Cincinnati Children's Hospital Medical Center, and University of Cincinnati, Cincinnati, Ohio
| | - Luis Murguia-Favela
- Section of Hematology/Immunology, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Suhag Parikh
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Fabien Touzot
- Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Morton J Cowan
- University of California San Francisco Benioff Children's Hospital, San Francisco, Calif
| | - Christopher C Dvorak
- University of California San Francisco Benioff Children's Hospital, San Francisco, Calif
| | - Elie Haddad
- Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Donald B Kohn
- Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Calif
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Sung-Yun Pai
- Immune Deficiency-Cellular Therapy Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Md
| | - Jennifer M Puck
- University of California San Francisco Benioff Children's Hospital, San Francisco, Calif
| | - Michael A Pulsipher
- Division of Pediatric Hematology and Oncology, Intermountain Primary Children's Hospital, Huntsman Cancer Institute at the University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, Utah
| | | | - Elizabeth M Kang
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Julia A Segre
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Md
| | - Clare E Bryant
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Emilia Liana Falcone
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montreal, Quebec, Canada; Center for Immunity, Inflammation and Infectious Diseases, IRCM, Montreal, Quebec, Canada; Department of Medicine, Université de Montréal, Montreal, Quebec, Canada.
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3
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Xing S, Shen S, Xu B, Li X, Huan T. BUDDY: molecular formula discovery via bottom-up MS/MS interrogation. Nat Methods 2023:10.1038/s41592-023-01850-x. [PMID: 37055660 DOI: 10.1038/s41592-023-01850-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/15/2023] [Indexed: 04/15/2023]
Abstract
A substantial fraction of metabolic features remains undetermined in mass spectrometry (MS)-based metabolomics, and molecular formula annotation is the starting point for unraveling their chemical identities. Here we present bottom-up tandem MS (MS/MS) interrogation, a method for de novo formula annotation. Our approach prioritizes MS/MS-explainable formula candidates, implements machine-learned ranking and offers false discovery rate estimation. Compared with the mathematically exhaustive formula enumeration, our approach shrinks the formula candidate space by 42.8% on average. Method benchmarking on annotation accuracy was systematically carried out on reference MS/MS libraries and real metabolomics datasets. Applied on 155,321 recurrent unidentified spectra, our approach confidently annotated >5,000 novel molecular formulae absent from chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global optimization to refine formula annotations while revealing peak interrelationships. This approach allowed the systematic annotation of 37 fatty acid amide molecules in human fecal data. All bioinformatics pipelines are available in a standalone software, BUDDY ( https://github.com/HuanLab/BUDDY ).
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Affiliation(s)
- Shipei Xing
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Shen
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Banghua Xu
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiaoxiao Li
- Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022; 414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although metabolomics, alone or combined with other omics data, has already demonstrated its relevance for patient stratification in the frame of research projects and clinical studies, much remains to be done to move this approach to the clinical practice. This is especially true in the perspective of being applied to personalized/precision medicine, which aims at stratifying patients according to their risk of developing diseases, and tailoring medical treatments of patients according to individual characteristics in order to improve their efficacy and limit their toxicity. In this review article, we discuss the main challenges linked to analytical chemistry that need to be addressed to foster the implementation of metabolomics in the clinics and the use of the data produced by this approach in personalized medicine. First of all, there are already well-known issues related to untargeted metabolomics workflows at the levels of data production (lack of standardization), metabolite identification (small proportion of annotated features and identified metabolites), and data processing (from automatic detection of features to multi-omic data integration) that hamper the inter-operability and reusability of metabolomics data. Furthermore, the outputs of metabolomics workflows are complex molecular signatures of few tens of metabolites, often with small abundance variations, and obtained with expensive laboratory equipment. It is thus necessary to simplify these molecular signatures so that they can be produced and used in the field. This last point, which is still poorly addressed by the metabolomics community, may be crucial in a near future with the increased availability of molecular signatures of medical relevance and the increased societal demand for participatory medicine.
