1
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Carlo MJ, Nanney ALM, Patrick AL. Energy-Resolved In-Source Collison-Induced Dissociation for Isomer Discrimination. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39016059 DOI: 10.1021/jasms.4c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
While mass spectrometry remains a gold-standard tool for analyte detection, characterization, and quantitation, isomer differentiation is often a challenge. Tandem mass spectrometry is a common approach to increase the selectivity of mass spectrometry and energy-resolved measurements can provide further improvements. However, not all mass spectrometers, especially those that are very compact and affordable, are amenable to such experiments. For instance, single-stage mass spectrometers with soft ionization provide no dissociation information and quadrupole ion trap instruments with resonant excitation do not necessarily provide as informative of energy-resolved curves, for instance when extensive sequential dissociation is responsible for much of the "fingerprint". In-source collision-induced dissociation (IS-CID) is one approach to overcoming these barriers to exploit the analytical selectivity of energy-resolved CID without the need for additional instrumentation; this approach could broaden the reach of these selectivity gains to additional user bases (e.g., educational settings, field portable devices). Here, we specifically investigate energy-resolved IS-CID with the goal of (1) comparing between energy-resolved appearance curves measured with true tandem mass spectrometry on a quadrupole time-of-flight instrument and those obtained using IS-CID, (2) evaluating the approach as a means of differentiating isomers/isobar sets, especially those with similar dissociation patterns, and (3) exploring additional analytical considerations relevant to method development and implementation. This proof-of-concept work establishes the analytical potential of this approach, opening doors for future method development for specific applications.
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Affiliation(s)
- Matthew J Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Andie L M Nanney
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Amanda L Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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2
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Adams C, Gabriel W, Laukens K, Picciani M, Wilhelm M, Bittremieux W, Boonen K. Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nat Commun 2024; 15:3956. [PMID: 38730277 PMCID: PMC11087512 DOI: 10.1038/s41467-024-48322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.
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Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wassim Gabriel
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Mario Picciani
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
- Munich Data Science Institute, Technical University of Munich, 85748, Garching, Germany
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Kurt Boonen
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
- Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium.
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3
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Chalet C, Lesage D, Darii E, Perret A, Alves S, Gimbert Y, Tabet JC. Enantioselective Reduction of Noncovalent Complexes of Amino Acids with Cu II via Resonant Collision-Induced Dissociation: Collision Energy, Activation Duration Effects, and RRKM Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:456-465. [PMID: 38372248 DOI: 10.1021/jasms.3c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Formation of noncovalent complexes is one of the approaches to perform chiral analysis with mass spectrometry. Enantiomeric distinction of amino acids (AAs) based on the relative rate constants of competitive fragmentations of quaternary copper complexes is an efficient method for chiral differentiation. Here, we studied the complex [CuII,(Phe,PhG,Pro-H)]+ (m/z 493) under resonant collision-induced dissociation conditions while varying the activation time. The precursor ion can yield two main fragments through the loss of the non-natural AA phenylglycine (PhG): the expected product ion [CuII,(Phe,Pro-H)]+ (m/z 342) and the reduced product ion [CuI,(Phe,Pro)]+ (m/z 343). Enantioselective reduction describes the difference in relative abundance of these ions, which depends on the chirality of the precursor ion: the formation of the reduced ion m/z 343 is favored in homochiral complexes (DDD) compared to heterochiral complexes (such as LDD). Energy-resolved mass spectrometry data show that reduction, which arises from rearrangement, is favored at a low collision energy (CE) and long activation time (ActT), whereas direct cleavage preferentially occurs at a high CE and short ActT. These results were confirmed with kinetic modeling based on RRKM theory. For this modeling, it was necessary to set a pre-exponential factor as a reference, so that the E0 values obtained are relative values. Interestingly, these simulations showed that the critical energy E0 required to form the reduced ion is comparable in both homochiral and heterochiral complexes. However, the formation of product ion m/z 342 through direct cleavage is associated with a lower E0 in heterochiral complexes. Consequently, enantioselectivity would not be caused by enhanced reduction in homochiral complexes but rather by direct cleavage being favored in heterochiral complexes.
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Affiliation(s)
- Clément Chalet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
- Sorbonne Université, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
| | - Denis Lesage
- Sorbonne Université, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Sandra Alves
- Sorbonne Université, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
| | - Yves Gimbert
- Sorbonne Université, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058 Grenoble, France
| | - Jean-Claude Tabet
- Sorbonne Université, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, F-91191 Gif sur Yvette, France
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4
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Asakawa D, Saikusa K. Pentafluorobenzylpyridinium: new thermometer ion for characterizing the ions produced by collisional activation during tandem mass spectrometry. ANAL SCI 2023; 39:2031-2039. [PMID: 37707776 DOI: 10.1007/s44211-023-00419-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/21/2023] [Indexed: 09/15/2023]
Abstract
In this study, pentafluorobenzylpyridinium (F5-BnPy+), which has the highest dissociation energy among the reported benzylpyridinium thermometer ion, is proposed to characterize the internal energy distributions of ions activated by higher energy collisional dissociation (HCD) and ion-trap collision-induced dissociation (CID) during tandem mass spectrometry. The dissociation threshold energies of F5-BnPy+ was determined using quantum chemistry calculations at the CCSD(T)/6-311++G(d,p)//M06-2X-D3/6-311++G(d,p) level of theory, and the appearance energies for ion dissociation in HCD and ion-trap CID were estimated using Rice-Ramsperger-Kassel-Marcus theory. The main differences between HCD and ion-trap CID are the collision energies used and the timescales of collisional activation. For both HCD and ion-trap CID, the average internal energy of the ions increased with increasing collision energy. In contrast, the average value for the internal energy of the ions activated by ion-trap CID was lower than that of ions activated by HCD, probably because of the smaller collisional energy and longer activation time of the ion-trap CID experiments. The reported method will aid in the determination of the optimum tandem mass spectrometry parameters for the analysis of small molecules such as metabolites.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8568, Japan.
