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Nie CZ, Liu H, Huang XH, Zhou DY, Wang XS, Qin L. Prediction of mass spectrometry ionization efficiency based on COSMO-RS and machine learning algorithms. Analyst 2024; 149:3140-3151. [PMID: 38629585 DOI: 10.1039/d4an00301b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Non-targeted analysis of high-resolution mass spectrometry (MS) can identify thousands of compounds, which also gives a huge challenge to their quantification. The aim of this study is to investigate the impact of mass spectrometry ionization efficiency on various compounds in food at different solvent ratios and to develop a predictive model for mass spectrometry ionization efficiency to enable non-targeted quantitative prediction of unknown compounds. This study covered 70 compounds in 14 different mobile phase ratio environments in positive ion mode to analyze the rules of the matrix effect. With the organic phase ratio from low to high, most compounds changed by 1.0 log units in log IE. The addition of formic acid enhanced the signal but also promoted the matrix effect, which often occurred in compounds with strong ionization capacity. It was speculated that the matrix effect was mainly in the form of competitive charge and charged droplet' gasification sites during MS detection. Subsequently, we present a log IE prediction method built using the COSMO-RS software and the artificial neural network (ANN) algorithm to address this difficulty and overcome the shortcomings of previous models, which always ignore the matrix effect. This model was developed following the principles of QSAR modeling recommended by the Organization for Economic Cooperation and Development (OECD). Furthermore, we validated this approach by predicting the log IE of 70 compounds, including those not involved in the log IE model development. The results presented demonstrate that the method we put forward has an excellent prediction accuracy for log IE (R2pred = 0.880), which means that it has the potential to predict the log IE of new compounds without authentic standards.
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Affiliation(s)
- Cheng-Zhen Nie
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
| | - Hao Liu
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
| | - Xu-Hui Huang
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
| | - Da-Yong Zhou
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
| | - Xu-Song Wang
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
| | - Lei Qin
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
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Guthrie JD, Rowell CER, Anyaeche RO, Alzarieni KZ, Kenttämaa HI. Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations. MASS SPECTROMETRY REVIEWS 2024; 43:369-408. [PMID: 36727592 DOI: 10.1002/mas.21832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Biomass-derived degraded lignin and cellulose serve as possible alternatives to fossil fuels for energy and chemical resources. Fast pyrolysis of lignocellulosic biomass generates bio-oil that needs further refinement. However, as pyrolysis causes massive degradation to lignin and cellulose, this process produces very complex mixtures. The same applies to degradation methods other than fast pyrolysis. The ability to identify the degradation products of lignocellulosic biomass is of great importance to be able to optimize methodologies for the conversion of these mixtures to transportation fuels and valuable chemicals. Studies utilizing tandem mass spectrometry have provided invaluable, molecular-level information regarding the identities of compounds in degraded biomass. This review focuses on the molecular-level characterization of fast pyrolysis and other degradation products of lignin and cellulose via tandem mass spectrometry based on collision-activated dissociation (CAD). Many studies discussed here used model compounds to better understand both the ionization chemistry of the degradation products of lignin and cellulose and their ions' CAD reactions in mass spectrometers to develop methods for the structural characterization of the degradation products of lignocellulosic biomass. Further, model compound studies were also carried out to delineate the mechanisms of the fast pyrolysis reactions of lignocellulosic biomass. The above knowledge was used to assign likely structures to many degradation products of lignocellulosic biomass.
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Affiliation(s)
- Jacob D Guthrie
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Ruth O Anyaeche
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Kawthar Z Alzarieni
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science & Technology, Irbid, Jordan
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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Dong X, Mayes HB, Morreel K, Katahira R, Li Y, Ralph J, Black BA, Beckham GT. Energy-Resolved Mass Spectrometry as a Tool for Identification of Lignin Depolymerization Products. CHEMSUSCHEM 2023; 16:e202201441. [PMID: 36197743 DOI: 10.1002/cssc.202201441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Lignin is the largest source of bio-based aromatic compounds in nature, and its valorization is essential to the sustainability of lignocellulosic biorefining. Characterizing lignin-derived compounds remains challenging due to the heterogeneity of this biopolymer. Tandem mass spectrometry is a promising tool for lignin structural analytics, as fragmentation patterns of model compounds can be extrapolated to identify characteristic moieties in complex samples. This work extended previous resonance excitation-type collision-induced dissociation (CID) methods that identified lignin oligomers containing β-O-4, β-5, and β-β bonds, to also identify characteristics of 5-5, β-1, and 4-O-5 dimers, enabled by quadrupole time-of-flight (QTOF) CID with energy-resolved mass spectrometry (ERMS). Overall, QTOF-ERMS offers in-depth structural information and could ultimately contribute to tools for high-throughput lignin dimer identification.
