Dany Jeanne Dit Fouque

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

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Antony Memboeuf

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Alicia Maroto

Université de Bretagne Occidentale

Rémy Lartia

Département de Chimie Moléculaire

Bénédicte Douziech

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Aurore Fraix

Centre Hospitalier Régional et Universitaire de Nancy

ÁR

Ágnes Révész

HUN-REN Research Centre for Natural Sciences

Nicolas Le Poul

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Yves Le Mest

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Claudio Iacobucci

University of L'Aquila

Tibor András Rokob

HUN-REN Research Centre for Natural Sciences

Cooperative Institutions

Centre National de la Recherche Scientifique

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Université de Bretagne Occidentale

Université Européenne de Bretagne

Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques

Université Paris Cité

Hungarian Academy of Sciences

HUN-REN Research Centre for Natural Sciences

Institute of Organic Chemistry

Eötvös Loránd University

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Analyses structurale et quantitative de composés iso-mères/bares en mélange par spectrométrie de masse tandem et multi-étapes

Dany Jeanne Dit Fouque

Ces travaux de these sont consacres au developpement de nouvelles methodologies pour l’analyse structurale et quantitative de composes isomeres ou isobares en melange par spectrometrie de masse en tandem (MS/MS) ainsi que par la technique des ions survivants (SY). A l’aide de cette technique, nous avons developpe une methode de « purification collisionnelle en phase gaz » consistant a purifier un compose par fragmentation selective du contaminant isomere ou isobare afin de permettre l’analyse structurale et quantitative du compose d’interet. Nous avons montre que cette approche peut etre utilisee avec succes a la fois lors de l’etape d’excitation collisionnelle (CID) d’une experience MS/MS, mais egalement lors du processus d’ionisation (in-source CID). Utilisant cette approche MS/MS sur une fenetre de 15 m/z, nous avons ainsi pu quantifier, par la methode de l’etalon interne, un peptide trypsique malgre la presence d’un contaminant isobare. L’optimisation des performances de quantification pour la technique SY a ensuite ete etudiee sur des peptides isomeres topologiques en melange et comparee a l’analyse par microscopie infrarouge. Parmi les alcalins, alcalino-terreux et metaux de transition testes, nous avons obtenu les meilleurs resultats avec les adduits au cesium. Des resultats comparables a la technique infrarouge ont confirme la pertinence de notre approche avec de surcroit de meilleures performances analytiques, en particulier en terme de rapidite d’execution, de sensibilite, d’erreur de prediction et de limite de quantification.

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Phosphonodithioformate-amine coupling reaction: from basic discovery to application for the functionalization of liposomes

Phosphorus, sulfur, and silicon and the related elements (2021)

Montassar Khalil Dany Jeanne Dit Fouque Mathieu Berchel Aurore Fraix Salvatore Sortino

This short review article is dedicated to the Phosphonodithioformate-Amine Coupling (PAC) reaction. This reaction occurs by mixing phosphonodithioformate with amine without any catalyst and produces, according to a fast second order kinetics, phosphonothioamide. This reaction was applied to the functionalization of liposomes and opens new possibilities for the functionalization of synthetic or biologic materials.

Surface Modification

Coupling reaction

10.1080/10426507.2021.2012177

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LC-MS accurate quantification of a tryptic peptide co-eluted with an isobaric interference by using in-source collisional purification

Analytical and Bioanalytical Chemistry (2023)

Alicia Maroto Dany Jeanne Dit Fouque Rémy Lartia Antony Memboeuf

Isobaric process

Isobaric labeling

10.1007/s00216-023-04989-w

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Optimal Collision Energies and Bioinformatics Tools for Efficient Bottom-up Sequence Validation of Monoclonal Antibodies

Analytical Chemistry (2019)

Ágnes Révész Tibor András Rokob Dany Jeanne Dit Fouque Dániel Hüse Viktor Háda

Rigorous validation of amino acid sequence is fundamental in the characterization of original and biosimilar protein biopharmaceuticals. Widely accepted workflows are based on bottom-up mass spectrometry, and they often require multiple techniques and significant manual work. Here, we demonstrate that optimization of a set of tandem mass spectroscopy (MS/MS) collision energies and automated combination of all available information in the measurements can increase the sequence validated by one technique close to the inherent limits. We created a software (called "Serac") that consumes results of the Mascot database search engine and identifies the amino acids validated by bottom-up MS/MS experiments using the most rigorous, industrially acceptable definition of sequence coverage (we term this "confirmed sequence coverage"). The software can combine spectra at the level of amino acids or fragment ions to exploit complementarity, provides full transparency to justify validation, and reduces manual effort. With its help, we investigated collision energy dependence of confirmed sequence coverage of individual peptides and full proteins on trypsin-digested monoclonal antibody samples (rituximab and trastuzumab). We found the energy dependence to be modest, but we demonstrated the benefit of using spectra taken at multiple energies. We describe a workflow based on 2-3 LC-MS/MS runs, carefully selected collision energies, and a fragment ion level combination, which yields ∼85% confirmed sequence coverage, 25%-30% above that from a basic proteomics protocol. Further increase can mainly be expected from alternative digestion enzymes or fragmentation techniques, which can be seamlessly integrated to the processing, thereby allowing effortless validation of full sequences.