| | - Kazumi Saikusa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8568, Japan
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5
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Matey JM, Zapata F, Menéndez-Quintanal LM, Montalvo G, García-Ruiz C. Identification of new psychoactive substances and their metabolites using non-targeted detection with high-resolution mass spectrometry through diagnosing fragment ions/neutral loss analysis. Talanta 2023; 265:124816. [PMID: 37423179 DOI: 10.1016/j.talanta.2023.124816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/24/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Affiliation(s)
- José Manuel Matey
- Department of Chemistry and Drugs, National Institute of Toxicology and Forensic Sciences, C/ José Echegaray Nº4, 28232, Las Rozas de Madrid, Madrid, Spain; Universidad de Alcalá, Instituto Universitario de Investigación en Ciencias Policiales (IUICP), calle Libreros 27, 28801, Alcalá de Henares, Madrid, España(1); Chemical and Forensic Sciences (CINQUIFOR) Research Group, University of Alcalá, Ctra. Madrid-Barcelona km 33.600, 28871, Alcalá de Henares, Madrid, Spain(2).
| | - Félix Zapata
- Department of Analytical Chemistry, University of Murcia, Campus Espinardo, 30100, Murcia, Spain.
| | - Luis Manuel Menéndez-Quintanal
- Department of Chemistry and Drugs, National Institute of Toxicology and Forensic Sciences, Campus de Ciencias de la Salud, La Cuesta, 38320, La Laguna (Sta. Cruz de Tenerife), Spain.
| | - Gemma Montalvo
- Universidad de Alcalá, Instituto Universitario de Investigación en Ciencias Policiales (IUICP), calle Libreros 27, 28801, Alcalá de Henares, Madrid, España(1); Chemical and Forensic Sciences (CINQUIFOR) Research Group, University of Alcalá, Ctra. Madrid-Barcelona km 33.600, 28871, Alcalá de Henares, Madrid, Spain(2); Universidad de Alcalá, Departamento de Química Analítica, Quimica Física e Ingeniería Química, Ctra. Madrid-Barcelona km 33,6, 28871 Alcalá de Henares, Madrid, España.
| | - Carmen García-Ruiz
- Universidad de Alcalá, Instituto Universitario de Investigación en Ciencias Policiales (IUICP), calle Libreros 27, 28801, Alcalá de Henares, Madrid, España(1); Chemical and Forensic Sciences (CINQUIFOR) Research Group, University of Alcalá, Ctra. Madrid-Barcelona km 33.600, 28871, Alcalá de Henares, Madrid, Spain(2); Universidad de Alcalá, Departamento de Química Analítica, Quimica Física e Ingeniería Química, Ctra. Madrid-Barcelona km 33,6, 28871 Alcalá de Henares, Madrid, España.
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6
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Lieng B, Quaile AT, Domingo-Almenara X, Röst HL, Montenegro-Burke JR. Computational Expansion of High-Resolution-MS n Spectral Libraries. Anal Chem 2023; 95:17284-17291. [PMID: 37963318 PMCID: PMC10688228 DOI: 10.1021/acs.analchem.3c03343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Commonly, in MS-based untargeted metabolomics, some metabolites cannot be confidently identified due to ambiguities in resolving isobars and structurally similar species. To address this, analytical techniques beyond traditional MS2 analysis, such as MSn fragmentation, can be applied to probe metabolites for additional structural information. In MSn fragmentation, recursive cycles of activation are applied to fragment ions originating from the same precursor ion detected on an MS1 spectrum. This resonant-type collision-activated dissociation (CAD) can yield information that cannot be ascertained from MS2 spectra alone, which helps improve the performance of metabolite identification workflows. However, most approaches for metabolite identification require mass-to-charge (m/z) values measured with high resolution, as this enables the determination of accurate mass values. Unfortunately, high-resolution-MSn spectra are relatively rare in spectral libraries. Here, we describe a computational approach to generate a database of high-resolution-MSn spectra by converting existing low-resolution-MSn spectra using complementary high-resolution-MS2 spectra generated by beam-type CAD. Using this method, we have generated a database, derived from the NIST20 MS/MS database, of MSn spectral trees representing 9637 compounds and 19386 precursor ions where at least 90% of signal intensity was converted from low-to-high resolution.
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Affiliation(s)
- Brandon
Y. Lieng
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S
3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, ON M5S 3G9, Canada
| | - Andrew T. Quaile
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S
3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, ON M5S 3G9, Canada
| | - Xavier Domingo-Almenara
- Centre
for Omics Sciences, Eurecat—Technology Centre of Catalonia
& Rovira i Virgili University Joint Unit, Reus 43204, Catalonia, Spain
- Department of Electrical, Electronic and Control
Engineering, Universitat Rovira i Virgili, Tarragona 43007, Catalonia, Spain
| | - Hannes L. Röst
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S
3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J. Rafael Montenegro-Burke
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S
3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, ON M5S 3G9, Canada
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7
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Murray KJ, Villalta PW, Griffin TJ, Balbo S. Discovery of Modified Metabolites, Secondary Metabolites, and Xenobiotics by Structure-Oriented LC-MS/MS. Chem Res Toxicol 2023; 36:1666-1682. [PMID: 37862059 DOI: 10.1021/acs.chemrestox.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Exogenous compounds and metabolites derived from therapeutics, microbiota, or environmental exposures directly interact with endogenous metabolic pathways, influencing disease pathogenesis and modulating outcomes of clinical interventions. With few spectral library references, the identification of covalently modified biomolecules, secondary metabolites, and xenobiotics is a challenging task using global metabolomics profiling approaches. Numerous liquid chromatography-coupled mass spectrometry (LC-MS) small molecule analytical workflows have been developed to curate global profiling experiments for specific compound groups of interest. These workflows exploit shared structural moiety, functional groups, or elemental composition to discover novel and undescribed compounds through nontargeted small molecule discovery pipelines. This Review introduces the concept of structure-oriented LC-MS discovery methodology and aims to highlight common approaches employed for the detection and characterization of covalently modified biomolecules, secondary metabolites, and xenobiotics. These approaches represent a combination of instrument-dependent and computational techniques to rapidly curate global profiling experiments to detect putative ions of interest based on fragmentation patterns, predictable phase I or phase II metabolic transformations, or rare elemental composition. Application of these methods is explored for the detection and identification of novel and undescribed biomolecules relevant to the fields of toxicology, pharmacology, and drug discovery. Continued advances in these methods expand the capacity for selective compound discovery and characterization that promise remarkable insights into the molecular interactions of exogenous chemicals with host biochemical pathways.
