1
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Hu Z, Zou Y, Ma Z, Liu W, Jin X, Yang J. Rapid screening and identification of targeted and non-targeted illegal added drugs in functional foods by MRSIT-HRMS based on NIST screening database. Food Chem 2024; 446:138913. [PMID: 38452505 DOI: 10.1016/j.foodchem.2024.138913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
The last few decades have witnessed the increasing consumption of functional foods, leading to the expansion of the worldwide market. However, the illegal addition drugs in functional foods remains incessant despite repeated prohibition, making it a key focus of strict crackdowns by regulatory authorities. Effective analytical tools and procedures are desperately needed to rapidly screen and identify illegally added drugs in a large number of samples, given the growing amount and diversity of these substances in functional foods. The MRSIT-HRMS (Multiple Sample Rapid Introduction combined with High Resolution Mass Spectrometry) without chromatographic separation, after direct sampling, utilizes NIST software (National Institute of Standards and Technology) matching with a home-built library to target identification and non-targeted screen of illegal additives. When applied to 50 batches of suspicious samples, the targeted method detected illegal added drugs in 41 batches of samples, while the non-targeted method screened a new phosphodiesterase-5 (PDE-5) inhibitor type structural derivative. The positive results obtained by the targeted method were consistent with LC-MS/MS (QQQ). The novel MRSIT-HRMS with a limit of quantification (LOD) of 1 μg/mL achieved 100 % correct identification for all 50 batches of actual samples, demonstrating its potential as a highly promising and powerful tool for fast screening of illegally added drugs in functional food, especially when compared to traditional LC-MS/MS methods. This is essential for ensuring drug safety and public health.
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Affiliation(s)
- Ziyan Hu
- Nanjing Institute for Food and Drug Control, Nanjing 211198, China; Key Laboratory of Food Authenticity Identification Technology for Jiangsu Province Market Regulation, Nanjing 211198, China.
| | - Yixuan Zou
- National Institute of Metrology, Beijing 100029, China
| | - Zhi Ma
- Nanjing Institute for Food and Drug Control, Nanjing 211198, China; Key Laboratory of Food Authenticity Identification Technology for Jiangsu Province Market Regulation, Nanjing 211198, China
| | - Wenting Liu
- Nanjing Institute for Food and Drug Control, Nanjing 211198, China; Key Laboratory of Food Authenticity Identification Technology for Jiangsu Province Market Regulation, Nanjing 211198, China
| | - Xin Jin
- Nanjing Institute for Food and Drug Control, Nanjing 211198, China; Key Laboratory of Food Authenticity Identification Technology for Jiangsu Province Market Regulation, Nanjing 211198, China
| | - Jun Yang
- Nanjing Institute for Food and Drug Control, Nanjing 211198, China; Key Laboratory of Food Authenticity Identification Technology for Jiangsu Province Market Regulation, Nanjing 211198, China.
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2
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Mahboubifar M, Zidorn C, Farag MA, Zayed A, Jassbi AR. Chemometric-based drug discovery approaches from natural origins using hyphenated chromatographic techniques. PHYTOCHEMICAL ANALYSIS : PCA 2024; 35:990-1016. [PMID: 38806406 DOI: 10.1002/pca.3382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
INTRODUCTION Isolation and characterization of bioactive components from complex matrices of marine or terrestrial biological origins are the most challenging issues for natural product chemists. Biochemometric is a new potential scope in natural product analytical science, and it is a methodology to find the compound's correlation to their bioactivity with the help of hyphenated chromatographic techniques and chemometric tools. OBJECTIVES The present review aims to evaluate the application of chemometric tools coupled to chromatographic techniques for drug discovery from natural resources. METHODS The searching keywords "biochemometric," "chemometric," "chromatography," "natural products bioassay," and "bioassay" were selected to search the published articles between 2010-2023 using different search engines including "Pubmed", "Web of Science," "ScienceDirect," and "Google scholar." RESULTS An initial stage in natural product analysis is applying the chromatographic hyphenated techniques in conjunction with biochemometric approaches. Among the applied chromatographic techniques, liquid chromatography (LC) techniques, have taken up more than half (53%) and also, mass spectroscopy (MS)-based chromatographic techniques such as LC-MS are the most widely used techniques applied in combination with chemometric methods for natural products bioassay. Considering the complexity of dataset achieved from chromatographic hyphenated techniques, chemometric tools have been increasingly employed for phytochemical studies in the context of determining botanicals geographical origin, quality control, and detection of bioactive compounds. CONCLUSION Biochemometric application is expected to be further improved with advancing in data acquisition methods, new efficient preprocessing, model validation and variable selection methods which would guarantee that the applied model to have good prediction ability in compound relation to its bioactivity.
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Affiliation(s)
- Marjan Mahboubifar
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Christian Zidorn
- Pharmazeutisches Institut, Abteilung Pharmazeutische Biologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed Zayed
- Pharmacognosy Department, College of Pharmacy, Tanta University, Tanta, Egypt
| | - Amir Reza Jassbi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmazeutisches Institut, Abteilung Pharmazeutische Biologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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3
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Rahman M, Marzullo B, Holman SW, Barrow M, Ray AD, O’Connor PB. Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:285-299. [PMID: 38197777 PMCID: PMC10853971 DOI: 10.1021/jasms.3c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/11/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are specialized molecules that bind to a target protein and a ubiquitin ligase to facilitate protein degradation. Despite their significance, native PROTACs have not undergone tandem mass spectrometry (MS) analysis. To address this gap, we conducted a pioneering investigation on the fragmentation patterns of two PROTACs in development, dBET1 and VZ185. Employing diverse cations (sodium, lithium, and silver) and multiple tandem-MS techniques, we enhanced their structural characterization. Notably, lithium cations facilitated comprehensive positive-mode coverage for dBET1, while negative polarity mode offered richer insights. Employing de novo structure determination on 2DMS data from degradation studies yielded crucial insights. In the case of VZ185, various charge states were observed, with [M + 2H]2+ revealing fewer moieties than [M + H]+ due to charge-related factors. Augmenting structural details through silver adducts suggested both charge-directed and charge-remote fragmentation. This comprehensive investigation identifies frequently dissociated bonds across multiple fragmentation techniques, pinpointing optimal approaches for elucidating PROTAC structures. The findings contribute to advancing our understanding of PROTACs, pivotal for their continued development as promising therapeutic agents.
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Affiliation(s)
- Mohammed Rahman
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
- Department
of Physics, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Bryan Marzullo
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Stephen W. Holman
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Mark Barrow
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Andrew D. Ray
- New
Modalities and Parenteral Development, Pharmaceutical Technology &
Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
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4
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Inoue K, Fujihara A. Differentiation of free d-amino acids and amino acid isomers in solution using tandem mass spectrometry of hydrogen-bonded clusters. J Pharm Biomed Anal 2023; 234:115567. [PMID: 37441889 DOI: 10.1016/j.jpba.2023.115567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/21/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
Free d-amino acids and amino acid isomers were differentiated using tandem mass spectrometry without chromatographic separation. Ultraviolet photodissociation and water adsorption of leucine (Leu) and isoleucine (Ile) enantiomers hydrogen-bonded with tryptophan (Trp) were investigated at 8 K in the gas phase. The enantiomer-selective Cα-Cβ bond cleavage of Trp was observed in the product ion spectra obtained by 285 nm photoexcitation, where the abundance of NH2CHCOOH-eliminated ion of heterochiral H+(d-Trp)(l-Leu) was higher than that of homochiral H+(l-Trp)(l-Leu). When comparing water adsorption on the surfaces of the heterochiral and homochiral clusters in a cold ion trap, the number of water molecules adsorbed on the heterochiral cluster was greater than that adsorbed on the homochiral cluster. These results indicate that the stronger intermolecular interactions within the homochiral H+(l-Trp)(l-Leu) compared to the heterochiral cluster inhibit enantiomer-selective photodissociation. Leu and Ile were differentiated by the isomer-selective Cα-Cβ bond cleavage of Trp in the clusters. Calibration curves for the differentiation of isomeric amino acids and their enantiomers were developed using monitoring isomer- and enantiomer-selective photodissociation, indicating that the molar fractions in solution could be determined from a single product ion spectrum.
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Affiliation(s)
- Kanako Inoue
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, Osaka 599-8531, Japan
| | - Akimasa Fujihara
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, Osaka 599-8531, Japan.
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5
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van Herwerden D, O’Brien JW, Lege S, Pirok BWJ, Thomas KV, Samanipour S. Cumulative Neutral Loss Model for Fragment Deconvolution in Electrospray Ionization High-Resolution Mass Spectrometry Data. Anal Chem 2023; 95:12247-12255. [PMID: 37549176 PMCID: PMC10448439 DOI: 10.1021/acs.analchem.3c00896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 08/09/2023]
Abstract
Clean high-resolution mass spectra (HRMS) are essential to a successful structural elucidation of an unknown feature during nontarget analysis (NTA) workflows. This is a crucial step, particularly for the spectra generated during data-independent acquisition or during direct infusion experiments. The most commonly available tools only take advantage of the time domain for spectral cleanup. Here, we present an algorithm that combines the time domain and mass domain information to perform spectral deconvolution. The algorithm employs a probability-based cumulative neutral loss (CNL) model for fragment deconvolution. The optimized model, with a mass tolerance of 0.005 Da and a scoreCNL threshold of 0.00, was able to achieve a true positive rate (TPr) of 95.0%, a false discovery rate (FDr) of 20.6%, and a reduction rate of 35.4%. Additionally, the CNL model was extensively tested on real samples containing predominantly pesticides at different concentration levels and with matrix effects. Overall, the model was able to obtain a TPr above 88.8% with FD rates between 33 and 79% and reduction rates between 9 and 45%. Finally, the CNL model was compared with the retention time difference method and peak shape correlation analysis, showing that a combination of correlation analysis and the CNL model was the most effective for fragment deconvolution, obtaining a TPr of 84.7%, an FDr of 54.4%, and a reduction rate of 51.0%.