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Affiliation(s)
- Xueming Dong
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Heather B Mayes
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Kris Morreel
- RIC Group, President Kennedypark 26, 8500, Kortrijk, Belgium
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Yanding Li
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave., Madison, WI, 53726, USA
| | - John Ralph
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave., Madison, WI, 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI, 53706, USA
| | - Brenna A Black
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Zhang Y, Li W, Lei H, Dong X, Kenttämaa H. Differentiation of Seven Isomeric n-Pentylquinoline Radical Cations Based on Energy-Resolved Medium-Energy Collision-Activated Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:48-63. [PMID: 36507850 DOI: 10.1021/jasms.2c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Asphaltenes, a major and undesirable component of heavy crude oil, contain many different types of large aromatic compounds. These compounds include nitrogen-containing heteroaromatic compounds that are thought to be the main culprit in the deactivation of catalysts in crude oil refinery processes. Unfortunately, prevention of this is challenging as the structures and properties of the nitrogen-containing heteroaromatic compounds are poorly understood. To facilitate their structural characterization, an approach based on ion-trap collision-activated dissociation (ITCAD) tandem mass spectrometry followed by energy-resolved medium-energy collision-activated dissociation (ER-MCAD) was developed for the differentiation of seven isomeric molecular radical cations of n-pentylquinoline. The fragmentation of each isomer was found to be distinctly different and depended largely on the site of the alkyl side chain in the quinoline ring. In order to better understand the observed fragmentation pathways, mechanisms for the formation of several fragment ions were delineated based on quantum chemical calculations. The fast benzylic α-bond cleavage that dominates the fragmentation of analogous nonheteroaromatic alkylbenzenes was only observed for the 3-isomer as the major pathway due to the lack of favorable low-energy rearrangement reactions. All the other isomeric ions underwent substantially lower-energy rearrangement reactions as their alkyl chains were found to interact mostly via 6-membered transition states either with the quinoline nitrogen (2- and 8-isomers) or the adjacent carbon atom in the quinoline core (4-, 5-, 6-, and 7-isomers), which lowered the activation energies of the fragmentation reactions. The presented analytical approach will facilitate the structural characterization of nitrogen-containing heteroaromatic compounds in asphaltenes.
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Affiliation(s)
- Yuyang Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Wanru Li
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Haoran Lei
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Xueming Dong
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hilkka Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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Letourneau DR, Volmer DA. Mass spectrometry-based methods for the advanced characterization and structural analysis of lignin: A review. MASS SPECTROMETRY REVIEWS 2023; 42:144-188. [PMID: 34293221 DOI: 10.1002/mas.21716] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Lignin is currently one of the most promising biologically derived resources, due to its abundance and application in biofuels, materials and conversion to value aromatic chemicals. The need to better characterize and understand this complex biopolymer has led to the development of many different analytical approaches, several of which involve mass spectrometry and subsequent data analysis. This review surveys the most important analytical methods for lignin involving mass spectrometry, first looking at methods involving gas chromatography, liquid chromatography and then continuing with more contemporary methods such as matrix assisted laser desorption ionization and time-of-flight-secondary ion mass spectrometry. Following that will be techniques that directly ionize lignin mixtures-without chromatographic separation-using softer atmospheric ionization techniques that leave the lignin oligomers intact. Finally, ultra-high resolution mass analyzers such as FT-ICR have enabled lignin analysis without major sample preparation and chromatography steps. Concurrent with an increase in the resolution of mass spectrometers, there have been a wealth of complementary data analyses and visualization methods that have allowed researchers to probe deeper into the "lignome" than ever before. These approaches extract trends such as compound series and even important analytical information about lignin substructures without performing lignin degradation either chemically or during MS analysis. These innovative methods are paving the way for a more comprehensive understanding of this important biopolymer, as we seek more sustainable solutions for our human species' energy and materials needs.
