1
|
Damont A, Legrand A, Cao C, Fenaille F, Tabet JC. Hydrogen/deuterium exchange mass spectrometry in the world of small molecules. MASS SPECTROMETRY REVIEWS 2023; 42:1300-1331. [PMID: 34859466 DOI: 10.1002/mas.21765] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/07/2023]
Abstract
The combined use of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS), referred to as HDX-MS, is a powerful tool for exploring molecular edifices and has been used for over 60 years. Initially for structural and mechanistic investigation of low-molecular weight organic compounds, then to study protein structure and dynamics, then, the craze to study small molecules by HDX-MS accelerated and has not stopped yet. The purpose of this review is to present its different facets with particular emphasis on recent developments and applications. Reversible H/D exchanges of mobilizable protons as well as stable exchanges of non-labile hydrogen are considered whether they are taking place in solution or in the gas phase, or enzymatically in a biological media. Some fundamental principles are restated, especially for gas-phase processes, and an overview of recent applications, ranging from identification to quantification through the study of metabolic pathways, is given.
Collapse
Affiliation(s)
- Annelaure Damont
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Anaïs Legrand
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Chenqin Cao
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, France
| |
Collapse
|
2
|
Tabet JC, Gimbert Y, Damont A, Touboul D, Fenaille F, Woods AS. Combining Chemical Knowledge and Quantum Calculation for Interpreting Low-Energy Product Ion Spectra of Metabolite Adduct Ions: Sodiated Diterpene Diester Species as a Case Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2499-2504. [PMID: 34469144 PMCID: PMC8903029 DOI: 10.1021/jasms.1c00154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We investigated the product ion spectra of [M + Na]+ from diterpene diester species and low molecular mass metabolites analyzed by electrospray ionization (ESI). Mainly, the formation of protonated salt structures was proposed to explain the observed neutral losses of carboxylic acids. It also facilitates understanding sodium retention on product ions or on neutral losses. In addition, the occurrence of consecutive carboxylic acid losses is rather unexpected under resonant excitation conditions. Quantum calculation demonstrated that the exothermic character of such neutral losses can represent a relevant explanation. There is no doubt that the formation and role of the protonated salt structures will be helpful for a better understanding and software-assisted interpretation of tandem mass spectra from small molecules, especially in the ever-growing metabolomics field.
Collapse
Affiliation(s)
- 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
| | - Yves Gimbert
- Sorbonne Université, Faculté des Sciences et de l’Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058 Grenoble, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Amina S. Woods
- NIDA IRP, NIH Structural Biology Unit Integrative Neuroscience Branch, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- The Johns Hopkins University School of Medicine, Pharmacology and Molecular Sciences, Baltimore, MD 21205
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Abstract
High-yield, chromatography-free syntheses of a ferrocene-templated molecular cage and its Pd-bearing derivative are presented. The formation of a symmetric cage-type structure was confirmed by single-crystal X-ray diffraction analysis. The Pd-bearing cage was used as an innovative catalyst for the efficient synthesis of 1,1'-biphenyls under mild conditions. The presented catalyst is reusable and 1,1'-biphenyls can be obtained efficiently in a gram scale process.
Collapse
Affiliation(s)
- Artur Kasprzak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego Str. 3, 00-664 Warsaw, Poland.
| | - Piotr A Guńka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego Str. 3, 00-664 Warsaw, Poland.
| |
Collapse
|
5
|
Damont A, Olivier MF, Warnet A, Lyan B, Pujos-Guillot E, Jamin EL, Debrauwer L, Bernillon S, Junot C, Tabet JC, Fenaille F. Proposal for a chemically consistent way to annotate ions arising from the analysis of reference compounds under ESI conditions: A prerequisite to proper mass spectral database constitution in metabolomics. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:567-582. [PMID: 31083780 DOI: 10.1002/jms.4372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Nowadays, high-resolution mass spectrometry is widely used for metabolomic studies. Thanks to its high sensitivity, it enables the detection of a large range of metabolites. In metabolomics, the continuous quest for a metabolite identification as complete and accurate as possible has led during the last decade to an ever increasing development of public MS databases (including LC-MS data) concomitantly with bioinformatic tool expansion. To facilitate the annotation process of MS profiles obtained from biological samples, but also to ease data sharing, exchange, and exploitation, the standardization and harmonization of the way to describe and annotate mass spectra seemed crucial to us. Indeed, under electrospray (ESI) conditions, a single metabolite does not produce a unique ion corresponding to its protonated or deprotonated form but could lead to a complex mixture of signals. These MS signals result from the existence of different natural isotopologues of the same compound and also to the potential formation of adduct ions, homomultimeric and heteromultimeric ions, fragment ions resulting from "prompt" in-source dissociations. As a joint reflection process within the French Infrastructure for Metabolomics and Fluxomics (MetaboHUB) and with the purpose of developing a robust and exchangeable annotated MS database made from pure reference compounds (chemical standards) analysis, it appeared to us that giving the metabolomics community some clues to standardize and unambiguously annotate each MS feature was a prerequisite to data entry and further efficient querying of the mass spectral database. The use of a harmonized notation is also mandatory for interlaboratory MS data exchange. Additionally, thorough description of the variety of MS signals arising from the analysis of a unique metabolite might provide greater confidence on its annotation.
Collapse
Affiliation(s)
- Annelaure Damont
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Marie-Françoise Olivier
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Anna Warnet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Bernard Lyan
- Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, INRA, UNH, F-63000, Clermont-Ferrand, France
| | - Estelle Pujos-Guillot
- Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, INRA, UNH, F-63000, Clermont-Ferrand, France
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology), Metatoul-AXIOM platform, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Metatoul-AXIOM platform, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France
| | - Stéphane Bernillon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux-MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine-Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75005, Paris, France
| | - François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| |
Collapse
|