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Affiliation(s)
- Denice van Herwerden
- Van
’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam 1012 WX, The Netherlands
| | - Jake W. O’Brien
- Van
’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam 1012 WX, The Netherlands
- Queensland
Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane 4102, Australia
| | - Sascha Lege
- Agilent
Technologies Deutschland GmbH, Waldbronn 76337, Germany
| | - Bob W. J. Pirok
- Van
’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam 1012 WX, The Netherlands
| | - Kevin V. Thomas
- Queensland
Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane 4102, Australia
| | - Saer Samanipour
- Van
’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam 1012 WX, The Netherlands
- Queensland
Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane 4102, Australia
- UvA
Data Science Center, University of Amsterdam, Amsterdam 1012 WP, The Netherlands
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6
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Feng YQ, Zhang P, Jian JZ, Wang ZW, Tian XL, Luo GY, Yang WD. Study on 2-arylbenzo[ b]furans from Itea omeiensis and their fragmentation patterns with Q-Orbitrap mass spectrometry. Nat Prod Res 2023:1-12. [PMID: 37245178 DOI: 10.1080/14786419.2023.2216344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/24/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
One new 2-arylbenzo[b]furan named iteafuranal F (1) as well as two known analogues (2-3) were isolated from the 95% EtOH extract of aerial parts of Itea omeiensis. Their chemical structures were constructed based on extensive analyses of UV, IR, 1D/2D NMR and HRMS spectra. Antioxidant assays revealed significant superoxide anion radical scavenging capacity of 1 with IC50 value of 0.66 mg/mL, which was comparable to the efficiency of positive control of luteolin. In addition, the preliminary MS fragmentation patterns in negative ion mode were established to distinguish 2-arylbenzo[b]furans with C-10 in different oxidation states: the characteristic loss of CO molecule [M-H-28]- was observed for 3-formyl-2-arylbenzo[b]furans, and the loss of CH2O fragment [M-H-30]- for 3-hydroxymethyl-2-arylbenzo[b]furans, and the loss of CO2 fragment [M-H-44]- for 2-arylbenzo[b]furan-3-carboxylic acids.
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Affiliation(s)
- Yun-Qian Feng
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Pan Zhang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Jin-Zhen Jian
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Zhi-Wei Wang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Xiao-Long Tian
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Guo-Yong Luo
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Wu-De Yang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
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7
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MAD HATTER Correctly Annotates 98% of Small Molecule Tandem Mass Spectra Searching in PubChem. Metabolites 2023; 13:metabo13030314. [PMID: 36984753 PMCID: PMC10053663 DOI: 10.3390/metabo13030314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics usually relies on mass spectrometry, a technology capable of detecting thousands of compounds in a biological sample. Metabolite annotation is executed using tandem mass spectrometry. Spectral library search is far from comprehensive, and numerous compounds remain unannotated. So-called in silico methods allow us to overcome the restrictions of spectral libraries, by searching in much larger molecular structure databases. Yet, after more than a decade of method development, in silico methods still do not reach the correct annotation rates that users would wish for. Here, we present a novel computational method called Mad Hatter for this task. Mad Hatter combines CSI:FingerID results with information from the searched structure database via a metascore. Compound information includes the melting point, and the number of words in the compound description starting with the letter ‘u’. We then show that Mad Hatter reaches a stunning 97.6% correct annotations when searching PubChem, one of the largest and most comprehensive molecular structure databases. Unfortunately, Mad Hatter is not a real method. Rather, we developed Mad Hatter solely for the purpose of demonstrating common issues in computational method development and evaluation. We explain what evaluation glitches were necessary for Mad Hatter to reach this annotation level, what is wrong with similar metascores in general, and why metascores may screw up not only method evaluations but also the analysis of biological experiments. This paper may serve as an example of problems in the development and evaluation of machine learning models for metabolite annotation.
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8
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van Outersterp R, Oosterhout J, Gebhardt CR, Berden G, Engelke UFH, Wevers RA, Cuyckens F, Oomens J, Martens J. Targeted Small-Molecule Identification Using Heartcutting Liquid Chromatography-Infrared Ion Spectroscopy. Anal Chem 2023; 95:3406-3413. [PMID: 36735826 PMCID: PMC9933049 DOI: 10.1021/acs.analchem.2c04904] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Infrared ion spectroscopy (IRIS) can be used to identify molecular structures detected in mass spectrometry (MS) experiments and has potential applications in a wide range of analytical fields. However, MS-based approaches are often combined with orthogonal separation techniques, in many cases liquid chromatography (LC). The direct coupling of LC and IRIS is challenging due to the mismatching timescales of the two technologies: an IRIS experiment typically takes several minutes, whereas an LC fraction typically elutes in several seconds. To resolve this discrepancy, we present a heartcutting LC-IRIS approach using a setup consisting of two switching valves and two sample loops as an alternative to direct online LC-IRIS coupling. We show that this automated setup enables us to record multiple IR spectra for two LC-features from a single injection without degrading the LC-separation performance. We demonstrate the setup for application in drug metabolism research by recording six m/z-selective IR spectra for two drug metabolites from a single 2 μL sample of cell incubation extract. Additionally, we measure the IR spectra of two closely eluting diastereomeric biomarkers for the inborn error of metabolism pyridoxine-dependent epilepsy (PDE-ALDH7A1), which shows that the heartcutting LC-IRIS setup has good sensitivity (requiring ∼μL injections of ∼μM samples) and that the separation between closely eluting isomers is maintained. We envision applications in a range of research fields, where the identification of molecular structures detected by LC-MS is required.
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Affiliation(s)
- Rianne
E. van Outersterp
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jitse Oosterhout
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | | | - Giel Berden
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F. H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Filip Cuyckens
- Drug
Metabolism & Pharmacokinetics, Janssen R&D, Beerse 2340, Belgium
| | - Jos Oomens
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Jonathan Martens
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,
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9
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Ramirez DA, Carazzone C. Small molecules putative structure elucidation in endemic Colombian fruits: CFM-ID approach. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2147539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Daniel Arias Ramirez
- Chemistry, Department, Universidad de Los Andes, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Bogotá, Colombia
- ICP-MS Spectrometry Laboratory, Deanship of Scientific Research-Faculty of Science, Universidad de Los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Chemistry, Department, Universidad de Los Andes, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Bogotá, Colombia
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10
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Cai Y, Zhou Z, Zhu ZJ. Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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11
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Wang X, Hebert DD, Runsewe DO, Pohlman GE, Hoffmann WD, Irvin JA. Electroactive Polymer-Based Spray Ionization for Direct Mass Spectrometric Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1840-1849. [PMID: 36149251 DOI: 10.1021/jasms.2c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Electrochemically deposited electroactive polymer (EAP) films were investigated for their potential to enhance the performance of ambient ionization mass spectrometry (MS). Several EAPs of varying hydrophobicity were evaluated, including the superhydrophobic polymer poly[3,4-(2-dodecylethylenedioxy)thiophene] (PEDOT-C12). The EAPs were electropolymerized onto indium tin oxide-coated glass, placed in front of the inlet of a mass spectrometer, and charged to 3.5-4.5 kV. Analyte solutions were then applied to the surface, initiating ionization events. Analytes including peptides and small molecule pharmaceuticals were studied in 0.1% formic acid in methanol/water ("spray solvent") as well as in synthetic biological fluid matrices, using both EAP spray ionization (EAPSI) and paper spray ionization (PSI). Each EAPSI analysis required as little as 0.1 μL of solution, and the resulting sprays were stable and reproducible. The sensitivity, limit of detection (LOD), and limit of quantification (LOQ) were evaluated using bradykinin, cannabinol, and cannabidiol, which were prepared in pure solvents, artificial urine, and artificial saliva. The limits of detection and quantitation for EAPSI were improved relative to PSI by 1-2 orders of magnitude for analytes prepared in methanol/water and on the same order of magnitude as PSI for analytes prepared in artificial saliva and urine. This EAP-based spray ionization technique offers possibilities for rapid MS analysis with small sample sizes, high accuracy, and miniaturization of MS instruments.