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Affiliation(s)
- Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Giulio Rosati
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Christian Moguet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Celia Fuentes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jose Marrugo-Ramírez
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Thibaud Lefebvre
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- Centre de Recherche sur l'Inflammation/CRI, Université de Paris, Inserm, Paris, France
- CRMR Porphyrie, Hôpital Louis Mourier, AP-HP Nord - Université de Paris, Colombes, France
| | - Hervé Volland
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France.
- MetaboHUB, Gif-sur-Yvette, France.
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5
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Neto FC, Raftery D. Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem 2021; 93:12001-12010. [PMID: 34436864 PMCID: PMC8530160 DOI: 10.1021/acs.analchem.1c02041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The urine metabolome constitutes a rich source of functional information reflecting physiological states that are influenced by distinct conditions and biological stresses, such as responses to drug treatments or disease manifestations. Although global liquid chromatography-mass spectrometry (MS) profiling provides the most comprehensive measurement of metabolites in complex biological samples, annotation remains a challenge, and computational approaches are necessary to translate the molecular composition into biological knowledge. Here, we investigated the use of tandem MS-based enhanced molecular networks (MolNetEnhancer) to improve the metabolite annotation of urine extracts. The samples (n = 10) were analyzed by hydrophilic interaction chromatography-quadrupole time-of-flight mass spectrometry in both electrospray ionization (ESI) modes. Consistent with other common data preprocessing software, the use of Progenesis QI led to the annotation of up to 20 metabolites based on MS2 library searches, showing a high fragmentation score (cosine similarity ≥ 0.7), that is, ∼2% of mass features containing MS2 spectra. Molecular networking based on library matching resulted in the annotation of up to 62 urinary compounds. Using a combination of unsupervised substructure discovery (MS2LDA), the in silico tool network annotation propagation (NAP), and ClassyFire chemical ontology, embedded in a multilayered molecular network by MolNetEnhancer, we were able to expand the chemical characterization to ∼50% of the data set. The integrative approach led to the annotation of 275 compounds at the metabolomics standards initiative (MSI) confidence level 2, as well as 459 and 578 urinary metabolites (MSI level 3) in both negative and positive ESI modes, respectively. The exhaustive MS2-based annotation outperformed similar studies applied to larger cohorts while offering the discovery of metabolites not identified by the MS2 library search. This is the first work that effectively integrates orthogonal annotation methods and MS2-based fragmentation studies to improve metabolite annotation in urine samples.
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Affiliation(s)
- Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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6
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Redefining dilute and shoot: The evolution of the technique and its application in the analysis of foods and biological matrices by liquid chromatography mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116284] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Collins SL, Koo I, Peters JM, Smith PB, Patterson AD. Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:467-487. [PMID: 34314226 DOI: 10.1146/annurev-anchem-091620-015205] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.
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Affiliation(s)
- Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeffrey M Peters
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Philip B Smith
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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8
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Cheng H, Yi L, Wu J, Li G, Zhao G, Xiao Z, Hu B, Zhao L, Tian J. Drug preconcentration and direct quantification in biofluids using 3D-Printed paper cartridge. Biosens Bioelectron 2021; 189:113266. [PMID: 34052581 DOI: 10.1016/j.bios.2021.113266] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/02/2021] [Accepted: 04/18/2021] [Indexed: 01/23/2023]
Abstract
Drug detection in biofluids has always been great importance for clinical diagnosis. Many detection technologies such as chromatography-mass spectrometry, have been applied to the detection of drugs. However, these technologies required multi-step operations, including complicated and time-consuming pretreatment processes and operations of bulky detection instruments, significantly limiting development of drug detection in clinical diagnosis. Herein, a portable 3D-printed paper cartridge was fabricated for fast sample preconcentration and direct drugs quantitative detection in biofluids by a portable Raman spectrometer. This cartridge contained both paper tip with silver nanowires to preconcentrate samples and achieve surface-enhanced Raman Scattering (SERS) measurement, and 3D-printed cartridge to build enclosed environment for the improvement of detection, which cost only one dollar. The preconcentration ability of the cartridge was up to 18.13-fold fluorescence enhancement and compared to the non-preconcentration method, it achieved 9.93-fold improvement of SERS performance. The anticancer drug of epirubicin hydrochloride, cyclophosphamide and their mixtures were quantitatively detected in the bovine serum or artificial urine. The integrated detection procedure required only 1 h, including sample pretreatment and preconcentration, drying, SERS measurements, and quantification analysis. This 3D-printed paper cartridge constituted a portable detection platform that would be potentially a practical and point-of-care detection tool for drug preconcentration and quantification on the clinical diagnosis.