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Affiliation(s)
- Kevin J Murray
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Silvia Balbo
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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8
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Ng CCA, Zhou Y, Yao ZP. Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review. Anal Chim Acta 2023; 1268:341330. [PMID: 37268337 DOI: 10.1016/j.aca.2023.341330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 06/04/2023]
Abstract
Peptide sequencing is of great significance to fundamental and applied research in the fields such as chemical, biological, medicinal and pharmaceutical sciences. With the rapid development of mass spectrometry and sequencing algorithms, de-novo peptide sequencing using tandem mass spectrometry (MS/MS) has become the main method for determining amino acid sequences of novel and unknown peptides. Advanced algorithms allow the amino acid sequence information to be accurately obtained from MS/MS spectra in short time. In this review, algorithms from exhaustive search to the state-of-art machine learning and neural network for high-throughput and automated de-novo sequencing are introduced and compared. Impacts of datasets on algorithm performance are highlighted. The current limitations and promising direction of de-novo peptide sequencing are also discussed in this review.
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Affiliation(s)
- Cheuk Chi A Ng
- State Key Laboratory of Chemical Biology and Drug Discovery, and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; Research Institute for Future Food, and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), and Shenzhen Key Laboratory of Food Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Yin Zhou
- State Key Laboratory of Chemical Biology and Drug Discovery, and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; Research Institute for Future Food, and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), and Shenzhen Key Laboratory of Food Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Zhong-Ping Yao
- State Key Laboratory of Chemical Biology and Drug Discovery, and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; Research Institute for Future Food, and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), and Shenzhen Key Laboratory of Food Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China.
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9
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Asakawa D. Phenyl Sulfate Derivatives: New Thermometer Ions for Characterization of Internal Energy of Negative Ions Produced by Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:435-440. [PMID: 36795600 DOI: 10.1021/jasms.2c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although positive thermometer ions are widely used for evaluating the internal energy distribution of gas-phase ions, negative thermometer ions have not yet been proposed. In this study, phenyl sulfate derivatives were tested as thermometer ions to characterize the internal energy distribution of ions produced by electrospray ionization (ESI) in the negative mode because the activation of phenyl sulfate preferentially undergoes SO3 loss, providing a phenolate anion. The dissociation threshold energies for the phenyl sulfate derivatives were determined using quantum chemistry calculations at the CCSD(T)/6-311++G(2df,p)//M06-2X-D3/6-311++G(d,p) level of theory. The values for the appearance energies of the fragment ions of the phenyl sulfate derivatives depend on the dissociation time scale in the experiment; therefore, the dissociation rate constants of the corresponding ions were estimated using the Rice-Ramsperger-Kassel-Marcus theory. The phenyl sulfate derivatives were used as thermometer ions to determine the internal energy distribution of negative ions activated by the in-source collision-induced dissociation (CID) and higher-energy collisional dissociation. Both mean and full width at half-maximum values increased with increasing ion collision energy. In the in-source CID experiments, the internal energy distributions obtained by phenyl sulfate derivatives are similar to that when all voltages are mirrored, and the traditional benzylpyridinium thermometer ions are used. The reported method will aid in determining the optimum voltage for ESI mass spectrometry and the subsequent tandem mass spectrometry of acidic analyte molecules.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
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10
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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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11
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Hissong R, Evans KR, Evans CR. Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics. Handb Exp Pharmacol 2023; 277:43-71. [PMID: 36409330 DOI: 10.1007/164_2022_617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The metabolome is composed of a vast array of molecules, including endogenous metabolites and lipids, diet- and microbiome-derived substances, pharmaceuticals and supplements, and exposome chemicals. Correct identification of compounds from this diversity of classes is essential to derive biologically relevant insights from metabolomics data. In this chapter, we aim to provide a practical overview of compound identification strategies for mass spectrometry-based metabolomics, with a particular eye toward pharmacologically-relevant studies. First, we describe routine compound identification strategies applicable to targeted metabolomics. Next, we discuss both experimental (data acquisition-focused) and computational (software-focused) strategies used to identify unknown compounds in untargeted metabolomics data. We then discuss the importance of, and methods for, assessing and reporting the level of confidence of compound identifications. Throughout the chapter, we discuss how these steps can be implemented using today's technology, but also highlight research underway to further improve accuracy and certainty of compound identification. For readers interested in interpreting metabolomics data already collected, this chapter will supply important context regarding the origin of the metabolite names assigned to features in the data and help them assess the certainty of the identifications. For those planning new data acquisition, the chapter supplies guidance for designing experiments and selecting analysis methods to enable accurate compound identification, and it will point the reader toward best-practice data analysis and reporting strategies to allow sound biological and pharmacological interpretation.
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12
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Xu F, Wang W, Ding L, Fang X, Ding CF. Synchronized Reverse Scan Collision Induced Dissociation in Digital Ion Trap Mass Spectrometer for Improving Fragment Ion Detection. Anal Chem 2022; 94:17827-17834. [PMID: 36512629 DOI: 10.1021/acs.analchem.2c03524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of fragment ion detection methods is of great importance for mass spectrometer advancement or substance identification. To date, collision induced dissociation (CID) remains the most commonly used ion activation method in MS/MS experiments, and the effectiveness of CID in an ion trap mass spectrometer is limited by low mass cutoff and weak fragmentation yields. Theoretically, controlling the q value is the key to maintain the fragment efficiency and trapping efficiency of MS/MS, thus improving the detection of fragment ion, while currently reported techniques usually require complex circuitry and often produce different CID patterns. In this paper, with the developed synchronized reversed scanning-collision induced dissociation (SRS-CID) technique, we demonstrate its effective improvement in fragment ion detection. The SRS-CID is implemented on a digital ion trap mass spectrometer (DITMS) by reverse scanning the q values during CID process, or specifically, the frequency is increased during the CID process. With the SRS-CID technique, the fragmentation efficiency of precursor ions can be slightly improved. For reserpine analyte, the trapping efficiency for low-mass fragment ions is improved at least 3 times, and for YGGFL, the trapping efficiency for low-mass fragment ions is improved at least 9 times. These experimental results can also be validated by simulations, and the kinetic energy variation plot suggests consecutive fragmentation occurs. In any case, the SRS-CID provides a solution to the low efficiency of fragment ion detection during tandem MS analysis, which will certainly be useful in the future.