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Affiliation(s)
- Xu Wang
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - David D Hebert
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Damilola O Runsewe
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - Gabriel E Pohlman
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - William D Hoffmann
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Jennifer A Irvin
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
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12
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Consonni V, Gosetti F, Termopoli V, Todeschini R, Valsecchi C, Ballabio D. Multi-Task Neural Networks and Molecular Fingerprints to Enhance Compound Identification from LC-MS/MS Data. Molecules 2022; 27:5827. [PMID: 36144564 PMCID: PMC9502453 DOI: 10.3390/molecules27185827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Mass spectrometry (MS) is widely used for the identification of chemical compounds by matching the experimentally acquired mass spectrum against a database of reference spectra. However, this approach suffers from a limited coverage of the existing databases causing a failure in the identification of a compound not present in the database. Among the computational approaches for mining metabolite structures based on MS data, one option is to predict molecular fingerprints from the mass spectra by means of chemometric strategies and then use them to screen compound libraries. This can be carried out by calibrating multi-task artificial neural networks from large datasets of mass spectra, used as inputs, and molecular fingerprints as outputs. In this study, we prepared a large LC-MS/MS dataset from an on-line open repository. These data were used to train and evaluate deep-learning-based approaches to predict molecular fingerprints and retrieve the structure of unknown compounds from their LC-MS/MS spectra. Effects of data sparseness and the impact of different strategies of data curing and dimensionality reduction on the output accuracy have been evaluated. Moreover, extensive diagnostics have been carried out to evaluate modelling advantages and drawbacks as a function of the explored chemical space.
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Affiliation(s)
| | | | | | | | | | - Davide Ballabio
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
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13
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Costalunga R, Tshepelevitsh S, Sepman H, Kull M, Kruve A. Sodium adduct formation with graph-based machine learning can aid structural elucidation in non-targeted LC/ESI/HRMS. Anal Chim Acta 2022; 1204:339402. [PMID: 35397906 DOI: 10.1016/j.aca.2021.339402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/07/2021] [Accepted: 12/23/2021] [Indexed: 11/01/2022]
Abstract
Non-targeted screening with LC/ESI/HRMS aims to identify the structure of the detected compounds using their retention time, exact mass, and fragmentation pattern. Challenges remain in differentiating between isomeric compounds. One untapped possibility to facilitate identification of isomers relies on different ionic species formed in electrospray. In positive ESI mode, both protonated molecules and adducts can be formed; however, not all isomeric structures form the same ionic species. The complicated mechanism of adduct formation has hindered the use of this molecular characteristic in the structural elucidation in non-targeted screening. Here, we have studied the adduct formation for 94 small molecules with ion mobility spectra and compared collision cross-sections of the respective ions. Based on the results we developed a fast support vector machine classifier with polynomial kernels for accurately predicting the sodium adduct formation in ESI/HRMS. The model is trained on five independent data sets from different laboratories and uses the graph-based connectivity of functional groups and PubChem fingerprints to predict the sodium adduct formation in ESI/HRMS. The validation of the model showed an accuracy of 74.7% (balanced accuracy 70.0%) on a dataset from an independent laboratory, which was not used in the training of the model. Lastly, we applied the classification algorithm to the SusDat database by NORMAN network to evaluate the proportion of isomeric compounds that could be distinguished based on predicted sodium adduct formation. It was observed that sodium adduct formation probability can provide additional selectivity for about one quarter of the exact masses and, therefore, shows practical utility for structural assignment in non-targeted screening.
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Affiliation(s)
- Riccardo Costalunga
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius väg 16, 106 91, Stockholm, Sweden; Department of Food and Drug, University of Parma, via Università, 12, I 43121, Parma, Italy
| | - Sofja Tshepelevitsh
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu, 50411, Estonia
| | - Helen Sepman
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius väg 16, 106 91, Stockholm, Sweden
| | - Meelis Kull
- Institute of Computer Science, University of Tartu, Narva mnt 18, 51009, Tartu, Estonia
| | - Anneli Kruve
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius väg 16, 106 91, Stockholm, Sweden.
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14
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Kumar M, Zheng Z, Nishshanka U, Xia H, Weisbecker C, Attygalle AB. Fragmentation pathways of deprotonated ortho-hydroxybenzyl alcohol. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4829. [PMID: 35581161 DOI: 10.1002/jms.4829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 06/15/2023]
Abstract
The ortho, meta, and para isomers of hydroxybenzyl alcohol can be unequivocally distinguished by the collision-induced dissociation mass spectra of their anions. The presence of a prominent peak at m/z 121 for an elimination of a dihydrogen molecule renders the ortho-isomer spectrum markedly different from those of its meta and para congeners. Investigations carried out with deuterium-labeled isotopologues of the ortho isomer verified that the labile hydrogen atom on the hydroxyl group and one of the benzylic hydrogen atoms are specifically removed in the formation of the m/z 121 ion. The ortho-isomer spectrum also showed a prominent peak at m/z 93. Experimental data indicated that the m/z 93 product ion originates either from a two-step H2 and CO elimination mechanism or from a direct loss of a HCHO molecule from the precursor anion. The intensity ratio of the m/z 93 and 94 peaks in the spectrum recorded from the m/z 124 ion generated from a sample of o-hydroxybenzyl alcohol dissolved in D2 O supported the notion that the direct HCHO loss is the more dominant pathway for the generation of the phenolate ion under low activation conditions. In contrast, the two-step mechanism becomes the more dominant pathway under high collisional activation conditions. The spectrum also showed a weak peak at m/z 105 for a water loss. Based on computational data, the m/z 105 ion generated in this way appears to be a composite generated from a common ion-neutral complex intermediate in which a hydroxyl anion is positioned equidistantly between one of the benzylic hydrogens and a nearby hydrogen atom of the benzene ring. Upon activation, the complex dissociates to form either a phenide or a quinone methide anion. The reaction forming a carbon dioxide adduct under ion-mobility conditions was used to support the proposed water-loss mechanism.
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Affiliation(s)
- Meenu Kumar
- Center for Mass Spectrometry, Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Zhaoyu Zheng
- Center for Mass Spectrometry, Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Upul Nishshanka
- Center for Mass Spectrometry, Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Hanxue Xia
- Center for Mass Spectrometry, Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Carl Weisbecker
- Center for Mass Spectrometry, Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Athula B Attygalle
- Center for Mass Spectrometry, Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
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15
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Man G, Xu L, Wang Y, Liao X, Xu Z. Profiling Phenolic Composition in Pomegranate Peel From Nine Selected Cultivars Using UHPLC-QTOF-MS and UPLC-QQQ-MS. Front Nutr 2022; 8:807447. [PMID: 35141267 PMCID: PMC8819070 DOI: 10.3389/fnut.2021.807447] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022] Open
Abstract
Pomegranate is widely cultivated across China, and the phenolics in its peel are principal components associated with health benefits. Ultra-high performance liquid chromatography coupled to a quadrupole time-of-flight mass spectrometer (UHPLC-QTOF-MS) and ultra-performance liquid chromatography coupled to a triple quadrupole mass spectrometer (UPLC-QQQ-MS) were used in this study, aiming at profiling the total phenolic composition in pomegranate peel from nine selected cultivars in 7 production areas. Sixty-four phenolic compounds were identified or annotated, and 23 of them were firstly reported in pomegranate peel. Principal component analysis (PCA) plots show differences and similarities of phenolics among nine cultivars. Furthermore, 15 phenolic compounds were quantified with the standards, and punicalagin, ellagic acid, gallocatechin, punicalin, catechin, and corilagin were found to be dominant. Punicalagin weighed the highest content (28.03–104.14 mg/g). This study can provide a deeper and more detailed insight into the phenolic composition in pomegranate peel and facilitate the health-promoting utilization of phenolics.
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Affiliation(s)
- Guowei Man
- College of Food Science and Nutritional Engineering, China Agricultural University; Beijing Key Laboratory for Food Non-thermal Processing; Key Lab of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lei Xu
- College of Food Science and Nutritional Engineering, China Agricultural University; Beijing Key Laboratory for Food Non-thermal Processing; Key Lab of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yongtao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University; Beijing Key Laboratory for Food Non-thermal Processing; Key Lab of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University; Beijing Key Laboratory for Food Non-thermal Processing; Key Lab of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- *Correspondence: Xiaojun Liao
| | - Zhenzhen Xu
- Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Beijing, China
- Zhenzhen Xu
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16
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Chen B, Kurita KL, Wong N, Crittenden CM. Ultraviolet photodissociation facilitates mass spectrometry-based structure elucidation with pyrrolidine and piperidine containing compounds. J Pharm Biomed Anal 2022; 211:114622. [DOI: 10.1016/j.jpba.2022.114622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
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17
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Tian Z, Liu F, Li D, Fernie AR, Chen W. Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples. Comput Struct Biotechnol J 2022; 20:5085-5097. [PMID: 36187931 PMCID: PMC9489805 DOI: 10.1016/j.csbj.2022.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022] Open
Abstract
LC–MS/MS is a major analytical platform for metabolomics, which has become a recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation of small molecules based on LC–MS/MS data remains a major challenge in the chemical and biological interpretation of untargeted metabolomics datasets. In recent years, several strategies for structure elucidation using LC–MS/MS data from complex biological samples have been proposed, these strategies can be simply categorized into two types, one based on structure annotation of mass spectra and for the other on retention time prediction. These strategies have helped many scientists conduct research in metabolite-related fields and are indispensable for the development of future tools. Here, we summarized the characteristics of the current tools and strategies for structure elucidation of small molecules based on LC–MS/MS data, and further discussed the directions and perspectives to improve the power of the tools or strategies for structure elucidation.
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18
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van Outersterp R, Engelke UF, Merx J, Berden G, Paul M, Thomulka T, Berkessel A, Huigen MC, Kluijtmans LA, Mecinović J, Rutjes FP, van Karnebeek CD, Wevers RA, Boltje TJ, Coene KL, Martens J, Oomens J. Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy. Anal Chem 2021; 93:15340-15348. [PMID: 34756024 PMCID: PMC8613736 DOI: 10.1021/acs.analchem.1c02896] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing "grand challenge" in the utilization of this approach is metabolite identification─confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico-predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids and that are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly provided novel insights into the pathophysiology of PDE-ALDH7A1.