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Affiliation(s)
- Dane R Letourneau
- Department of Chemistry, Humboldt University Berlin, Berlin, Germany
| | - Dietrich A Volmer
- Department of Chemistry, Humboldt University Berlin, Berlin, Germany
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Li Y, Zhao S, Sun Y, Li J, Wang Y, Xu W, Luo J, Kong L. Automatic MS/MS Data Mining Strategy for Discovering Target Natural Products: A Case of Lindenane Sesquiterpenoids. Anal Chem 2022; 94:8514-8522. [PMID: 35637569 DOI: 10.1021/acs.analchem.2c01559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used method for discovering natural products (NPs); however, automatic MS/MS data mining for the discovery of NPs remains a challenge. In this work, LindenaneExtractor, a program based on characteristic MS/MS ions of lindenane sesquiterpenoids (LSs) was developed to automatically extract the LSs features for target LS discovery in plant extracts. To build this program, fragmentation mechanisms of characteristic ions of LSs were elucidated and confirmed by quantum chemical calculation and deuterium-labeled compounds. Subsequently, the information of characteristic ions was integrated and coded to develop LindenaneExtractor, which was further examined by standards and several public databases. Finally, the target LS features in Sarcandra hainanensis extract were automatically extracted by LindenaneExtractor and visualized by feature-based molecular networking and two-dimensional (2D) retention time-m/z plot, leading to the discovery of 96 target LSs in total, 37 of these compounds were potentially new NPs and one was confirmed by further isolation. This work proposed a new strategy for target NP analysis and discovery based on automatic MS/MS data mining, which could significantly improve the efficiency and accuracy of NP discovery.
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Affiliation(s)
- Yongyi Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Shuai Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Yunpeng Sun
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Jixin Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Yongyue Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Wenjun Xu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
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Darii E, Gimbert Y, Alves S, Damont A, Perret A, Woods AS, Fenaille F, Tabet JC. First Direct Evidence of Interpartner Hydride/Deuteride Exchanges for Stored Sodiated Arginine/Fructose-6-phosphate Complex Anions within Salt-Solvated Structures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1424-1440. [PMID: 33929837 DOI: 10.1021/jasms.1c00040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mass spectrometric investigations of noncovalent binding between low molecular weight compounds revealed the existence of gas-phase (GP) noncovalent complex (NCC) ions involving zwitterionic structures. ESI MS is used to prove the formation of stable sodiated NCC anions between fructose (F6P) and arginine (R) moieties. Theoretical calculations indicate a folded solvated salt (i.e., sodiated carboxylate interacting with phosphate) rather than a charge-solvated form. Under standard CID conditions, [(F6P+R-H+Na)-H]- competitively forms two major product ions (PIs) through partner splitting [(R-H+Na) loss] and charge-induced cross-ring cleavage while preserving the noncovalent interactions (noncovalent product ions (NCPIs)). MS/MS experiments combined with in-solution proton/deuteron exchanges (HDXs) demonstrated an unexpected labeling of PIs, i.e., a correlated D-enrichment/D-depletion. An increase in activation time up to 3000 ms favors such processes when limited to two H/D exchanges. These results are rationalized by interpartner hydride/deuteride exchanges (⟨HDX⟩) through stepwise isomerization/dissociation of sodiated NCC-d11 anions. In addition, the D-enrichment/D-depletion discrepancy is further explained by back HDX with residual water in LTQ (selective for the isotopologue NCPIs as shown by PI relaxation experiments). Each isotopologue leads to only one back HDX unlike multiple HDXs generally observed in GP. This behavior shows that NCPIs are zwitterions with charges solvated by a single water molecule, thus generating a back HDX through a relay mechanism, which quenches the charges and prevents further back HDX. By estimating back HDX impact on D-depletion, the interpartner ⟨HDX⟩ complementarity was thus illustrated. This is the first description of interpartner ⟨HDX⟩ and selective back HDX validating salt-solvated structures.
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Affiliation(s)
- Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Yves Gimbert
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058 Grenoble, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Amina S Woods
- NIDA IRP, NIH Structural Biology Unit Cellular Neurobiology Branch, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- The Johns Hopkins University School of Medicine, Pharmacology and Molecular Sciences, Baltimore, Maryland 21205, United States
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Jean-Claude Tabet
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
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