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Affiliation(s)
- Fuxing Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Weimin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Li Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Xiang Fang
- National Institute of Metrology, Chemical Metrology & Analytical Science Division, Beijing 100029, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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13
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Bayat P, Gatineau D, Lesage D, Martinez A, Cole RB. Benchmarking higher energy collision dissociation (HCD) by investigation of binding energies of gas-phase host-guest complexes of hemicryptophane cages. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4879. [PMID: 36098385 DOI: 10.1002/jms.4879] [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: 05/10/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Synthesis of host molecules that feature well-defined characteristics for molecular recognition of guest molecules is often a major aim of synthetic host-guest (H-G) chemistry. A key consideration in evaluating the selectivity of hosts and the affinities of guests is the measurement of binding energies of obtained H-G complexes. In contrast to nuclear magnetic resonance (NMR) or fluorescence measurements that are capable of measuring binding strengths in solution, mass spectrometry offers the opportunity to measure gas-phase binding energies. Presented in this article is a higher energy collision dissociation (HCD) approach for determining critical energies of dissociation of H-G complexes. Experiments were performed on electrospray ionization (ESI)-generated H-G pairs in an LTQ-XL/Orbitrap hybrid instrument. The presented HCD approach requires preliminary calibration of the internal energy distribution of generated ions that was achieved by the use of activation parameters that were known from previous low-energy collision-induced dissociation (low-energy CID) experiments. Internal energy deposition was modeled based on a truncated Maxwell-Boltzmann distribution and characteristic temperature (Tchar ). Using this method, critical energies of dissociation were determined for 10 H-G biologically relevant complexes of the heteroditopic hemicryptophane cage host (Host). Obtained results are compared with those found previously by low-energy CID. The use of this HCD technique is relatively straightforward, although its implementation does require knowledge (or a presumption) about the Arrhenius pre-exponential factor of the complexes to obtain their critical energies of dissociation.
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Affiliation(s)
- Parisa Bayat
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, UMR 8232, CNRS, Paris, France
| | - David Gatineau
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, UMR 8232, CNRS, Paris, France
- Département de Chimie Moléculaire, Université Grenoble Alpes, UMR 5250, CNRS, Grenoble, France
| | - Denis Lesage
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, UMR 8232, CNRS, Paris, France
| | - Alexandre Martinez
- Centrale Marseille, iSm2, Aix Marseille Université, CNRS, Marseille, France
| | - Richard B Cole
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, UMR 8232, CNRS, Paris, France
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14
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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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15
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Evaluating the Performance of 193 nm Ultraviolet Photodissociation for Tandem Mass Tag Labeled Peptides. ANALYTICA 2021. [DOI: 10.3390/analytica2040014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite the successful application of tandem mass tags (TMT) for peptide quantitation, missing reporter ions in higher energy collisional dissociation (HCD) spectra remains a challenge for consistent quantitation, especially for peptides with labile post-translational modifications. Ultraviolet photodissociation (UVPD) is an alternative ion activation method shown to provide superior coverage for sequencing of peptides and intact proteins. Here, we optimized and evaluated 193 nm UVPD for the characterization of TMT-labeled model peptides, HeLa proteome, and N-glycopeptides from model proteins. UVPD yielded the same TMT reporter ions as HCD, at m/z 126–131. Additionally, UVPD produced a wide range of fragments that yielded more complete characterization of glycopeptides and less frequent missing TMT reporter ion channels, whereas HCD yielded a strong tradeoff between characterization and quantitation of TMT-labeled glycopeptides. However, the lower fragmentation efficiency of UVPD yielded fewer peptide identifications than HCD. Overall, 193 nm UVPD is a valuable tool that provides an alternative to HCD for the quantitation of large and highly modified peptides with labile PTMs. Continued development of instrumentation specific to UVPD will yield greater fragmentation efficiency and fulfil the potential of UVPD to be an all-in-one spectrum ion activation method for broad use in the field of proteomics.
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16
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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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17
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Delvaux A, Rathahao-Paris E, Alves S. An emerging powerful technique for distinguishing isomers: Trapped ion mobility spectrometry time-of-flight mass spectrometry for rapid characterization of estrogen isomers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8928. [PMID: 32833266 DOI: 10.1002/rcm.8928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/28/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Isomer metabolites are involved in metabolic pathways, and their characterization is essential but remains challenging even using high-performance analytical platforms. The addition of ion mobility prior to mass analysis can help to separate isomers. Here, the ability of a recently developed trapped ion mobility spectrometry system to separate metabolite isomers was examined. METHODS Three pairs of estrogen isomers were studied as a model of isomeric metabolites under both negative and positive electrospray ionization (ESI) modes using a commercial trapped ion mobility spectrometry-TOF mass spectrometer. The standard metabolites were also spiked into human urine to evaluate the efficiency of trapped ion mobility spectrometry to separate isomers in complex mixtures. RESULTS The estradiol glucuronide isomers (E2 β-3G and E2 β-17G) could be distinguished as deprotonated species, while the estradiol epimers (E2 β and E2 α) and the methoxyestradiol isomers (2-MeO-E2 β and 4-MeO-E2 β) were separated as lithiated adducts in positive ionization mode. When performing analyses in the urine matrix, no alteration in the ion mobility resolving power was observed and the measured collision cross section (CCS) values varied by less than 1.0%. CONCLUSIONS The trapped ion mobility spectrometry-TOF mass spectrometer enabled the separation of the metabolite isomers with very small differences in CCS values (ΔCCS% = 2%). It is shown to be an effective tool for the rapid characterization of isomers in complex matrices.
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Affiliation(s)
- Aurélie Delvaux
- Institut Parisien de Chimie Moléculaire, CNRS, Faculté des Sciences et de l'Ingénierie, Sorbonne Université, Paris, F-75005, France
| | - Estelle Rathahao-Paris
- Institut Parisien de Chimie Moléculaire, CNRS, Faculté des Sciences et de l'Ingénierie, Sorbonne Université, Paris, F-75005, France
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, Gif-sur-Yvette, F-91191, France
| | - Sandra Alves
- Institut Parisien de Chimie Moléculaire, CNRS, Faculté des Sciences et de l'Ingénierie, Sorbonne Université, Paris, F-75005, France
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18
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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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19
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Mass spectrometry-based metabolomics for an in-depth questioning of human health. Adv Clin Chem 2020; 99:147-191. [PMID: 32951636 DOI: 10.1016/bs.acc.2020.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Today, metabolomics is becoming an indispensable tool to get a more comprehensive analysis of complex living systems, providing insights on multiple aspects of physiology. Although its application in large scale population-based studies is very challenging due to the processing of large sample sets as well as the complexity of data information, its potential to characterize human health is well recognized. Technological advances in metabolomics pave the way for the efficient biomarker discovery of disease etiology, diagnosis and prognosis. Here, different steps of the metabolomics workflow, particularly mass spectrometry-based approaches, are discussed to demonstrate the potential of metabolomics to address biological questioning in human health. First an overview of metabolomics is provided with its interest in human health studies. Analytical development and advances in mass spectrometry instrumentation and computational tools are discussed regarding their application limits. Advancing metabolomics for applicability in human health and large-scale studies is presented and discussed in conclusion.
