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Brunet TA, Clément Y, Calabrese V, Lemoine J, Geffard O, Chaumot A, Degli-Esposti D, Salvador A, Ayciriex S. Concomitant investigation of crustacean amphipods lipidome and metabolome during the molting cycle by Zeno SWATH data-independent acquisition coupled with electron activated dissociation and machine learning. Anal Chim Acta 2024; 1304:342533. [PMID: 38637034 DOI: 10.1016/j.aca.2024.342533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND DIA (Data-Independent Acquisition) is a powerful technique in Liquid Chromatography coupled with high-resolution tandem Mass Spectrometry (LC-MS/MS) initially developed for proteomics studies and recently emerging in metabolomics and lipidomics. It provides a comprehensive and unbiased coverage of molecules with improved reproducibility and quantitative accuracy compared to Data-Dependent Acquisition (DDA). Combined with the Zeno trap and Electron-Activated Dissociation (EAD), DIA enhances data quality and structural elucidation compared to conventional fragmentation under CID. These tools were applied to study the lipidome and metabolome of the freshwater amphipod Gammarus fossarum, successfully discriminating stages and highlighting significant biological features. Despite being underused, DIA, along with the Zeno trap and EAD, holds great potential for advancing research in the omics field. RESULTS DIA combined with the Zeno trap enhances detection reproducibility compared to conventional DDA, improving fragmentation spectra quality and putative identifications. LC coupled with Zeno-SWATH-DIA methods were used to characterize molecular changes in reproductive cycle of female gammarids. Multivariate data analysis including Principal Component Analysis and Partial Least Square Discriminant Analysis successfully identified significant features. EAD fragmentation helped to identify unknown features and to confirm their molecular structure using fragmentation spectra database annotation or machine learning. EAD database matching accurately annotated five glycerophospholipids, including the position of double bonds on fatty acid chain moieties. SIRIUS database predicted structures of unknown features based on experimental fragmentation spectra to compensate for database incompleteness. SIGNIFICANCE Reproducible detection of features and confident identification of putative compounds are pivotal stages within analytical pipelines. The DIA approach combined with Zeno pulsing enhances detection sensitivity and targeted fragmentation with EAD in positive polarity provides orthogonal fragmentation information. In our study, Zeno-DIA and EAD thereby facilitated a comprehensive and insightful exploration of pertinent biological molecules associated with the reproductive cycle of gammarids. The developed methodology holds great promises for identifying informative biomarkers on the health status of an environmental sentinel species.
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Affiliation(s)
- Thomas Alexandre Brunet
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Yohann Clément
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Valentina Calabrese
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625, Villeurbanne, France
| | | | - Arnaud Salvador
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Sophie Ayciriex
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France.
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Girod M, Arquier D, Helms A, Juetten K, Brodbelt JS, Lemoine J, MacAleese L. Characterization of Phosphorylated Peptides by Electron-Activated and Ultraviolet Dissociation Mass Spectrometry: A Comparative Study with Collision-Induced Dissociation. J Am Soc Mass Spectrom 2024; 35:1040-1054. [PMID: 38626331 DOI: 10.1021/jasms.4c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.
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Affiliation(s)
- Marion Girod
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Delphine Arquier
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Juetten
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jérôme Lemoine
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Luke MacAleese
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, F-69100 Villeurbanne, France
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Deforet F, Jehanne Q, Bénéjat L, Aptel J, Prat R, Desbiolles C, Ducournau A, Jauvain M, Bonnet R, Vandenesch F, Lemoine J, Lehours P. Combined genomic-proteomic approach in the identification of Campylobacter coli amoxicillin-clavulanic acid resistance mechanism in clinical isolates. Front Microbiol 2023; 14:1285236. [PMID: 38029165 PMCID: PMC10666280 DOI: 10.3389/fmicb.2023.1285236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Aminopenicillins resistance among Campylobacter jejuni and Campylobacter coli strains is associated with a single mutation in the promoting region of a chromosomal beta-lactamase blaOXA61, allowing its expression. Clavulanic acid is used to restore aminopenicillins activity in case of blaOXA61 expression and has also an inherent antimicrobial activity over Campylobacter spp. Resistance to amoxicillin-clavulanic acid is therefore extremely rare among these species: only 0.1% of all Campylobacter spp. analyzed in the French National Reference Center these last years (2017-2022). Material and methods Whole genome sequencing with bioinformatic resistance identification combined with mass spectrometry (MS) was used to identify amoxicillin-acid clavulanic resistance mechanism in Campylobacters. Results A G57T mutation in blaOXA61 promoting region was identified in all C. jejuni and C. coli ampicillin resistant isolates and no mutation in ampicillin susceptible isolates. Interestingly, three C. coli resistant to both ampicillin and amoxicillin-clavulanic acid displayed a supplemental deletion in the promoting region of blaOXA61 beta-lactamase, at position A69. Using MS, a significant difference in the expression of BlaOXA61 was observed between these three isolates and amoxicillin-clavulanic acid susceptible C. coli. Conclusion A combined genomics/proteomics approach allowed here to identify a rare putative resistance mechanism associated with amoxicillin-clavulanic acid resistance for C. coli.