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Affiliation(s)
- Rianne
E. van Outersterp
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F.H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jona Merx
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Mathias Paul
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Thomas Thomulka
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Albrecht Berkessel
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Marleen C.D.G. Huigen
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo A.J. Kluijtmans
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jasmin Mecinović
- University
of Southern Denmark, Department of Physics,
Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark
| | - Floris P.J.T. Rutjes
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Clara D.M. van Karnebeek
- Department
of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial
Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Karlien L.M. Coene
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 908, 1098XH Amsterdam, The Netherlands
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19
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Evaluation of Sample Preparation Methods for Non-Target Screening of Organic Micropollutants in Urban Waters Using High-Resolution Mass Spectrometry. Molecules 2021; 26:molecules26237064. [PMID: 34885646 PMCID: PMC8659043 DOI: 10.3390/molecules26237064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 02/02/2023] Open
Abstract
Non-target screening (NTS) has gained interest in recent years for environmental monitoring purposes because it enables the analysis of a large number of pollutants without predefined lists of molecules. However, sample preparation methods are diverse, and few have been systematically compared in terms of the amount and relevance of the information obtained by subsequent NTS analysis. The goal of this work was to compare a large number of sample extraction methods for the unknown screening of urban waters. Various phases were tested for the solid-phase extraction of micropollutants from these waters. The evaluation of the different phases was assessed by statistical analysis based on the number of detected molecules, their range, and physicochemical properties (molecular weight, standard recoveries, polarity, and optical properties). Though each cartridge provided its own advantages, a multilayer cartridge combining several phases gathered more information in one single extraction by benefiting from the specificity of each one of its layers.
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20
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Viana L, English M. The application of chromatography in the study of off-flavour compounds in pulses and pulse by-products. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Cave JR, Parker E, Lebrilla C, Waterhouse AL. Normal-phase chromatographic separation of pigmented wine tannin by nano-HPLC quadrupole time-of-flight tandem mass spectrometry and identification of candidate molecular features. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:4699-4704. [PMID: 33491784 DOI: 10.1002/jsfa.11115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/28/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND As a wine ages, altered sensory properties lead to changes in perceived quality and value. Concurrent modifications of anthocyanin and tannin occur forming pigmented tannin, softening astringency and retaining persistent color. Wine tannin extracts of 1990 and 2010 vintages of Oakville Station Cabernet Sauvignon have been analyzed using normal-phase chromatography with tandem quadrupole time-of-flight mass spectrometry (QToF) to investigate the compositional differences in their pigmented tannin fractions. RESULTS The older wine demonstrates much greater structural diversity and a range of more polar compounds, while the younger wine contains fewer observed ion peaks. Several hundred molecular features are observable, and, as expected, there is progression to higher molecular weights after long aging. Between 7% and 16% of molecular features could be matched to a database of anticipated pigmented tannin compounds. Many signals had multiple possible isomeric identities, but fragmentation to resolve their identity was stymied by low sensitivity of the tandem mass spectrometric capability provided by QToF, so isomeric disambiguation is incomplete. CONCLUSIONS The chromatography displayed a high degree of resolution in aged wines, separating many of the known pigment types, including aldehyde bridged compounds, pyranoanthocyanins and direct condensation products among others, as well as resolving a great number of unknown compounds. Expanding our understanding of red wine pigments will lead to better wines as winemakers will be able to associate quality with particular wine pigment profiles once we can distinguish the relevant patterns in those pigments. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jonathan R Cave
- Agricultural and Environmental Chemistry, University of California, Davis, CA, USA
- Department of Viticulture and Enology, University of California, Davis, CA, USA
| | - Evan Parker
- Department of Chemistry, University of California, Davis, CA, USA
| | - Carlito Lebrilla
- Department of Chemistry, University of California, Davis, CA, USA
| | - Andrew L Waterhouse
- Department of Viticulture and Enology, University of California, Davis, CA, USA
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22
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Plachká K, Pezzatti J, Musenga A, Nicoli R, Kuuranne T, Rudaz S, Nováková L, Guillarme D. Ion mobility-high resolution mass spectrometry in doping control analysis. Part II: Comparison of acquisition modes with and without ion mobility. Anal Chim Acta 2021; 1175:338739. [PMID: 34330438 DOI: 10.1016/j.aca.2021.338739] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022]
Abstract
In the second part of this study, a systematic comparison was made between two ion fragmentation acquisition modes, namely data-independent acquisition (DIA) and DIA with ion mobility spectrometry (IMS) technology. These two approaches were applied to the analysis of 192 doping agents in urine. Group I included 102 compounds such as stimulants, diuretics, narcotics, and β2-agonists, while Group II contained 90 compounds included steroids, glucocorticoids, and hormone and metabolic modulators. Important method parameters were examined and compared, including the fragmentation, sensitivity, and assignment capability with the minimum occurrence of false positive hits. The results differed between Group I and II in number of detected fragments when exploring the MS/MS spectra. In Group I only 13%, while in the Group II 64% of the substances had a higher number of fragments in DIA-IMS mode vs. DIA. In terms of sensitivity, the performance of the two modes with and without activated IMS dimension was identical for about 50% of the doping agents. The sensitivity was higher without IMS, i.e. in simple DIA mode, for 20-40% of remaining doping agents. Despite this sensitivity reduction with IMS, 82% of compounds from both Groups met the minimum required performance level (MRPL) criteria of the World Anti-Doping Agency (WADA) when the DIA-IMS mode was applied. Automated data processing is important in routine doping analysis. Therefore, processing methods were optimized and evaluated for the prevalence of false peak assignments by analysing the target substances at different concentrations in urine samples. Overall, a significantly higher number of misidentified compounds was observed in Group II, with an almost 2-fold higher number of misidentifications in DIA compared to DIA-IMS. This result highlights the benefit of the IMS dimension to reduce the rate of false positive in screening analysis. The optimized UHPLC-IM-HRMS method was finally applied to the analysis of urine samples from administration studies including nine doping agents from both Groups. However, to limit the number of interferences from the biological matrix, an emphasis is needed on the adequate settings of the data processing method.
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Affiliation(s)
- Kateřina Plachká
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Julian Pezzatti
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211, Geneva 4, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211, Geneva 4, Switzerland
| | - Alessandro Musenga
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine Lausanne and Geneva, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Raul Nicoli
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine Lausanne and Geneva, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Tiia Kuuranne
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine Lausanne and Geneva, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211, Geneva 4, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211, Geneva 4, Switzerland
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211, Geneva 4, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211, Geneva 4, Switzerland.
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23
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Zheng S, Zhang X, Li Z, Hoene M, Fritsche L, Zheng F, Li Q, Fritsche A, Peter A, Lehmann R, Zhao X, Xu G. Systematic, Modifying Group-Assisted Strategy Expanding Coverage of Metabolite Annotation in Liquid Chromatography-Mass Spectrometry-Based Nontargeted Metabolomics Studies. Anal Chem 2021; 93:10916-10924. [PMID: 34328315 DOI: 10.1021/acs.analchem.1c01715] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
From microbes to human beings, nontargeted metabolic profiling by liquid chromatography (LC)-mass spectrometry (MS) has been commonly used to investigate metabolic alterations. Still, a major challenge is the annotation of metabolites from thousands of detected features. The aim of our research was to go beyond coverage of metabolite annotation in common nontargeted metabolomics studies by an integrated multistep strategy applying data-dependent acquisition (DDA)-based ultrahigh-performance liquid chromatography (UHPLC)-high-resolution mass spectrometry (HRMS) analysis followed by comprehensive neutral loss matches for characteristic metabolite modifications and database searches in a successive manner. Using pooled human urine as a model sample for method establishment, we found 22% of the detected compounds having modifying structures. Major types of metabolite modifications in urine were glucuronidation (33%), sulfation (20%), and acetylation (6%). Among the 383 annotated metabolites, 100 were confirmed by standard compounds and 50 modified metabolites not present in common databases such as human metabolite database (HMDB) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were structurally elucidated. Practicability was tested by the investigation of urines from pregnant women diagnosed with gestational diabetes mellitus vs healthy controls. Overall, 83 differential metabolites were annotated and 67% of them were modified metabolites including five previously unreported compounds. To conclude, the systematic modifying group-assisted strategy can be taken as a useful tool to extend the number of annotated metabolites in biological and biomedical nontargeted studies.
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Affiliation(s)
- Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miriam Hoene
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, Tuebingen 72076, Germany
| | - Louise Fritsche
- German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany.,Internal Medicine 4, University Hospital Tuebingen, Otfried-Mueller-Str. 10, Tuebingen 72076, Germany
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Andreas Fritsche
- German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany.,Internal Medicine 4, University Hospital Tuebingen, Otfried-Mueller-Str. 10, Tuebingen 72076, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, Tuebingen 72076, Germany.,German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, Tuebingen 72076, Germany.,German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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24
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Muhr M, Heiß P, Schütz M, Bühler R, Gemel C, Linden MH, Linden HB, Fischer RA. Enabling LIFDI-MS measurements of highly air sensitive organometallic compounds: a combined MS/glovebox technique. Dalton Trans 2021; 50:9031-9036. [PMID: 33970171 DOI: 10.1039/d1dt00978h] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A new setup combining a ThermoFisher Exactive Plus Orbitrap Mass Spectrometer with a liquid injection field desorption ionization (LIFDI) source directly connected to an inert atmosphere glovebox is presented. The described setup allows for the analysis of very air- and moisture sensitive samples. Furthermore, the soft nature of LIFDI ionization gives access to the molecular ions of fragile molecules. This new setup is therefore especially useful for sensitive organometallic complexes. The functionality of the new setup is tested against [(Cp)2TiCl]˙, which is known for its notorious sensitivity to air and moisture. Its drastic colour change from green to orange upon exposure to air further supports the easy detection of traces of oxygen during the experiment. In addition, we applied this setup to the mass spectrometric analysis of the qualitative composition of a Cu/Al cluster mixture, which is not accessible by other analytical methods.