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20
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Danquah BD, Yefremova Y, Opuni KFM, Röwer C, Koy C, Glocker MO. Intact Transition Epitope Mapping - Thermodynamic Weak-force Order (ITEM - TWO). J Proteomics 2019; 212:103572. [PMID: 31683061 DOI: 10.1016/j.jprot.2019.103572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 01/17/2023]
Abstract
We have developed an electrospray mass spectrometry method which is capable to determine antibody affinity in a gas phase experiment. A solution with the immune complex is electrosprayed and multiply charged ions are translated into the gas phase. Then, the intact immune-complex ions are separated from unbound peptide ions. Increasing the voltage difference in a collision cell results in collision induced dissociation of the immune-complex by which bound peptide ions are released. When analyzing a peptide mixture, measuring the mass of the complex-released peptide ions identifies which of the peptides contains the epitope. A step-wise increase in the collision cell voltage difference changes the intensity ratios of the surviving immune complex ions, the released peptide ions, and the antibody ions. From all the ions´ normalized intensity ratios are deduced the thermodynamic quasi equilibrium dissociation constants (KDm0g#) from which are calculated the apparent gas phase Gibbs energies of activation over temperature (ΔGm0g#T). The order of the apparent gas phase dissociation constants of four antibody - epitope peptide pairs matched well with those obtained from in-solution measurements. The determined gas phase values for antibody affinities are independent from the source of the investigated peptides and from the applied instrument. Data are available via ProteomeXchange with identifier PXD016024. SIGNIFICANCE: ITEM - TWO enables rapid epitope mapping and determination of apparent dissociation energies of immune complexes with minimal in-solution handling. Mixing of antibody and antigen peptide solutions initiates immune complex formation in solution. Epitope binding strengths are determined in the gas phase after electrospraying the antibody / antigen peptide mixtures and mass spectrometric analysis of immune complexes under different collision induced dissociation conditions. Since the order of binding strengths in the gas phase is the same as that in solution, ITEM - TWO characterizes two most important antibody properties, specificity and affinity.
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Affiliation(s)
- Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Claudia Röwer
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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21
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Lesage D, Mezzache S, Gimbert Y, Dossmann H, Tabet JC. Extended kinetic method and RRKM modeling to reinvestigate proline's proton affinity and approach the meaning of effective temperature. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:219-228. [PMID: 30630370 DOI: 10.1177/1469066718822054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proline proton affinity PA(Pro) was previously measured by extended kinetic methods with several amines as reference bases using a triple quadrupole mass spectrometer ( J Mass Spectrom 2005; 40: 1300). The measured value of 947.5 ± 5 kJ.mol-1 differs by more than 10 kJ.mol-1 from previous reported experimental or calculated values. This difference may be explained in part by the existence of relatively large entropy difference between the two dissociation channels (ΔΔS‡avg = 31 ± 10 J.mol-1.K-1) and by the inaccuracy of the amines proton affinity used as reference bases. In the present work, these experimental measurements were reinvestigated by RRKM modeling using MassKinetics software. From this modeling, a new PA value of 944.5 ± 5 kJ.mol-1 and a ΔΔS‡avg(600K) value of 33 ± 10 J.mol-1.K-1 are determined. However, the difference between experiment and recent theoretical calculations remains large (10 kJ.mol-1). These RRKM simulations allow also accessing to the effective temperature parameter (T eff) and to discuss the meaning of this term. As previously reported, T eff mainly depends on the internal energy and on the decomposition time as well. It also depends on the critical energies and on the transition state. Considering the entrance of the collision cell as a new ion source, T eff is finally shown to be close to a characteristic temperature (T char).
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Affiliation(s)
- Denis Lesage
- 1 CNRS, Institut Parisien de Chimie Moléculaire, Sorbonne Université, IPCM, Paris, France
| | - Sakina Mezzache
- 1 CNRS, Institut Parisien de Chimie Moléculaire, Sorbonne Université, IPCM, Paris, France
| | - Yves Gimbert
- 1 CNRS, Institut Parisien de Chimie Moléculaire, Sorbonne Université, IPCM, Paris, France
- 2 Université Grenoble Alpes and CNRS, DCM (UMR 5250) Grenoble Cedex 9, France
| | - Héloïse Dossmann
- 1 CNRS, Institut Parisien de Chimie Moléculaire, Sorbonne Université, IPCM, Paris, France
| | - Jean-Claude Tabet
- 1 CNRS, Institut Parisien de Chimie Moléculaire, Sorbonne Université, IPCM, Paris, France
- 3 Service de Pharmacologie et d'Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
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22
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Bayat P, Gatineau D, Lesage D, Robert V, Martinez A, Cole RB. Investigation of Hemicryptophane Host-Guest Binding Energies Using High-Pressure Collision-Induced Dissociation in Combination with RRKM Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:509-518. [PMID: 30478817 DOI: 10.1007/s13361-018-2109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/20/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
In advancing host-guest (H-G) chemistry, considerable effort has been spent to synthesize host molecules with specific and well-defined molecular recognition characteristics including selectivity and adjustable affinity. An important step in the process is the characterization of binding strengths of the H-G complexes that is typically performed in solution using NMR or fluorescence. Here, we present a mass spectrometry-based multimodal approach to obtain critical energies of dissociation for two hemicryptophane cages with three biologically relevant guest molecules. A combination of blackbody infrared radiative dissociation (BIRD) and high-pressure collision-induced dissociation (high-pressure CID), along with RRKM modeling, was employed for this purpose. For the two tested hemicryptophane hosts, the cage containing naphthyl linkages exhibited stronger interactions than the cage bearing phenyl linkages. For both cages, the order of guest stability is choline > acetylcholine > betaine. The information obtained by these types of mass spectrometric studies can provide new insight into the structural features that most influence the stability of H-G pairs, thereby providing guidance for future syntheses. Graphical Abstract.