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Affiliation(s)
- Francis Deforet
- Institut des Sciences Analytiques, Université Claude Bernard Lyon 1, Lyon, France
| | - Quentin Jehanne
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Lucie Bénéjat
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Johanna Aptel
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Roxane Prat
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Chloé Desbiolles
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Astrid Ducournau
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Marine Jauvain
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, Université de Bordeaux, Bordeaux, France
| | - Richard Bonnet
- Laboratoire Associé CNR de la Résistance aux Antibiotiques, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université Claude Bernard Lyon 1, Lyon, France
| | - Philippe Lehours
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, Université de Bordeaux, Bordeaux, France
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Cochard C, Caby M, Gruau P, Madec E, Marceau M, Macavei I, Lemoine J, Le Danvic C, Bouchart F, Delrue B, Bontemps-Gallo S, Lacroix JM. Emergence of the Dickeya genus involved duplication of the OmpF porin and the adaptation of the EnvZ-OmpR signaling network. Microbiol Spectr 2023; 11:e0083323. [PMID: 37642428 PMCID: PMC10581057 DOI: 10.1128/spectrum.00833-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/06/2023] [Indexed: 08/31/2023] Open
Abstract
Genome evolution, and more specifically gene duplication, is a key process shaping host-microorganism interaction. The conserved paralogs usually provide an advantage to the bacterium to thrive. If not, these genes become pseudogenes and disappear. Here, we show that during the emergence of the genus Dickeya, the gene encoding the porin OmpF was duplicated. Our results show that the ompF2 expression is deleterious to the virulence of Dickeya dadantii, the agent causing soft rot disease. Interestingly, ompF2 is regulated while ompF is constitutive but activated by the EnvZ-OmpR two-component system. In vitro, acidic pH triggers the system. The pH measured in four eudicotyledons increased from an initial pH of 5.5 to 7 within 8 h post-infection. Then, the pH decreased to 5.5 at 10 h post-infection and until full maceration of the plant tissue. Yet, the production of phenolic acids by the plant's defenses prevents the activation of the EnvZ-OmpR system to avoid the ompF2 expression even though environmental conditions should trigger this system. We highlight that gene duplication in a pathogen is not automatically an advantage for the infectious process and that, there was a need for our model organism to adapt its genetic regulatory networks to conserve these duplicated genes. IMPORTANCE Dickeya species cause various diseases in a wide range of crops and ornamental plants. Understanding the molecular program that allows the bacterium to colonize the plant is key to developing new pest control methods. Unlike other enterobacterial pathogens, Dickeya dadantii, the causal agent of soft rot disease, does not require the EnvZ-OmpR system for virulence. Here, we showed that during the emergence of the genus Dickeya, the gene encoding the porin OmpF was duplicated and that the expression of ompF2 was deleterious for virulence. We revealed that while the EnvZ-OmpR system was activated in vitro by acidic pH and even though the pH was acidic when the plant is colonized, this system was repressed by phenolic acid (generated by the plant's defenses). These results provide a unique- biologically relevant-perspective on the consequence of gene duplication and the adaptive nature of regulatory networks to retain the duplicated gene.