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Affiliation(s)
- He Cheng
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China
| | - Langlang Yi
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China
| | - Jianduo Wu
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China
| | - Guoqian Li
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China
| | - Gang Zhao
- Pucheng Hospital, Pucheng, 715500, Shaanxi, PR China
| | - Zhixiang Xiao
- Pucheng Hospital, Pucheng, 715500, Shaanxi, PR China
| | - Bo Hu
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China; Xi'an Doctor Biotechnology Co. Ltd., Xi'an, 710075, Shaanxi, PR China.
| | - Lei Zhao
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China.
| | - Jie Tian
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, PR China; Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, PR China.
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Telu KH, Marupaka R, Andriamaharavo NR, Simón-Manso Y, Liang Y, Mirokhin YA, Bukhari TH, Preston RJ, Kashi L, Kelman Z, Stein SE. Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components. Biotechnol Bioeng 2021; 118:1491-1510. [PMID: 33404064 PMCID: PMC8048470 DOI: 10.1002/bit.27661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/02/2020] [Accepted: 12/13/2020] [Indexed: 02/02/2023]
Abstract
This paper reports the first implementation of a new type of mass spectral library for the analysis of Chinese hamster ovary (CHO) cell metabolites that allows users to quickly identify most compounds in any complex metabolite sample. We also describe an annotation methodology developed to filter out artifacts and low‐quality spectra from recurrent unidentified spectra of metabolites. CHO cells are commonly used to produce biological therapeutics. Metabolic profiles of CHO cells and media can be used to monitor process variability and look for markers that discriminate between batches of product. We have created a comprehensive library of both identified and unidentified metabolites derived from CHO cells that can be used in conjunction with tandem mass spectrometry to identify metabolites. In addition, we present a workflow that can be used for assigning confidence to a NIST MS/MS Library search match based on prior probability of general utility. The goal of our work is to annotate and identify (when possible), all liquid chromatography‐mass spectrometry generated metabolite ions as well as create automatable library building and identification pipelines for use by others in the field.
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Affiliation(s)
- Kelly H Telu
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Ramesh Marupaka
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Nirina R Andriamaharavo
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Yamil Simón-Manso
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Yuxue Liang
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Yuri A Mirokhin
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Tallat H Bukhari
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Renae J Preston
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA
| | - Lila Kashi
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA
| | - Zvi Kelman
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA
| | - Stephen E Stein
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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10
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Correia MSP, Lin W, Aria AJ, Jain A, Globisch D. Rapid Preparation of a Large Sulfated Metabolite Library for Structure Validation in Human Samples. Metabolites 2020; 10:metabo10100415. [PMID: 33081284 PMCID: PMC7603051 DOI: 10.3390/metabo10100415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolomics analysis of biological samples is widely applied in medical and natural sciences. Assigning the correct chemical structure in the metabolite identification process is required to draw the correct biological conclusions and still remains a major challenge in this research field. Several metabolite tandem mass spectrometry (MS/MS) fragmentation spectra libraries have been developed that are either based on computational methods or authentic libraries. These libraries are limited due to the high number of structurally diverse metabolites, low commercial availability of these compounds, and the increasing number of newly discovered metabolites. Phase II modification of xenobiotics is a compound class that is underrepresented in these databases despite their importance in diet, drug, or microbiome metabolism. The O-sulfated metabolites have been described as a signature for the co-metabolism of bacteria and their human host. Herein, we have developed a straightforward chemical synthesis method for rapid preparation of sulfated metabolite standards to obtain mass spectrometric fragmentation pattern and retention time information. We report the preparation of 38 O-sulfated alcohols and phenols for the determination of their MS/MS fragmentation pattern and chromatographic properties. Many of these metabolites are regioisomers that cannot be distinguished solely by their fragmentation pattern. We demonstrate that the versatility of this method is comparable to standard chemical synthesis. This comprehensive metabolite library can be applied for co-injection experiments to validate metabolites in different human sample types to explore microbiota-host co-metabolism, xenobiotic, and diet metabolism.