10.1021/acs.analchem.9b03362

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Purification and Quantification of an Isomeric Compound in a Mixture by Collisional Excitation in Multistage Mass Spectrometry Experiments

Analytical Chemistry (2016)

Dany Jeanne Dit Fouque Alicia Maroto Antony Memboeuf

The differentiation, characterization, and quantification of isomers and/or isobars in mixtures is a recurrent problem in mass spectrometry and more generally in analytical chemistry. Here we present a new strategy to assess the purity of a compound that is susceptible to be contaminated with another isomeric side-product in trace levels. Providing one of the isomers is available as pure sample, this new strategy allows the detection of isomeric contamination. This is done thanks to a "gas-phase collisional purification" inside an ion trap mass spectrometer paving the way for an improved analysis of at least similar samples. This strategy consists in using collision induced dissociation (CID) multistage mass spectrometry (MS2 and MS3) experiments and the survival yield (SY) technique. It has been successfully applied to mixtures of cyclic poly(L-lactide) (PLA) with increasing amounts of its linear topological isomer. Purification in gas phase of PLA mixtures was established based on SY curves obtained in MS3 mode: all samples gave rise to the same SY curve corresponding then to the pure cyclic component. This new strategy was sensitive enough to detect traces of linear PLA (<3%) in a sample of cyclic PLA that was supposedly pure according to other characterization techniques (1H NMR, MALDI-HRMS, and size-exclusion chromatography). Moreover, in this case, the presence of linear isomer was undetectable according to MS/MS or MS/MS/MS analysis only as fragment ions are also of the same m/z values. This type of approach could easily be implemented in hyphenated mass spectrometric techniques to improve the structural and quantitative analysis of complex samples.

Isobar

Quadrupole ion trap

Mass

Collision-induced dissociation

Characterization

10.1021/acs.analchem.6b03490

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Citations (32)

Structural and quantitative analysis of iso-meric/baric compounds in mixtures using tandem and multi-stage mass spectrometry.

Dany Jeanne Dit Fouque

Tandem

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Removal of isobaric interference using pseudo‐multiple reaction monitoring and energy‐resolved mass spectrometry for the isotope dilution quantification of a tryptic peptide

Journal of Mass Spectrometry (2024)

Alicia Maroto Dany Jeanne Dit Fouque Rémy Lartia Antony Memboeuf

Abstract Energy‐resolved mass spectrometry (ERMS) and an isotopically labelled internal standard were successfully combined to accurately quantify a tryptic peptide despite the presence of an isobaric interference. For this purpose, electrospray ionisation tandem mass spectrometry (ESI‐MS/MS) experiments were conducted into an ion trap instrument using an unconventional 8 m / z broadband isolation window, which encompassed both the tryptic peptide and its internal standard. Interference removal was assessed by determining an excitation voltage that was high enough to maintain a constant value for the analyte/internal standard peaks intensity ratio, thus ensuring accurate quantification even in the presence of isobaric contamination. Pseudo‐multiple reaction monitoring (MRM) was employed above this excitation voltage to quantify the trypic peptide. The internal standard calibration model showed no lack of fit and exhibited a linear dynamic range from 0.5 μM up to 2.5 μM. The detection limit was 0.08 μM. The accuracy of the method was evaluated by quantifying the tryptic peptide of three reference samples intentionally contaminated with the isobaric interference. All the reference samples were accurately quantified with ∼1% deviation despite the isobaric contamination. Furthermore, we have demonstrated that this methodology can also be applied to quantify the isobaric peptide by standard additions down to 0.2 μM. Finally, liquid chromatography ERMS (LC ERMS) experiments yielded similar results, suggesting the potential of the proposed methodology for analysing complex samples.

Isobaric process

Isobaric labeling

Isotope dilution

10.1002/jms.5025

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Selection of Collision Energies in Proteomics Mass Spectrometry Experiments for Best Peptide Identification: Study of Mascot Score Energy Dependence Reveals Double Optimum

Journal of Proteome Research (2018)

Ágnes Révész Tibor András Rokob Dany Jeanne Dit Fouque Lilla Turiák Antony Memboeuf

Collision energy is a key parameter determining the information content of beam-type collision induced dissociation tandem mass spectrometry (MS/MS) spectra, and its optimal choice largely affects successful peptide and protein identification in MS-based proteomics. For an MS/MS spectrum, quality of peptide match based on sequence database search, often characterized in terms of a single score, is a complex function of spectrum characteristics, and its collision energy dependence has remained largely unexplored. We carried out electrospray ionization-quadrupole-time of flight (ESI-Q-TOF)-MS/MS measurements on 2807 peptides from tryptic digests of HeLa and E. coli at 21 different collision energies. Agglomerative clustering of the resulting Mascot score versus energy curves revealed that only few of them display a single, well-defined maximum; rather, they feature either a broad plateau or two clear peaks. Nonlinear least-squares fitting of one or two Gaussian functions allowed the characteristic energies to be determined. We found that the double peaks and the plateaus in Mascot score can be associated with the different energy dependence of b- and y-type fragment ion intensities. We determined that the energies for optimum Mascot scores follow separate linear trends for the unimodal and bimodal cases with rather large residual variance even after differences in proton mobility are taken into account. This leaves room for experiment optimization and points to the possible influence of further factors beyond m/z.

Mascot

10.1021/acs.jproteome.7b00912

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Citations (18)

CCDC 981248: Experimental Crystal Structure Determination

The Cambridge Structural Database (2020)

Nicolas Le Poul Benoît Colasson Grégory Thiabaud Dany Jeanne Dit Fouque Claudio Iacobucci

10.5517/ccdc.csd.cc11y257

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Quantification of intramolecular click chemistry modified synthetic peptide isomers in mixtures using tandem mass spectrometry and the survival yield technique

Analytical and Bioanalytical Chemistry (2018)

Dany Jeanne Dit Fouque Rémy Lartia Alicia Maroto Antony Memboeuf

10.1007/s00216-018-1258-5

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Citations (17)