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Affiliation(s)
- Clémence Cochard
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marine Caby
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Peggy Gruau
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Edwige Madec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Michael Marceau
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Iulia Macavei
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, Villeurbanne, France
| | - Jérôme Lemoine
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, Villeurbanne, France
| | - Chrystelle Le Danvic
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- R&D Department, ALLICE, Paris, France
| | - Franck Bouchart
- Université Polytechnique Hauts-de-France, EA 2443 - LMCPA - Laboratoire des Matériaux Céramiques et Procédés Associés, Valenciennes, France
| | - Brigitte Delrue
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Bontemps-Gallo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Marie Lacroix
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Brunet TA, Ayciriex S, Arquier D, Lemoine J, Randon J, Salvador A. Scout triggered multiple reaction monitoring mass spectrometry for the rapid transfer of large multiplexed targeted methods in metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123849. [PMID: 37634392 DOI: 10.1016/j.jchromb.2023.123849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023]
Abstract
The field of metabolomics based on mass spectrometry has grown considerably in recent years due to the need to detect and, above all, quantify a very large number of metabolites, simultaneously. Up to now, targeted multiplexed analysis on complex samples by Liquid Chromatography coupled with tandem Mass Spectrometry (LC-MS/MS) has relied almost exclusively on compound detection based on absolute retention times, as in the Scheduled-MRM (sMRM) approach. Those methods turn out to be poorly transferable from one instrument to another and result in a time-consuming and tedious method development involving a significant number of critical parameters that need specific re-optimisation. To address this challenge, we introduce a novel acquisition mode called scout-triggered MRM (stMRM). In stMRM, a marker transition is used to trigger MS analysis for a group of dependent target analytes. These marker transitions are strategically distributed throughout the chromatographic run, and the dependent analytes are associated based on their retention times. The result is a targeted assay that remains robust even in the presence of retention time shifts. A 3 to 5-fold increase in the number of detected transitions associated to plasma metabolites was obtained when transferring from a direct application of a published sMRM to a stMRM method. This significant improvement highlights the universal applicability of the stMRM method, as it can be implemented on any LC system without the need for extensive method development. We subsequently illustrate the robustness of stMRM in modified chromatographic elution conditions. Despite a large change in metabolite's selectivity, the multiplexed assay successfully recovered 70% of the monitored transitions when consequently modifying the gradient method. These findings demonstrate the versatility and adaptability of stMRM, opening new avenues for the development of highly multiplexed LC-MS/MS methods in metabolomics. These methods are characterized by their analytical transparency and straightforward implementation using existing literature data.
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Affiliation(s)
- Thomas Alexandre Brunet
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Sophie Ayciriex
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Delphine Arquier
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Jérôme Randon
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Arnaud Salvador
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.
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Pivard M, Bastien S, Macavei I, Mouton N, Rasigade JP, Couzon F, Youenou B, Tristan A, Carrière R, Moreau K, Lemoine J, Vandenesch F. Targeted proteomics links virulence factor expression with clinical severity in staphylococcal pneumonia. Front Cell Infect Microbiol 2023; 13:1162617. [PMID: 37077532 PMCID: PMC10106754 DOI: 10.3389/fcimb.2023.1162617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionThe bacterial pathogen Staphylococcus aureus harbors numerous virulence factors that impact infection severity. Beyond virulence gene presence or absence, the expression level of virulence proteins is known to vary across S. aureus lineages and isolates. However, the impact of expression level on severity is poorly understood due to the lack of high-throughput quantification methods of virulence proteins.MethodsWe present a targeted proteomic approach able to monitor 42 staphylococcal proteins in a single experiment. Using this approach, we compared the quantitative virulomes of 136 S. aureus isolates from a nationwide cohort of French patients with severe community-acquired staphylococcal pneumonia, all requiring intensive care. We used multivariable regression models adjusted for patient baseline health (Charlson comorbidity score) to identify the virulence factors whose in vitro expression level predicted pneumonia severity markers, namely leukopenia and hemoptysis, as well as patient survival.ResultsWe found that leukopenia was predicted by higher expression of HlgB, Nuc, and Tsst-1 and lower expression of BlaI and HlgC, while hemoptysis was predicted by higher expression of BlaZ and HlgB and lower expression of HlgC. Strikingly, mortality was independently predicted in a dose-dependent fashion by a single phage-encoded virulence factor, the Panton-Valentine leucocidin (PVL), both in logistic (OR 1.28; 95%CI[1.02;1.60]) and survival (HR 1.15; 95%CI[1.02;1.30]) regression models.DiscussionThese findings demonstrate that the in vitro expression level of virulence factors can be correlated with infection severity using targeted proteomics, a method that may be adapted to other bacterial pathogens.