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11
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Yan X, Markey SP, Marupaka R, Dong Q, Cooper BT, Mirokhin YA, Wallace WE, Stein SE. Mass Spectral Library of Acylcarnitines Derived from Human Urine. Anal Chem 2020; 92:6521-6528. [PMID: 32271007 DOI: 10.1021/acs.analchem.0c00129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC-MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of acylcarnitines and developed a set of rules, derived from spectra in the NIST17 Tandem MS Library and those identified in urine, using the newly developed hybrid search method. Acylcarnitine tandem spectra were annotated with fragments from carnitine and acyl moieties as well as neutral loss peaks from precursors. Consensus spectra were derived from spectra having similar retention time, fragmentation pattern, and the same precursor m/z and collision energy. The library contains 157 different precursor masses, 586 unique acylcarnitines, and 4 332 acylcarnitine consensus spectra. Furthermore, from spectra that partially satisfied the fragmentation rules of acylcarnitines, we identified 125 conjugated acylcarnitines represented by 987 consensus spectra, which appear to originate from Phase II biotransformation reactions. To our knowledge, this is the first report of conjugated acylcarnitines. The mass spectra provided by this work may be useful for clinical screening of acylcarnitines as well as for studying relationships among fragmentation patterns, collision energies, structures, and retention times of acylcarnitines. Further, these methods are extensible to other classes of metabolites.
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Affiliation(s)
- Xinjian Yan
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Sanford P Markey
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Ramesh Marupaka
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Qian Dong
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Brian T Cooper
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Yuri A Mirokhin
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - William E Wallace
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Stephen E Stein
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
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12
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Petrov AP, Sherman LM, Camden JP, Dovichi NJ. Database of free solution mobilities for 276 metabolites. Talanta 2020; 209:120545. [PMID: 31892063 PMCID: PMC6956853 DOI: 10.1016/j.talanta.2019.120545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 11/23/2022]
Abstract
Although databases are available that provide mass spectra and chromatographic retention information for small-molecule metabolites, no publicly available database provides electrophoretic mobility for common metabolites. As a result, most compounds found in electrophoretic-based metabolic studies are unidentified and simply annotated as "features". To begin to address this issue, we analyzed 460 metabolites from a commercial library using capillary zone electrophoresis coupled with electrospray mass spectrometry. To speed analysis, a sequential injection method was used wherein six compounds were analyzed per run. An uncoated fused silica capillary was used for the analysis at 20 °C with a 0.5% (v/v) formic acid and 5% (v/v) methanol background electrolyte. A Prince autosampler was used for sample injection and the capillary was coupled to an ion trap mass spectrometer using an electrokinetically-pumped nanospray interface. We generated mobility values for 276 metabolites from the library (60% success rate) with an average standard deviation of 0.01 × 10-8 m2V-1s-1. As expected, cationic and anionic compounds were well resolved from neutral compounds. Neutral compounds co-migrated with electro-osmotic flow. Most of the compounds that were not detected were neutral and presumably suffered from adsorption to the capillary wall or poor ionization efficiency.
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Affiliation(s)
- Alexander P Petrov
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556-5670, USA
| | - Lindy M Sherman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556-5670, USA
| | - Jon P Camden
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556-5670, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556-5670, USA.