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Affiliation(s)
- Maximilian Muhr
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85748 Garching, Germany. and Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, D-85748 Garching, Germany
| | - Patricia Heiß
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85748 Garching, Germany. and Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, D-85748 Garching, Germany
| | - Max Schütz
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85748 Garching, Germany. and Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, D-85748 Garching, Germany
| | - Raphael Bühler
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85748 Garching, Germany. and Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, D-85748 Garching, Germany
| | - Christian Gemel
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85748 Garching, Germany. and Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, D-85748 Garching, Germany
| | | | | | - Roland A Fischer
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85748 Garching, Germany. and Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, D-85748 Garching, Germany
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25
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Murashima H, Fujihara A. Gas-Phase Adsorption of N 2 on Protonated Molecules and Its Application to the Structural Elucidation of Small Molecules. Mass Spectrom (Tokyo) 2021; 10:A0096. [PMID: 34136324 PMCID: PMC8188007 DOI: 10.5702/massspectrometry.a0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
The gas-phase adsorption of N2 on protonated serine (Ser, C3H7NO3), threonine (Thr, C4H9NO3), glycine (Gly, C2H5NO2), and 2-aminoethanol (C2H7NO) was investigated using a tandem mass spectrometer equipped with an electrospray ionization source and a cold ion trap. N2 molecules were adsorbed on the free X–H (X=O and N) groups of protonated molecules. Gas-phase N2 adsorption-mass spectrometry detected the presence of free X–H groups in the molecular structures, and was applied to the structural elucidation of small molecules. When the 93 structures with an elemental composition of C3H7NO3 were filtered using the gas-phase N2 adsorption-mass spectrometry results for Ser, the number of possible molecular structures was reduced to 8 via the quantification of the X–H groups. Restricting and minimizing the number of possible candidates were effective steps in the structural elucidation process. Gas-phase N2 adsorption-mass spectrometry combined with mass spectrometry-based techniques has the potential for being useful for elucidating the molecular structures of a variety of molecules.
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Affiliation(s)
- Hiromori Murashima
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Akimasa Fujihara
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
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26
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van Outersterp RE, Martens J, Berden G, Koppen V, Cuyckens F, Oomens J. Mass spectrometry-based identification of ortho-, meta- and para-isomers using infrared ion spectroscopy. Analyst 2021; 145:6162-6170. [PMID: 32924040 DOI: 10.1039/d0an01119c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Distinguishing positional isomers, such as compounds having different substitution patterns on an aromatic ring, presents a significant challenge for mass spectrometric analyses and is a frequently encountered difficulty in, for example, drug metabolism research. In contrast to mass spectrometry, IR spectroscopy is a well-known and powerful tool in the distinction of ortho-, meta- and para-isomers, but is not applicable to low-abundance compounds in complex mixtures such as often targeted in bioanalytical studies. Here, we demonstrate the use of infrared ion spectroscopy (IRIS) as a novel method that facilitates the differentiation between positional isomers of disubstituted phenyl-containing compounds and that can be applied in mass spectrometry-based complex mixture analysis. By analyzing different substitution patterns over several sets of isomeric compounds, we show that IRIS is able to consistently probe the diagnostic CH out-of-plane vibrations that are sensitive to positional isomerism. We show that these modes are largely independent of the chemical functionality contained in the ring substituents and of the type of ionization. We also show that IRIS spectra often identify the positional isomer directly, even in the absence of reference spectra obtained from physical standards or from computational prediction. We foresee that this method will be generally applicable to the identification of disubstituted phenyl-containing compounds.
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Affiliation(s)
- Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands.
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27
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Liu Y, De Vijlder T, Bittremieux W, Laukens K, Heyndrickx W. Current and future deep learning algorithms for tandem mass spectrometry (MS/MS)-based small molecule structure elucidation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021:e9120. [PMID: 33955607 DOI: 10.1002/rcm.9120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/13/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Structure elucidation of small molecules has been one of the cornerstone applications of mass spectrometry for decades. Despite the increasing availability of software tools, structure elucidation from tandem mass spectrometry (MS/MS) data remains a challenging task, leaving many spectra unidentified. However, as an increasing number of reference MS/MS spectra are being curated at a repository scale and shared on public servers, there is an exciting opportunity to develop powerful new deep learning (DL) models for automated structure elucidation. ARCHITECTURES Recent early-stage DL frameworks mostly follow a "two-step approach" that translates MS/MS spectra to database structures after first predicting molecular descriptors. The related architectures could suffer from: (1) computational complexity because of the separate training of descriptor-specific classifiers, (2) the high dimensional nature of mass spectral data and information loss due to data preprocessing, (3) low substructure coverage and class imbalance problem of predefined molecular fingerprints. Inspired by successful DL frameworks employed in drug discovery fields, we have conceptualized and designed hypothetical DL architectures to tackle the above issues. For (1), we recommend multitask learning to achieve better performance with fewer classifiers by grouping structurally related descriptors. For (2) and (3), we introduce feature engineering to extract condensed and higher-order information from spectra and structure data. For instance, encoding spectra with subtrees and pre-calculated spectral patterns add peak interactions to the model input. Encoding structures with graph convolutional networks incorporates connectivity within a molecule. The joint embedding of spectra and structures can enable simultaneous spectral library and molecular database search. CONCLUSIONS In principle, given enough training data, adapted DL architectures, optimal hyperparameters and computing power, DL frameworks can predict small molecule structures, completely or at least partially, from MS/MS spectra. However, their performance and general applicability should be fairly evaluated against classical machine learning frameworks.
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Affiliation(s)
| | | | - Wout Bittremieux
- University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (biomina), University of Antwerp, Antwerp, Belgium
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Kris Laukens
- University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (biomina), University of Antwerp, Antwerp, Belgium
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28
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Ara T, Sakurai N, Takahashi S, Waki N, Suganuma H, Aizawa K, Matsumura Y, Kawada T, Shibata D. TOMATOMET: A metabolome database consists of 7118 accurate mass values detected in mature fruits of 25 tomato cultivars. PLANT DIRECT 2021; 5:e00318. [PMID: 33969254 PMCID: PMC8082711 DOI: 10.1002/pld3.318] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/18/2021] [Accepted: 03/09/2021] [Indexed: 06/02/2023]
Abstract
The total number of low-molecular-weight compounds in the plant kingdom, most of which are secondary metabolites, is hypothesized to be over one million, although only a limited number of plant compounds have been characterized. Untargeted analysis, especially using mass spectrometry (MS), has been useful for understanding the plant metabolome; however, due to the limited availability of authentic compounds for MS-based identification, the identities of most of the ion peaks detected by MS remain unknown. Accurate mass values of peaks obtained by high accuracy mass measurement and, if available, MS/MS fragmentation patterns provide abundant annotation for each peak. Here, we carried out an untargeted analysis of compounds in the mature fruit of 25 tomato cultivars using liquid chromatography-Orbitrap MS for accurate mass measurement, followed by manual curation to construct the metabolome database TOMATOMET (http://metabolites.in/tomato-fruits/). The database contains 7,118 peaks with accurate mass values, in which 1,577 ion peaks are annotated as members of a chemical group. Remarkably, 71% of the mass values are not found in the accurate masses detected previously in Arabidopsis thaliana, Medicago truncatula or Jatropha curcas, indicating significant chemical diversity among plant species that remains to be solved. Interestingly, substantial chemical diversity exists also among tomato cultivars, indicating that chemical profiling from distinct cultivars contributes towards understanding the metabolome, even in a single organ of a species, and can prioritize some desirable metabolic targets for further applications such as breeding.
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Affiliation(s)
- Takeshi Ara
- Graduate School of AgricultureKyoto UniversityUjiJapan
| | - Nozomu Sakurai
- Kazusa DNA Research InstituteKisarazuJapan
- National Institute of GeneticsMishimaJapan
| | - Shingo Takahashi
- Graduate School of AgricultureKyoto UniversityUjiJapan
- KAGOME CO., LTD.NasushiobaraJapan
| | - Naoko Waki
- Graduate School of AgricultureKyoto UniversityUjiJapan
- KAGOME CO., LTD.NasushiobaraJapan
| | | | | | | | - Teruo Kawada
- Graduate School of AgricultureKyoto UniversityUjiJapan
| | - Daisuke Shibata
- Graduate School of AgricultureKyoto UniversityUjiJapan
- Kazusa DNA Research InstituteKisarazuJapan
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29
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Krettler CA, Thallinger GG. A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics. Brief Bioinform 2021; 22:6184408. [PMID: 33758925 DOI: 10.1093/bib/bbab073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/29/2021] [Accepted: 02/12/2021] [Indexed: 12/27/2022] Open
Abstract
Metabolomics, the comprehensive study of the metabolome, and lipidomics-the large-scale study of pathways and networks of cellular lipids-are major driving forces in enabling personalized medicine. Complicated and error-prone data analysis still remains a bottleneck, however, especially for identifying novel metabolites. Comparing experimental mass spectra to curated databases containing reference spectra has been the gold standard for identification of compounds, but constructing such databases is a costly and time-demanding task. Many software applications try to circumvent this process by utilizing cutting-edge advances in computational methods-including quantum chemistry and machine learning-and simulate mass spectra by performing theoretical, so called in silico fragmentations of compounds. Other solutions concentrate directly on experimental spectra and try to identify structural properties by investigating reoccurring patterns and the relationships between them. The considerable progress made in the field allows recent approaches to provide valuable clues to expedite annotation of experimental mass spectra. This review sheds light on individual strengths and weaknesses of these tools, and attempts to evaluate them-especially in view of lipidomics, when considering complex mixtures found in biological samples as well as mass spectrometer inter-instrument variability.