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Affiliation(s)
- Parisa Bayat
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France
| | - David Gatineau
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France
- CNRS, UMR 5250, DCM, University of Grenoble Alpes, Grenoble, France
| | - Denis Lesage
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France
| | - Vincent Robert
- Laboratoire de Chimie Quantique, Université de Strasbourg, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Alexandre Martinez
- UMR CNRS 7313-iSm2, Equipe Chirosciences, Aix Marseille Université, Av. Escadrille Normandie-Niemen, 13397, Marseille, France
| | - Richard B Cole
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France.
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23
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Gatineau D, Lesage D, Clavier H, Dossmann H, Chan CH, Milet A, Memboeuf A, Cole RB, Gimbert Y. Bond dissociation energies of carbonyl gold complexes: a new descriptor of ligand effects in gold(i) complexes? Dalton Trans 2018; 47:15497-15505. [PMID: 30338332 DOI: 10.1039/c8dt03721c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ligand electronic effects in gold(i) chemistry have been evaluated by means of the experimental determination of M-CO bond dissociation energies for 16 [L-Au-CO]+ complexes, bearing L ligands widely used in gold catalysis. Energy-resolved analyses have been made using tandem mass spectrometry with collision-induced dissociation. Coupled with DFT calculations, this approach enables the quantification of ligand effects based on the LAu-CO bond strength. A further energy decomposition analysis gives access to detailed insights into this bond's characteristics. Whereas small differences are observed between phosphine- and phosphite-containing gold complexes, carbene ligands are shown to stabilize the gold-carbonyl bond much more efficiently.
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Affiliation(s)
- David Gatineau
- Univ. Grenoble Alpes and CNRS, DCM (UMR 5250) BP 53, 38041 Grenoble Cedex9, France.
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24
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Bayat P, Lesage D, Cole RB. Low-energy collision-induced dissociation (low-energy CID), collision-induced dissociation (CID), and higher energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:705-716. [PMID: 29813177 DOI: 10.1002/jms.4205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/11/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision-induced dissociation (low-energy CID), collision-induced dissociation (CID), and higher energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using 3 techniques shows that, generally, when working with monolithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with dilithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a nonresonant activation technique, and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of monolithiated and dilithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages vs glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on dilithiated and trilithiated sugars reveal that intensities of product ions containing 2 Li+ or 3 Li+ , respectively, are higher than those bearing only 1 Li+ . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl-adducted lithiated sugar and NaCl-adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system.
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Affiliation(s)
- Parisa Bayat
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, 75005, Paris, France
| | - Denis Lesage
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, 75005, Paris, France
| | - Richard B Cole
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, 75005, Paris, France
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Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O. Identification of small molecules using accurate mass MS/MS search. MASS SPECTROMETRY REVIEWS 2018; 37:513-532. [PMID: 28436590 PMCID: PMC8106966 DOI: 10.1002/mas.21535] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/17/2017] [Accepted: 03/18/2017] [Indexed: 05/03/2023]
Abstract
Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in MS/MS-based annotation of chemical structures is impacted by instrumental settings and requirements, data acquisition modes including data-dependent and data-independent methods, library scoring algorithms, as well as post-curation steps. We critically discuss parameters that influence search results, such as mass accuracy, precursor ion isolation width, intensity thresholds, centroiding algorithms, and acquisition speed. A range of publicly and commercially available MS/MS databases such as NIST, MassBank, MoNA, LipidBlast, Wiley MSforID, and METLIN are surveyed. In addition, software tools including NIST MS Search, MS-DIAL, Mass Frontier, SmileMS, Mass++, and XCMS2 to perform fast MS/MS search are discussed. MS/MS scoring algorithms and challenges during compound annotation are reviewed. Advanced methods such as the in silico generation of tandem mass spectra using quantum chemistry and machine learning methods are covered. Community efforts for curation and sharing of tandem mass spectra that will allow for faster distribution of scientific discoveries are discussed.
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Affiliation(s)
- Tobias Kind
- Genome Center, Metabolomics, UC Davis, Davis, California
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Tomas Cajka
- Genome Center, Metabolomics, UC Davis, Davis, California
| | - Yan Ma
- National Institute of Biological Sciences, Beijing, People’s Republic of China
| | - Zijuan Lai
- Genome Center, Metabolomics, UC Davis, Davis, California
| | | | | | | | | | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Oliver Fiehn
- Genome Center, Metabolomics, UC Davis, Davis, California
- Faculty of Sciences, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
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Cao X, Cai X, Mo W. Comparing the fragmentation reactions of protonated cyclic indolyl α-amino esters in quadrupole/orbitrap and quadrupole time-of-flight mass spectrometers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:543-551. [PMID: 29369433 DOI: 10.1002/rcm.8063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 06/07/2023]
Abstract
RATIONALE The comparative study of higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) mechanisms for protonated cyclic indolyl α-amino esters in quadrupole/orbitrap (Q/Orbitrap) and quadrupole time-of-flight (QTOF) mass spectrometers, respectively, is helpful to study the structures and properties of biologically active indole derivatives using tandem mass spectrometry (MS/MS) technology. METHODS HCD and CID experiments were carried out using electrospray ionization Q/Orbitrap MS and QTOFMS in positive ion mode, respectively. Only the labile hydrogens were exchanged with deuterium in hydrogen/deuterium exchange (HDX) experiments and only the aromatic indole C-H hydrogens were substituted with deuterium in regiospecific hydrogen-deuterium labeling experiments. Theoretical calculations were carried out using the density functional theory (DFT) method at the B3LYP level with the 6-311G(d,p) basis set in the Gaussian 03 package of programs. RESULTS In Q/Orbitrap MS/MS, when the added proton on the N8 position of protonated cyclic indolyl α-amino esters migrated in a stepwise fashion to the C3 position via two sequential 1,4-H shifts, an ion-neutral complex INC1 of [protonated cyclic N-sulfonyl ketimino esters/indoles] was formed by a charge-directed heterolytic cleavage of the C3 -C10 bond, while an ion-neutral complex INC3 of [cyclic N-sulfonyl ketimino esters/protonated indoles] was formed when another labile hydrogen on the N8 position successively migrated to the C4 position. Direct decomposition of INC1 and INC3 resulted in protonated cyclic N-sulfonyl ketimino esters and protonated indoles, respectively, while proton transfer led to protonated indoles and protonated cyclic N-sulfonyl ketimino esters. The HDX reaction with residual water in the HCD cell was also observed. In QTOF-MS/MS, protonated cyclic N-sulfonyl ketimino esters and protonated indoles resulted from direct decomposition of INC1 and INC3 , respectively, rather than proton transfer. CONCLUSIONS Due to the specific construction of the Q/Orbitrap and QTOF mass spectrometers, different fragmentation mechanisms medicated by ion-neutral complexes of protonated cyclic indolyl α-amino esters were proposed. This study is desirable for qualitative and quantitive investigation of indole derivatives using MS/MS technology.