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Affiliation(s)
- Mariane Pivard
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Sylvère Bastien
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Iulia Macavei
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Nicolas Mouton
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Florence Couzon
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Benjamin Youenou
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Anne Tristan
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Romain Carrière
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
- *Correspondence: François Vandenesch,
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Faugere J, Brunet TA, Clément Y, Espeyte A, Geffard O, Lemoine J, Chaumot A, Degli-Esposti D, Ayciriex S, Salvador A. Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum. Talanta 2023; 253:123806. [PMID: 36113334 DOI: 10.1016/j.talanta.2022.123806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/24/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.
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Affiliation(s)
- Julien Faugere
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Thomas Alexandre Brunet
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Yohann Clément
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | | | - Sophie Ayciriex
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France.
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Amor M, Lemoine J, Angioi M, Breton C, Chati Z, Simon JP, Maigrat CH. Intravascular lithotripsy for heavily calcified peripheral artery lesions. Preliminary experience. Archives of Cardiovascular Diseases Supplements 2023. [DOI: 10.1016/j.acvdsp.2022.10.214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Relative quantification of sulfenic acids in plasma proteins using differential labelling and mass spectrometry coupled with 473 nm photo-dissociation analysis: A multiplexed approach applied to an Alzheimer's disease cohort. Talanta 2022; 250:123745. [PMID: 35870285 DOI: 10.1016/j.talanta.2022.123745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 10/17/2022]
Abstract
Cysteine (Cys) is subject to a variety of reversible post-translational modifications such as formation of sulfenic acid (Cys-SOH). If this modification is often involved in normal biological activities, it can also be the result of oxidative damage. Indeed, oxidative stress yields abnormal cysteine oxidations that affect protein function and structure and can lead to neurodegenerative diseases. In a context of population ageing, validation of novel biomarkers for detection of neurodegenerative diseases is important. However, Cys-SOH proteins investigation in large human cohorts is challenging due to their low abundance and lability under endogenous conditions. To improve the detection specificity towards the oxidized protein subpopulation, we developed a method that makes use of a mass spectrometer coupled with visible laser induced dissociation (LID) to add a stringent optical specificity to the mass selectivity. Since peptides do not naturally absorb in the visible range, this approach relies on the proper chemical derivatization of Cys-SOH with a chromophore functionalized with a cyclohexanedione. To compensate for the significant variability in total protein expression within the samples and any experimental bias, a normalizing strategy using free thiol (Cys-SH) cysteine peptides derivatized with a maleimide chromophore as internal references was used. Thanks to the differential tagging, oxidative ratios were then obtained for 69 Cys-containing peptides from 19 proteins tracked by parallel reaction monitoring (PRM) LID, in a cohort of 49 human plasma samples from Alzheimer disease (AD) patients. A statistical analysis indicated that, for the proteins monitored, the Cys oxidative ratio does not correlate with the diagnosis of AD. Nevertheless, the PRM-LID method allows the unbiased, sensitive and robust relative quantification of Cys oxidation within cohorts of samples.
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Affiliation(s)
- Jean-Valery Guillaubez
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Delphine Pitrat
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Yann Bretonnière
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marion Girod
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France.