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Affiliation(s)
- Christoph A Krettler
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16/I, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16/I, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
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30
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Non-targeted screening of trace organic contaminants in surface waters by a multi-tool approach based on combinatorial analysis of tandem mass spectra and open access databases. Talanta 2021; 230:122293. [PMID: 33934765 DOI: 10.1016/j.talanta.2021.122293] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 01/04/2023]
Abstract
Non-targeted screening (NTS) in mass spectrometry (MS) helps alleviate the shortcoming of targeted analysis such as missing the presence of concerning compounds that are not monitored and its lack of retrospective analysis to subsequently look for new contaminants. Most NTS workflows include high resolution tandem mass spectrometry (HRMS2) and structure annotation with libraries which are still limited. However, in silico combinatorial fragmentation tools that simulate MS2 spectra are available to help close the gap of missing compounds in empirical libraries. Three NTS tools were combined and used to detect and identify unknown contaminants at ultra-trace levels in surface waters in real samples in this qualitative study. Two of them were based on combinatorial fragmentation databases, MetFrag and the Similar Partition Searching algorithm (SPS), and the third, the Global Natural Products Social Networking (GNPS), was an ensemble of empirical databases. The three NTS tools were applied to the analysis of real samples from a local river. A total of 253 contaminants were identified by combining all three tools: 209 were assigned a probable structure and 44 were confirmed using reference standards. The two major classes of contaminants observed were pharmaceuticals and consumer product additives. Among the confirmed compounds, octylphenol ethoxylates, denatonium, irbesartan and telmisartan are reported for the first time in surface waters in Canada. The workflow presented in this work uses three highly complementary NTS tools and it is a powerful approach to help identify and strategically select contaminants and their transformation products for subsequent targeted analysis and uncover new trends in surface water contamination.
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31
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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32
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Zhou Z, Luo M, Chen X, Yin Y, Xiong X, Wang R, Zhu ZJ. Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics. Nat Commun 2020; 11:4334. [PMID: 32859911 PMCID: PMC7455731 DOI: 10.1038/s41467-020-18171-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/07/2020] [Indexed: 01/04/2023] Open
Abstract
The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility - mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. Here, we curate an ion mobility CCS atlas, namely AllCCS, and develop an integrated strategy for metabolite annotation using known or unknown chemical structures. The AllCCS atlas covers vast chemical structures with >5000 experimental CCS records and ~12 million calculated CCS values for >1.6 million small molecules. We demonstrate the high accuracy and wide applicability of AllCCS with medium relative errors of 0.5-2% for a broad spectrum of small molecules. AllCCS combined with in silico MS/MS spectra facilitates multi-dimensional match and substantially improves the accuracy and coverage of both known and unknown metabolite annotation from biological samples. Together, AllCCS is a versatile resource that enables confident metabolite annotation, revealing comprehensive chemical and metabolic insights towards biological processes.
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Affiliation(s)
- Zhiwei Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Mingdu Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xi Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Yandong Yin
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China
| | - Xin Xiong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China
| | - Ruohong Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, People's Republic of China.
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33
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Coley CW, Eyke NS, Jensen KF. Autonomous Discovery in the Chemical Sciences Part I: Progress. Angew Chem Int Ed Engl 2020; 59:22858-22893. [DOI: 10.1002/anie.201909987] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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34
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Coley CW, Eyke NS, Jensen KF. Autonome Entdeckung in den chemischen Wissenschaften, Teil I: Fortschritt. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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35
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Ferrer I, Sweeney DL, Thurman EM, Zweigenbaum JA. Nontargeted Screening of Water Samples Using Data-Dependent Acquisition with Similar Partition Searching. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1189-1204. [PMID: 32356661 DOI: 10.1021/jasms.0c00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A rapid screening method for the detection of nontargeted compounds in surface water samples was developed using MS-MS high-resolution mass spectrometry and data-dependent acquisition. The key parameters for the acquisition method were optimized using five model compounds with diverse chemical characteristics. The parameter selection required optimization between the total number of precursor ions that could be selected in an LC-MS run, the quality of each MS (full range) spectrum, and the quality of each MS-MS fragmentation spectrum. After the acquisition method was optimized, 18 surface water samples from rivers, reservoirs, and effluents from wastewater treatment plants were analyzed, generating 41625 MS-MS spectra in about 14 h. The raw data were then converted into two generic formats using the open-access program MSConvert. A combinatorial approach, similar partition searching (SPS), was then used to putatively identify analytes from the accurate mass of each analyte (adjusted for the adduct mass) and the corresponding MS-MS spectra were obtained. In this approach, the structures of about 250000 common compounds, stored in a large database as mathematical partitions of their exact mass, were compared directly to each MS-MS spectrum. Compounds with a similar mass and retention time were grouped together and labeled as "Analytes", using an Excel Add-In. The isotope ratio data from the MS spectrum, the corresponding MS-MS spectra, and the putative identifications were then imported into an Access relational database to facilitate sorting, searching, filtering, and querying the results. This allowed final inspection to assess confidence of the identifications made through the nontargeted screening.
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Affiliation(s)
- Imma Ferrer
- University of Colorado, Boulder, Colorado 80303, United States
| | - Daniel L Sweeney
- MathSpec, Inc., Arlington Heights, Illinois 60004, United States
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36
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Errabelli R, Zheng Z, Attygalle AB. Formation of Protonated ortho-Quinonimide from ortho-Iodoaniline in the Gas Phase by a Molecular-Oxygen-Mediated, ortho-Isomer-Specific Fragmentation Mechanism. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:864-872. [PMID: 32233379 DOI: 10.1021/jasms.9b00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Upon collisional activation under mass spectrometric conditions, protonated 2-, 3-, and 4-iodoanilines lose an iodine radical to generate primarily dehydroanilinium radical cations (m/z 93), which are the distonic counterparts of the conventional molecular ion of aniline. When briefly accumulated in the Trap region of a Triwave cell in a SYNAPT G2 instrument, before being released for ion-mobility separation, these dehydroanilinium cations react readily with traces of oxygen present in the mobility gas to form peroxyl radical cations. Although all three isomeric dehydroanilinium ions showed avid affinity for O2, their reactivities were distinctly different. For example, the product-ion spectra recorded from mass-selected m/z 93 ion from 3- and 4-iodoanilines showed a peak at m/z 125 for the respective peroxylbenzenaminium ion. In contrast, an analogous peak at m/z 125 was absent in the spectrum of the 2-dehydroanilinium ion generated from 2-iodoaniline. Evidently, the 2-peroxylbenzenaminium ion generated from the 2-dehydroanilinium ion immediately loses a •OH to form protonated ortho-quinonimide (m/z 108).
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Affiliation(s)
- Ramu Errabelli
- Center for Mass Spectrometry, Department of Chemistry, and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Zhaoyu Zheng
- Center for Mass Spectrometry, Department of Chemistry, and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Athula B Attygalle
- Center for Mass Spectrometry, Department of Chemistry, and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
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37
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Guo J, Turesky RJ, Tarifa A, DeCaprio AP, Cooke MS, Walmsley SJ, Villalta PW. Development of a DNA Adductome Mass Spectral Database. Chem Res Toxicol 2020; 33:852-854. [PMID: 32223224 DOI: 10.1021/acs.chemrestox.0c00031] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based DNA adductomics is an emerging approach for the human biomonitoring of hazardous chemicals. A mass spectral database of DNA adducts will be created for the scientific community to investigate the associations between chemical exposures, DNA damage, and disease risk.
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Affiliation(s)
- Jingshu Guo
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert J Turesky
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anamary Tarifa
- Forensic & Analytical Toxicology Facility, Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Anthony P DeCaprio
- Forensic & Analytical Toxicology Facility, Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, Florida 33199, United States
| | - Scott J Walmsley
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute of Health Informatics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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38
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Fine JA, Rajasekar AA, Jethava KP, Chopra G. Spectral deep learning for prediction and prospective validation of functional groups. Chem Sci 2020; 11:4618-4630. [PMID: 34122917 PMCID: PMC8152587 DOI: 10.1039/c9sc06240h] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/13/2020] [Indexed: 01/06/2023] Open
Abstract
State-of-the-art identification of the functional groups present in an unknown chemical entity requires the expertise of a skilled spectroscopist to analyse and interpret Fourier transform infra-red (FTIR), mass spectroscopy (MS) and/or nuclear magnetic resonance (NMR) data. This process can be time-consuming and error-prone, especially for complex chemical entities that are poorly characterised in the literature, or inefficient to use with synthetic robots producing molecules at an accelerated rate. Herein, we introduce a fast, multi-label deep neural network for accurately identifying all the functional groups of unknown compounds using a combination of FTIR and MS spectra. We do not use any database, pre-established rules, procedures, or peak-matching methods. Our trained neural network reveals patterns typically used by human chemists to identify standard groups. Finally, we experimentally validated our neural network, trained on single compounds, to predict functional groups in compound mixtures. Our methodology showcases practical utility for future use in autonomous analytical detection.