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Affiliation(s)
- Xiaoji Cao
- Research Center of Analysis and Measurement, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R. China
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R. China
| | - Xue Cai
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R. China
| | - Weimin Mo
- Research Center of Analysis and Measurement, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R. China
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R. China
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Solano EA, Mohamed S, Mayer PM. Modeling collision energy transfer in APCI/CID mass spectra of PAHs using thermal-like post-collision internal energy distributions. J Chem Phys 2016; 145:164311. [PMID: 27802636 DOI: 10.1063/1.4966186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The internal energy transferred when projectile molecular ions of naphthalene collide with argon gas atoms was extracted from the APCI-CID (atmospheric-pressure chemical ionization collision-induced dissociation) mass spectra acquired as a function of collision energy. Ion abundances were calculated by microcanonical integration of the differential rate equations using the Rice-Ramsperger-Kassel-Marcus rate constants derived from a UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) fragmentation mechanism and thermal-like vibrational energy distributions pME,Tchar. The mean vibrational energy excess of the ions was characterized by the parameter Tchar ("characteristic temperature"), determined by fitting the theoretical ion abundances to the experimental breakdown graph (a plot of relative abundances of the ions as a function of kinetic energy) of activated naphthalene ions. According to these results, the APCI ion source produces species below Tchar = 1457 K, corresponding to 3.26 eV above the vibrational ground state. Subsequent collisions heat the ions up further, giving rise to a sigmoid curve of Tchar as a function of Ecom (center-of-mass-frame kinetic energy). The differential internal energy absorption per kinetic energy unit (dEvib/dEcom) changes with Ecom according to a symmetric bell-shaped function with a maximum at 6.38 ± 0.32 eV (corresponding to 6.51 ± 0.27 eV of vibrational energy excess), and a half-height full width of 6.30 ± 1.15 eV. This function imposes restrictions on the amount of energy that can be transferred by collisions, such that a maximum is reached as kinetic energy is increased. This behavior suggests that the collisional energy transfer exhibits a pronounced increase around some specific value of energy. Finally, the model is tested against the CID mass spectra of anthracene and pyrene ions and the corresponding results are discussed.
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Affiliation(s)
- Eduardo A Solano
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Sabria Mohamed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Paul M Mayer
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Atypical cleavage of protonated N-fatty acyl amino acids derived from aspartic acid evidenced by sequential MS 3 experiments. Amino Acids 2016; 48:2717-2729. [PMID: 27565657 DOI: 10.1007/s00726-016-2286-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/21/2016] [Indexed: 01/30/2023]
Abstract
Lipidomics calls for information on detected lipids and conjugates whose structural elucidation by mass spectrometry requires to rationalization of their gas phase dissociations toward collision-induced dissociation (CID) processes. This study focused on activated dissociations of two lipoamino acid (LAA) systems composed of N-palmitoyl acyl coupled with aspartic and glutamic acid mono ethyl esters (as LAA(*D) and LAA(*E)). Although in MS/MS, their CID spectra show similar trends, e.g., release of water and ethanol, the [(LAA(*D/*E)+H)-C2H5OH]+ product ions dissociate via distinct pathways in sequential MS3 experiments. The formation of all the product ions is rationalized by charge-promoted cleavages often involving stepwise processes with ion isomerization into ion-dipole prior to dissociation. The latter explains the maleic anhydride or ketene neutral losses from N-palmitoyl acyl aspartate and glutamate anhydride fragment ions, respectively. Consequently, protonated palmitoyl acid amide is generated from LAA(*D), whereas LAA(*E) leads to the [*E+H-H2O]+ anhydride. The former releases ammonia to provide acylium, which gives the C n H(2n-1) and C n H(2n-3) carbenium series. This should offer structural information, e.g., to locate either unsaturation(s) or alkyl group branching present on the various fatty acyl moieties of lipo-aspartic acid in further studies based on MS n experiments.
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Barbier Saint Hilaire P, Warnet A, Gimbert Y, Hohenester UM, Giorgi G, Olivier MF, Fenaille F, Colsch B, Junot C, Tabet JC. Mechanistic study of competitive releases of H 2O, NH 3 and CO 2 from deprotonated aspartic and glutamic acids: Role of conformation. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1047:64-74. [PMID: 27592168 DOI: 10.1016/j.jchromb.2016.08.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 07/22/2016] [Accepted: 08/22/2016] [Indexed: 11/27/2022]
Abstract
The aims of this study were to highlight the impact of minor structural differences (e.g. an aminoacid side chain enlargement by one methylene group), on ion dissociation under collision-induced dissociation conditions, and to determine the underlying chemical mechanisms. Therefore, we compared fragmentations of deprotonated aspartic and glutamic acids generated in negative electrospray ionization. Energy-resolved mass spectrometry breakdown curves were recorded and MS3 experiments performed on an Orbitrap Fusion for high-resolution and high-mass accuracy measurements. Activated fragmentations were performed using both the resonant and non-resonant excitation modes (i.e., CID and HCD, respectively) in order to get complementary information on the competitive and consecutive dissociative pathways. These experiments showed a specific loss of ammonia from the activated aspartate but not from the activated glutamate. We mainly focused on this specific observed loss from aspartate. Two different mechanisms based on intramolecular reactions (similar to those occurring in organic chemistry) were proposed, such as intramolecular elimination (i.e. Ei-like) and nucleophilic substitution (i.e. SNi-like) reactions, respectively, yielding anions as fumarate and α lactone from a particular conformation with the lowest steric hindrance (i.e. with antiperiplanar carboxyl groups). The detected deaminated aspartate anion can then release CO2 as observed in the MS3 experimental spectra. However, quantum calculations did not indicate the formation of such a deaminated aspartate product ion without loss of carbon dioxide. Actually, calculations displayed the double neutral (NH3+CO2) loss as a concomitant pathway (from a particular conformation) with relative high activation energy instead of a consecutive process. This disagreement is apparent since the concomitant pathway may be changed into consecutive dissociations according to the collision energy i.e., at higher collision energy and at lower excitation conditions, respectively. The latter takes place by stabilization of the deaminated aspartate solvated with two residual molecules of water (present in the collision cell). This desolvated anion formed is an α lactone substituted by a methylene carboxylate group. The vibrational excitation acquired by [(D-H)-NH3]-during its isolation is enough to allow its prompt decarboxylation with a barrier lower than 8.4kJ/mol. In addition, study of glutamic acid-like diastereomers constituted by a cyclopropane, hindering any side chain rotation, confirms the impact of the three-dimensional geometry on fragmentation pathways. A significant specific loss of water is only observed for one of these diastereomers. Other experiments, such as stable isotope labeling, need to be performed to elucidate all the observed losses from activated aspartate and glutamate anions. These first mechanistic interpretations enhance understanding of this dissociative pathway and underline the necessity of studying fragmentation of a large number of various compounds to implement properly new algorithms for de novo elucidation of unknown metabolites.