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10
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Mohan P, Lemoine J, Trotter C, Rakova I, Billings P, Peacock S, Kao C, Wang Y, Xia F, Eng CM, Benn P. Clinical experience with non-invasive prenatal screening for single-gene disorders. Ultrasound Obstet Gynecol 2022; 59:33-39. [PMID: 34358384 PMCID: PMC9302116 DOI: 10.1002/uog.23756] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 05/10/2023]
Abstract
OBJECTIVE To assess the performance of a non-invasive prenatal screening test (NIPT) for a panel of dominant single-gene disorders (SGD) with a combined population incidence of 1 in 600. METHODS Cell-free fetal DNA isolated from maternal plasma samples accessioned from 14 April 2017 to 27 November 2019 was analyzed by next-generation sequencing, targeting 30 genes, to look for pathogenic or likely pathogenic variants implicated in 25 dominant conditions. The conditions included Noonan spectrum disorders, skeletal disorders, craniosynostosis syndromes, Cornelia de Lange syndrome, Alagille syndrome, tuberous sclerosis, epileptic encephalopathy, SYNGAP1-related intellectual disability, CHARGE syndrome, Sotos syndrome and Rett syndrome. NIPT-SGD was made available as a clinical service to women with a singleton pregnancy at ≥ 9 weeks' gestation, with testing on maternal and paternal genomic DNA to assist in interpretation. A minimum of 4.5% fetal fraction was required for test interpretation. Variants identified in the mother were deemed inconclusive with respect to fetal carrier status. Confirmatory prenatal or postnatal diagnostic testing was recommended for all screen-positive patients and follow-up information was requested. The screen-positive rates with respect to the clinical indication for testing were evaluated. RESULTS A NIPT-SGD result was available for 2208 women, of which 125 (5.7%) were positive. Elevated test-positive rates were observed for referrals with a family history of a disorder on the panel (20/132 (15.2%)) or a primary indication of fetal long-bone abnormality (60/178 (33.7%)), fetal craniofacial abnormality (6/21 (28.6%)), fetal lymphatic abnormality (20/150 (13.3%)) or major fetal cardiac defect (4/31 (12.9%)). For paternal age ≥ 40 years as a sole risk factor, the test-positive rate was 2/912 (0.2%). Of the 125 positive cases, follow-up information was available for 67 (53.6%), with none classified as false-positive. No false-negative cases were identified. CONCLUSIONS NIPT can assist in the early detection of a set of SGD, particularly when either abnormal ultrasound findings or a family history is present. Additional clinical studies are needed to evaluate the optimal design of the gene panel, define target populations and assess patient acceptability. NIPT-SGD offers a safe and early prenatal screening option. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
| | | | | | | | | | | | | | - Y. Wang
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - F. Xia
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - C. M. Eng
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - P. Benn
- Department of Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
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11
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Abcha F, Lemoine J, Bizot M, Amor M. Rotational atherectomy: In hospital results of a real life experience for the treatment of complex calcified coronary lesions. Archives of Cardiovascular Diseases Supplements 2022. [DOI: 10.1016/j.acvdsp.2021.09.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Michelon H, Larabi IA, Lemoine J, Alvarez JC, Genevée A, Lillo-Lelouet A, Azouvi P, Lefèvre-Dognin C, Paquereau J. Atropine-induced toxicity after off-label sublingual administration of eyedrop for sialorrhoea treatment in neurological disabled patients. Br J Clin Pharmacol 2021; 87:3364-3369. [PMID: 33521988 DOI: 10.1111/bcp.14757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022] Open
Abstract
Sialorrhea is a troublesome and disabling symptom defined by the unintentional loss of saliva from the mouth, usually associated with swallowing disorders. Today there is no consensus about the management of sialorrhoea, but off-label use of ophthalmic atropine eyedrop administered sublingually may offer benefits, despite limited safety data. We report 2 cases of atropine overdose after sublingual administration illustrating that atropine can expose to severe adverse effects when administered sublingually. The noncompartmental pharmacokinetic study of atropine performed in 1 patient highlighted that systemic absorption of sublingual atropine was effective (Cmax [1 h] = 2.2 ng mL-1 ; approximately) after a single dose of 1 mg.