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Affiliation(s)
- Jonathan A Fine
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette IN 47907 USA
| | - Anand A Rajasekar
- Department of Biological Engineering, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras Chennai 600036 India
| | - Krupal P Jethava
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette IN 47907 USA
| | - Gaurav Chopra
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette IN 47907 USA
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Chao A, Al-Ghoul H, McEachran AD, Balabin I, Transue T, Cathey T, Grossman JN, Singh RR, Ulrich EM, Williams AJ, Sobus JR. In silico MS/MS spectra for identifying unknowns: a critical examination using CFM-ID algorithms and ENTACT mixture samples. Anal Bioanal Chem 2020; 412:1303-1315. [PMID: 31965249 PMCID: PMC7021669 DOI: 10.1007/s00216-019-02351-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/27/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022]
Abstract
High-resolution mass spectrometry (HRMS) enables rapid chemical annotation via accurate mass measurements and matching of experimentally derived spectra with reference spectra. Reference libraries are generated from chemical standards and are therefore limited in size relative to known chemical space. To address this limitation, in silico spectra (i.e., MS/MS or MS2 spectra), predicted via Competitive Fragmentation Modeling-ID (CFM-ID) algorithms, were generated for compounds within the U.S. Environmental Protection Agency's (EPA) Distributed Structure-Searchable Toxicity (DSSTox) database (totaling, at the time of analysis, ~ 765,000 substances). Experimental spectra from EPA's Non-Targeted Analysis Collaborative Trial (ENTACT) mixtures (n = 10) were then used to evaluate the performance of the in silico spectra. Overall, MS2 spectra were acquired for 377 unique compounds from the ENTACT mixtures. Approximately 53% of these compounds were correctly identified using a commercial reference library, whereas up to 50% were correctly identified as the top hit using the in silico library. Together, the reference and in silico libraries were able to correctly identify 73% of the 377 ENTACT substances. When using the in silico spectra for candidate filtering, an examination of binary classifiers showed a true positive rate (TPR) of 0.90 associated with false positive rates (FPRs) of 0.10 to 0.85, depending on the sample and method of candidate filtering. Taken together, these findings show the abilities of in silico spectra to correctly identify true positives in complex samples (at rates comparable to those observed with reference spectra), and efficiently filter large numbers of potential false positives from further consideration. Graphical abstract.
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Affiliation(s)
- Alex Chao
- Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA.
- Student Contractor, U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA.
| | - Hussein Al-Ghoul
- Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
- Student Contractor, U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
| | - Andrew D McEachran
- Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
- Agilent Technologies Inc., Santa Clara, CA, 95051, USA
| | - Ilya Balabin
- General Dynamics Information Technology, 79 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Tom Transue
- General Dynamics Information Technology, 79 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Tommy Cathey
- General Dynamics Information Technology, 79 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Jarod N Grossman
- Student Contractor, U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
- Agilent Technologies Inc., Santa Clara, CA, 95051, USA
| | - Randolph R Singh
- Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4365, Esch-sur-Alzette, Luxembourg
| | - Elin M Ulrich
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
| | - Antony J Williams
- U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA
| | - Jon R Sobus
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27711, USA.
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Reisdorph NA, Walmsley S, Reisdorph R. A Perspective and Framework for Developing Sample Type Specific Databases for LC/MS-Based Clinical Metabolomics. Metabolites 2019; 10:metabo10010008. [PMID: 31877765 PMCID: PMC7023092 DOI: 10.3390/metabo10010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics has the potential to greatly impact biomedical research in areas such as biomarker discovery and understanding molecular mechanisms of disease. However, compound identification (ID) remains a major challenge in liquid chromatography mass spectrometry-based metabolomics. This is partly due to a lack of specificity in metabolomics databases. Though impressive in depth and breadth, the sheer magnitude of currently available databases is in part what makes them ineffective for many metabolomics studies. While still in pilot phases, our experience suggests that custom-built databases, developed using empirical data from specific sample types, can significantly improve confidence in IDs. While the concept of sample type specific databases (STSDBs) and spectral libraries is not entirely new, inclusion of unique descriptors such as detection frequency and quality scores, can be used to increase confidence in results. These features can be used alone to judge the quality of a database entry, or together to provide filtering capabilities. STSDBs rely on and build upon several available tools for compound ID and are therefore compatible with current compound ID strategies. Overall, STSDBs can potentially result in a new paradigm for translational metabolomics, whereby investigators confidently know the identity of compounds following a simple, single STSDB search.
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Affiliation(s)
- Nichole A. Reisdorph
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, CO 80045, USA;
- Correspondence: ; Tel.: +1-303-724-9234
| | - Scott Walmsley
- Masonic Cancer Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA;
- Institute for Health Informatics, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Rick Reisdorph
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, CO 80045, USA;
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Cave JR, Parker E, Lebrilla C, Waterhouse AL. Omics Forecasting: Predictive Calculations Permit the Rapid Interpretation of High-Resolution Mass Spectral Data from Complex Mixtures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13318-13326. [PMID: 31604012 DOI: 10.1021/acs.jafc.9b04384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
For some complex mixtures, chromatographic techniques are insufficient to separate the large numbers of compounds present. In addition, these mixtures often contain compounds with similar or identical molecular masses and shared fragmentation transitions. Advancements in mass spectrometry have provided more and more detailed molecular profiles with significant increases in resolution. This has led to a capacity to distinguish a very large number of compounds in complex mixtures, providing overwhelming data sets. The approach of calculating molecular formulas from a mass list has become more and more problematic as the number of signals has increased exponentially, to the point that it has become impossible to manually interpret the thousands of mass signals. The current approach is to calculate a list of possible formulas that fall within a specific mass error of the observed signal. Then, one must look for possible structures that can be derived from each entry on the list of formulas. However, an alternative approach is to anticipate the possible structures of a particular set of compounds, such as red wine pigments, and then compare the ion signals against a predicted list. To that end, starting with known wine pigment types, we have generated a set of expected wine pigment variants based on known derivatives of condensed tannin oligomers, anthocyanins, and fermentation products. After the ability to distinguish compounds by mass spectrometry was accounted for, over 1 million results were generated consisting of known and anticipated wine pigments. A comparison with a small sample of wine phenolic fractions show a large number of matches, suggesting that this approach may be helpful.
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Liu Y, Romijn EP, Verniest G, Laukens K, De Vijlder T. Mass spectrometry-based structure elucidation of small molecule impurities and degradation products in pharmaceutical development. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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43
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Velasco-Alzate KY, Bauermeister A, Tangerina MMP, Lotufo TMC, Ferreira MJP, Jimenez PC, Padilla G, Lopes NP, Costa-Lotufo LV. Marine Bacteria from Rocas Atoll as a Rich Source of Pharmacologically Active Compounds. Mar Drugs 2019; 17:md17120671. [PMID: 31795148 PMCID: PMC6949966 DOI: 10.3390/md17120671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022] Open
Abstract
Rocas Atoll is a unique environment in the equatorial Atlantic Ocean, hosting a large number of endemic species, however, studies on the chemical diversity emerging from this biota are rather scarce. Therefore, the present work aims to assess the metabolomic diversity and pharmacological potential of the microbiota from Rocas Atoll. A total of 76 bacteria were isolated and cultured in liquid culture media to obtain crude extracts. About one third (34%) of these extracts were recognized as cytotoxic against human colon adenocarcinoma HCT-116 cell line. 16S rRNA gene sequencing analyses revealed that the bacteria producing cytotoxic extracts were mainly from the Actinobacteria phylum, including Streptomyces, Salinispora, Nocardiopsis, and Brevibacterium genera, and in a smaller proportion from Firmicutes phylum (Bacillus). The search in the spectral library in GNPS (Global Natural Products Social Molecular Networking) unveiled a high chemodiversity being produced by these bacteria, including rifamycins, antimycins, desferrioxamines, ferrioxamines, surfactins, surugamides, staurosporines, and saliniketals, along with several unidentified compounds. Using an original approach, molecular networking successfully highlighted groups of compounds responsible for the cytotoxicity of crude extracts. Application of DEREPLICATOR+ (GNPS) allowed the annotation of macrolide novonestimycin derivatives as the cytotoxic compounds existing in the extracts produced by Streptomyces BRB-298 and BRB-302. Overall, these results highlighted the pharmacological potential of bacteria from this singular atoll.
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Affiliation(s)
- Karen Y. Velasco-Alzate
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil; (K.Y.V.-A.); (A.B.)
| | - Anelize Bauermeister
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil; (K.Y.V.-A.); (A.B.)