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Affiliation(s)
| | - Anna Warnet
- CEA, iBiTec-S, SPI, LEMM, Metabohub Gif Sur Yvette, France; Université Paris VI (UPMC), CNRS UMR 7201, Paris Cedex 05, France.
| | - Yves Gimbert
- Université Grenoble Alpes et CNRS, DCM UMR 5250, Grenoble, France
| | | | - Gianluca Giorgi
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, Via Aldo Moro, I-53100 Siena, Italy
| | | | | | - Benoît Colsch
- CEA, iBiTec-S, SPI, LEMM, Metabohub Gif Sur Yvette, France
| | | | - Jean-Claude Tabet
- CEA, iBiTec-S, SPI, LEMM, Metabohub Gif Sur Yvette, France; Université Paris VI (UPMC), CNRS UMR 7201, Paris Cedex 05, France
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Viglino E, Shaffer CJ, Tureček F. UV/Vis Action Spectroscopy and Structures of Tyrosine Peptide Cation Radicals in the Gas Phase. Angew Chem Int Ed Engl 2016; 55:7469-73. [DOI: 10.1002/anie.201602604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Emilie Viglino
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | | | - František Tureček
- Department of Chemistry University of Washington Seattle WA 98195 USA
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31
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Viglino E, Shaffer CJ, Tureček F. UV/Vis Action Spectroscopy and Structures of Tyrosine Peptide Cation Radicals in the Gas Phase. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Emilie Viglino
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | | | - František Tureček
- Department of Chemistry University of Washington Seattle WA 98195 USA
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32
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Aretz I, Meierhofer D. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology. Int J Mol Sci 2016; 17:ijms17050632. [PMID: 27128910 PMCID: PMC4881458 DOI: 10.3390/ijms17050632] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.
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Affiliation(s)
- Ina Aretz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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33
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Liang Y, Neta P, Simón-Manso Y, Stein SE. Reaction of arylium ions with the collision gas N2 in electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:629-636. [PMID: 26212280 DOI: 10.1002/rcm.7147] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 05/18/2023]
Abstract
RATIONALE The tandem mass spectra of many compounds contained peaks which could not have arisen from the precursor ion. Such peaks were found to be due to reaction of arylium ions with N2 in the collision cell. Therefore, this reaction was studied in detail with representative compounds. METHODS Various classes of compounds were dissolved in acetonitrile/water/formic acid and studied by electrospray ionization mass spectrometry to record their MS(2) and pseudo-MS(3) spectra in a QqQ mass spectrometer and their accurate m/z values in an Orbitrap Elite instrument. Arylium ions were found to react with N2 in the collision cell. The reaction was confirmed by pseudo-MS(3) studies, by comparison with authentic diazonium ions, and by the pressure dependence of the product ion survival yield. RESULTS Reactions of arylium ions with N2 were observed with p-toluenesulfonic acid, o-toluenesulfonamide, phenylphosphonic acid, phenol, aniline, aminonaphthalenes, benzoic acid, benzophenone, and other compounds. By using a QqQ mass spectrometer, we observed that the protonated compounds produce arylium ions, which then react with N2 to form diazonium ions. The diazonium ion was produced with N2 but not with Ar in the collision cell, and its abundance increased with increasing N2 pressure. CONCLUSIONS Arylium ions generated from a wide variety of compounds in electrospray ionization tandem mass spectrometry may react with N2 to form diazonium ions. The abundance of the diazonium ions is affected by collision energy and N2 pressure. This reaction should be considered when annotating peaks in MS/MS libraries. Published in 2015. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Yuxue Liang
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Pedatsur Neta
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Yamil Simón-Manso
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Stephen E Stein
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
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34
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Martín-Sómer A, Yáñez M, Gaigeot MP, Spezia R. Unimolecular Fragmentation Induced By Low-Energy Collision: Statistically or Dynamically Driven? J Phys Chem A 2014; 118:10882-93. [DOI: 10.1021/jp5076059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Martín-Sómer
- Departamento
de Química, Facultad de Ciencias, Módulo
13. Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC. Cantoblanco, E-28049 Madrid, Spain
- Université d’Evry Val d’Essonne, UMR 8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
| | - Manuel Yáñez
- Departamento
de Química, Facultad de Ciencias, Módulo
13. Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC. Cantoblanco, E-28049 Madrid, Spain
| | - Marie-Pierre Gaigeot
- Université d’Evry Val d’Essonne, UMR 8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse
et Modélisation pour la Biologie et
l’Environnement, UMR 8587, Boulevard
F. Mitterrand, 91025 Evry Cedex, France
- Institut Universitaire de France (IUF), 103 Blvd St Michel, 75005 Paris, France
| | - Riccardo Spezia
- Université d’Evry Val d’Essonne, UMR 8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse
et Modélisation pour la Biologie et
l’Environnement, UMR 8587, Boulevard
F. Mitterrand, 91025 Evry Cedex, France
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