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13
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Bearden DW, Sheen DA, Simón-Manso Y, Benner BA, Rocha WFC, Blonder N, Lippa KA, Beger RD, Schnackenberg LK, Sun J, Mehta KY, Cheema AK, Gu H, Marupaka R, Nagana Gowda GA, Raftery D. Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite. Metabolites 2019; 9:metabo9110270. [PMID: 31703392 PMCID: PMC6918257 DOI: 10.3390/metabo9110270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022] Open
Abstract
There is a lack of experimental reference materials and standards for metabolomics measurements, such as urine, plasma, and other human fluid samples. Reasons include difficulties with supply, distribution, and dissemination of information about the materials. Additionally, there is a long lead time because reference materials need their compositions to be fully characterized with uncertainty, a labor-intensive process for material containing thousands of relevant compounds. Furthermore, data analysis can be hampered by different methods using different software by different vendors. In this work, we propose an alternative implementation of reference materials. Instead of characterizing biological materials based on their composition, we propose using untargeted metabolomic data such as nuclear magnetic resonance (NMR) or gas and liquid chromatography-mass spectrometry (GC-MS and LC-MS) profiles. The profiles are then distributed with the material accompanying the certificate, so that researchers can compare their own metabolomic measurements with the reference profiles. To demonstrate this approach, we conducted an interlaboratory study (ILS) in which seven National Institute of Standards and Technology (NIST) urine Standard Reference Material®s (SRM®s) were distributed to participants, who then returned the metabolomic data to us. We then implemented chemometric methods to analyze the data together to estimate the uncertainties in the current measurement techniques. The participants identified similar patterns in the profiles that distinguished the seven samples. Even when the number of spectral features is substantially different between platforms, a collective analysis still shows significant overlap that allows reliable comparison between participants. Our results show that a urine suite such as that used in this ILS could be employed for testing and harmonization among different platforms. A limited quantity of test materials will be made available for researchers who are willing to repeat the protocols presented here and contribute their data.
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Affiliation(s)
- Daniel W. Bearden
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - David A. Sheen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
- Correspondence: ; Tel.: +1-301-975-2603
| | - Yamil Simón-Manso
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
| | - Bruce A. Benner
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - Werickson F. C. Rocha
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
- National Institute of Metrology, Quality, and Technology—INMETRO, 25250-020 Duque de Caxias, RJ, Brazil
| | - Niksa Blonder
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - Katrice A. Lippa
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - Richard D. Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (R.D.B.); (L.K.S.); (J.S.)
| | - Laura K. Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (R.D.B.); (L.K.S.); (J.S.)
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (R.D.B.); (L.K.S.); (J.S.)
| | - Khyati Y. Mehta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (K.Y.M.); (A.K.C.)
| | - Amrita K. Cheema
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (K.Y.M.); (A.K.C.)
- Departments of Oncology and Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA;
| | - Ramesh Marupaka
- Clinical Toxicology at CIAN Diagnostics, Frederick, MD 21703, USA;
| | - G. A. Nagana Gowda
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98109, USA; (G.A.N.G.); (D.R.)
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98109, USA; (G.A.N.G.); (D.R.)
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14
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Cooper BT, Yan X, Simón-Manso Y, Tchekhovskoi DV, Mirokhin YA, Stein SE. Hybrid Search: A Method for Identifying Metabolites Absent from Tandem Mass Spectrometry Libraries. Anal Chem 2019; 91:13924-13932. [PMID: 31600070 PMCID: PMC7299168 DOI: 10.1021/acs.analchem.9b03415] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics has a critical need for better tools for mass spectral identification. Common metabolites may be identified by searching libraries of tandem mass spectra, which offers important advantages over other approaches to identification. But tandem libraries are not nearly complete enough to represent the full molecular diversity present in complex biological samples. We present a novel hybrid search method that can help identify metabolites not in the library by similarity to compounds that are. We call it "hybrid" searching because it combines conventional, direct peak matching with the logical equivalent of neutral-loss matching. A successful hybrid search requires the library to contain "cognates" of the unknown: similar compounds with a structural difference confined to a single region of the molecule, that does not substantially alter its fragmentation behavior. We demonstrate that the hybrid search is highly likely to find similar compounds under such circumstances.
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Affiliation(s)
- Brian T. Cooper
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Xinjian Yan
- Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Yamil Simón-Manso
- Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Dmitrii V. Tchekhovskoi
- Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Yuri A. Mirokhin
- Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Stephen E. Stein
- Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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