- NPPNS, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto/SP, Brazil;
| | - Marcelo M. P. Tangerina
- Departamento do Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo/SP, Brazil (M.J.P.F.)
| | - Tito M. C. Lotufo
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, 05508-120 São Paulo/SP, Brazil;
| | - Marcelo J. P. Ferreira
- Departamento do Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo/SP, Brazil (M.J.P.F.)
| | - Paula C. Jimenez
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, 11015-020 Santos/SP, Brazil;
| | - Gabriel Padilla
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil;
| | - Norberto P. Lopes
- NPPNS, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto/SP, Brazil;
| | - Letícia V. Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil; (K.Y.V.-A.); (A.B.)
- Correspondence: or ; Tel.: +55-11-30917316
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Cordell GA. Cyberecoethnopharmacolomics. JOURNAL OF ETHNOPHARMACOLOGY 2019; 244:112134. [PMID: 31377262 DOI: 10.1016/j.jep.2019.112134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Development of a new term which describes the contemporary, composite, constituent sciences of ethnopharmacology. AIM OF THE STUDY To discuss the polysyllabic term cyberecoethnopharmacolomics in the context of the future of ethnopharmacology in global health care. MATERIALS AND METHODS Literature background and assessment from the prior literature, diverse databases, and personal discussions. RESULTS The profiles and literature background with contemporary and future thoughts regarding the concepts and practices of cyber-, eco-, ethno-, pharmacol-, and -omics, and their impact in ethnopharmacology for the future are presented in the context of integrated health care systems. CONCLUSIONS Ethnopharmacology has a major role to play in global health care if the relevant sciences and cutting-edge technologies can coalesce synergistically as a responsive, evidence-based health care practice.
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Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, IL, USA; Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
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45
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Moumbock AFA, Ntie-Kang F, Akone SH, Li J, Gao M, Telukunta KK, Günther S. An overview of tools, software, and methods for natural product fragment and mass spectral analysis. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Abstract
One major challenge in natural product (NP) discovery is the determination of the chemical structure of unknown metabolites using automated software tools from either GC–mass spectrometry (MS) or liquid chromatography–MS/MS data only. This chapter reviews the existing spectral libraries and predictive computational tools used in MS-based untargeted metabolomics, which is currently a hot topic in NP structure elucidation. We begin by focusing on spectral databases and the general workflow of MS annotation. We then describe software and tools used in MS, particularly those used to predict fragmentation patterns, mass spectral classifiers, and tools for fragmentation trees analysis. We then round up the chapter by looking at more advanced approaches implemented in tools for competitive fragmentation modeling and quantum chemical approaches.
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46
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Kepceoğlu A, Gündoğdu Y, Ledingham KWD, Kilic HS. Real-Time Distinguishing of the Xylene Isomers Using Photoionization and Dissociation Mass Spectra Obtained by Femtosecond Laser Mass Spectrometry (FLMS). ANAL LETT 2019. [DOI: 10.1080/00032719.2019.1647227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Abdullah Kepceoğlu
- Faculty of Science, Department of Physics, Selçuk University, Konya, Turkey
| | - Yasemin Gündoğdu
- Faculty of Science, Department of Physics, Selçuk University, Konya, Turkey
| | - Kenneth William David Ledingham
- Faculty of Science, Department of Physics, Selçuk University, Konya, Turkey
- SUPA, Department of Physics, University of Strathclyde, Glasgow, Scotland
| | - Hamdi Sukur Kilic
- Faculty of Science, Department of Physics, Selçuk University, Konya, Turkey
- Directorate of High Technology Research and Application Centre, Selçuk University, Konya, Turkey
- Directorate of Laser Induced Proton Therapy Research and Application Centre, Selçuk University, Konya, Turkey
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47
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Stopka SA, Samarah LZ, Shaw JB, Liyu AV, Veličković D, Agtuca BJ, Kukolj C, Koppenaal DW, Stacey G, Paša-Tolić L, Anderton CR, Vertes A. Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry. Anal Chem 2019; 91:5028-5035. [PMID: 30821434 DOI: 10.1021/acs.analchem.8b05084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is an indispensable analytical tool to capture the array of metabolites within complex biological systems. However, conventional MS-based metabolomic workflows require extensive sample processing and separation resulting in limited throughput and potential alteration of the native molecular states in these systems. Ambient ionization methods, capable of sampling directly from tissues, circumvent some of these issues but require high-performance MS to resolve the molecular complexity within these samples. Here, we demonstrate a unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 tesla Fourier transform ion cyclotron resonance (21T-FTICR) for direct MS analysis and imaging applications. This analytical platform provides isotopic fine structure information directly from biological tissues, enabling the rapid assignment of molecular formulas and delivering a higher degree of confidence for molecular identification.
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Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Laith Z Samarah
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Caroline Kukolj
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Akos Vertes
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
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48
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Djoumbou-Feunang Y, Pon A, Karu N, Zheng J, Li C, Arndt D, Gautam M, Allen F, Wishart DS. CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification. Metabolites 2019; 9:metabo9040072. [PMID: 31013937 PMCID: PMC6523630 DOI: 10.3390/metabo9040072] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/31/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM-ID) was developed to accurately predict electrospray ionization-MS/MS (ESI-MS/MS) spectra from chemical structures and to aid in compound identification via MS/MS spectral matching. While earlier versions of CFM-ID performed very well, CFM-ID's performance for predicting the MS/MS spectra of certain classes of compounds, including many lipids, was quite poor. Furthermore, CFM-ID's compound identification capabilities were limited because it did not use experimentally available MS/MS spectra nor did it exploit metadata in its spectral matching algorithm. Here, we describe significant improvements to CFM-ID's performance and speed. These include (1) the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID; (2) the inclusion of experimental MS/MS spectra and other metadata to enhance CFM-ID's compound identification abilities; (3) the development of new scoring functions that improves CFM-ID's accuracy by 21.1%; and (4) the implementation of a chemical classification algorithm that correctly classifies unknown chemicals (based on their MS/MS spectra) in >80% of the cases. This improved version called CFM-ID 3.0 is freely available as a web server. Its source code is also accessible online.
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Affiliation(s)
| | - Allison Pon
- OMx Personal Health Analytics, Edmonton, AB T5J 1B9, Canada.
| | - Naama Karu
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jiamin Zheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Carin Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - David Arndt
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Maheswor Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Felicity Allen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
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49
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Ladd MP, Giannone RJ, Abraham PE, Wullschleger SD, Hettich RL. Evaluation of an untargeted nano-liquid chromatography-mass spectrometry approach to expand coverage of low molecular weight dissolved organic matter in Arctic soil. Sci Rep 2019; 9:5810. [PMID: 30967565 PMCID: PMC6456581 DOI: 10.1038/s41598-019-42118-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/14/2019] [Indexed: 11/17/2022] Open
Abstract
Characterizing low molecular weight (LMW) dissolved organic matter (DOM) in soils and evaluating the availability of this labile pool is critical to understanding the underlying mechanisms that control carbon storage or release across terrestrial systems. However, due to wide-ranging physicochemical diversity, characterizing this complex mixture of small molecules and how it varies across space remains an analytical challenge. Here, we evaluate an untargeted approach to detect qualitative and relative-quantitative variations in LMW DOM with depth using water extracts from a soil core from the Alaskan Arctic, a unique system that contains nearly half the Earth's terrestrial carbon and is rapidly warming due to climate change. We combined reversed-phase and hydrophilic interaction liquid chromatography, and nano-electrospray ionization coupled with high-resolution tandem mass spectrometry in positive- and negative-ionization mode. The optimized conditions were sensitive, robust, highly complementary, and enabled detection and putative annotations of a wide range of compounds (e.g. amino acids, plant/microbial metabolites, sugars, lipids, peptides). Furthermore, multivariate statistical analyses revealed subtle but consistent and significant variations with depth. Thus, this platform is useful not only for characterizing LMW DOM, but also for quantifying relative variations in LMW DOM availability across space, revealing hotspots of biogeochemical activity for further evaluation.
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Affiliation(s)
- Mallory P Ladd
- Bredesen Center for Interdisciplinary Research & Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Stan D Wullschleger
- Bredesen Center for Interdisciplinary Research & Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Bredesen Center for Interdisciplinary Research & Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA.
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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50
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Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JP, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Expanding the Use of Spectral Libraries in Proteomics. J Proteome Res 2018; 17:4051-4060. [PMID: 30270626 PMCID: PMC6443480 DOI: 10.1021/acs.jproteome.8b00485] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
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Affiliation(s)
- Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington, 98109, United States
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert J. Chalkley
- University of California San Francisco, San Francisco, 94158, California, United States
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 85354, Germany
| | | | - Timo Sachsenberg
- Department of Computer Science, Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Mathias Walzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH − Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Bernard Delanghe
- Thermo Fisher Scientific Bremen, Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Viktoria Dorfer
- University of Applied Sciences Upper Austria, Bioinformatics Research Group, Hagenberg, 4232, Austria
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 85354, Germany
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, 85354, Germany
| | | | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Dennis W. Wolan
- Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, California, United States
| | - Ana Y. Wang
- Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, California, United States
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, Washington, 98109, United States
| | - Jim Shofstahl
- Thermo Fisher Scientific, 355 River Oaks Parkway San Jose, CA 95134
| | - Andrew W. Dowsey
- Department of Population Health Sciences and Bristol Veterinary School, Faculty of Health Sciences, University of Bristol, Bristol BS9 1BN, UK
| | - Johannes Griss
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Reza M. Salek
- The International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Pierre-Alain Binz
- Clinical Chemistry Service, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Henry Lam
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093-0404, USA
| | - Hannes Röst
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, ON, M5S 3E1, Canada
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