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Affiliation(s)
- Hugues Michelon
- Service de Pharmacie, Hôpital Sainte-Périne, APHP. Université Paris-Saclay, Paris, France.,Service de Pharmacie, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
| | - Islam Amine Larabi
- Service de Pharmacologie - Toxicologie, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
| | - Jérôme Lemoine
- Unité de Soins de Rééducation Post-Réanimation, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
| | - Jean-Claude Alvarez
- Service de Pharmacologie - Toxicologie, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
| | - Anne Genevée
- Unité de Soins de Rééducation Post-Réanimation, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
| | - Agnès Lillo-Lelouet
- Centre Régional de Pharmacovigilance de Paris, Hôpital Européen Georges Pompidou, AP-HP.Centre - Université de Paris, Paris, France
| | - Philippe Azouvi
- Unité de Soins de Rééducation Post-Réanimation, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
| | - Clémence Lefèvre-Dognin
- Unité de Soins de Rééducation Post-Réanimation, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France.,Unité de Soins Prolongés Complexes, Hôpital Sainte-Périne, APHP. Université Paris-Saclay, Paris, France
| | - Julie Paquereau
- Unité de Soins de Rééducation Post-Réanimation, Hôpital Raymond Poincaré, APHP. Université Paris-Saclay, Garches, France
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13
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Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Unbiased Detection of Cysteine Sulfenic Acid by 473 nm Photodissociation Mass Spectrometry: Toward Facile In Vivo Oxidative Status of Plasma Proteins. Anal Chem 2021; 93:2907-2915. [PMID: 33522244 DOI: 10.1021/acs.analchem.0c04484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine (Cys) is prone to diverse post-translational modifications in proteins, including oxidation into sulfenic acid (Cys-SOH) by reactive oxygen species generated under oxidative stress. Detection of low-concentration and metastable Cys-SOH within complex biological matrices is challenging due to the dynamic concentration range of proteins in the samples. Herein, visible laser-induced dissociation (LID) implemented in a mass spectrometer was used for streamlining the detection of Cys oxidized proteins owing to proper derivatization of Cys-SOH with a chromophore tag functionalized with a cyclohexanedione group. Once grafted, peptides undergo a high fragmentation yield under LID, leading concomitantly to informative backbone ions and to a chromophore reporter ion. Seventy-nine percent of the Cys-containing tryptic peptides derived from human serum albumin and serotransferrin tracked by parallel reaction monitoring (PRM) were detected as targets subjected to oxidation. These candidates as well as Cys-containing peptides predicted by in silico trypsin digestion of five other human plasma proteins were then tracked in real plasma samples to pinpoint the endogenous Cys-SOH subpopulation. Most of the targeted peptides were detected in all plasma samples by LID-PRM, with significant differences in their relative amounts. By eliminating the signal of interfering co-eluted compounds, LID-PRM surpasses conventional HCD (higher-energy collisional dissociation)-PRM in detecting grafted Cys-SOH-containing peptides and allows now to foresee clinical applications in large human cohorts.
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Affiliation(s)
- Jean-Valery Guillaubez
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Delphine Pitrat
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Yann Bretonnière
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Marion Girod
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
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14
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Leprêtre M, Palos-Ladeiro M, Faugere J, Almunia C, Lemoine J, Armengaud J, Geffard A, Salvador A. From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha. Anal Bioanal Chem 2020; 412:7333-7347. [DOI: 10.1007/s00216-020-02868-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
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15
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Salvador A, Carrière R, Ayciriex S, Margoum C, Leblanc Y, Lemoine J. Scout-multiple reaction monitoring: A liquid chromatography tandem mass spectrometry approach for multi-residue pesticide analysis without time scheduling. J Chromatogr A 2020; 1621:461046. [DOI: 10.1016/j.chroma.2020.461046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/15/2020] [Accepted: 03/12/2020] [Indexed: 11/24/2022]
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16
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Ayciriex S, Carrière R, Bardet C, Blanc JCYL, Salvador A, Fortin T, Lemoine J. Streamlined Development of Targeted Mass Spectrometry‐Based Method Combining Scout‐MRM and a Web‐Based Tool Indexed with Scout Peptides. Proteomics 2020; 20:e1900254. [DOI: 10.1002/pmic.201900254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 12/10/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Sophie Ayciriex
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
| | - Romain Carrière
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
| | - Chloé Bardet
- Anaquant 5 rue de la Doua F‐69100 Villeurbanne France
| | | | - Arnaud Salvador
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
| | - Tanguy Fortin
- Anaquant 5 rue de la Doua F‐69100 Villeurbanne France
| | - Jérôme Lemoine
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
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17
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Solla F, Lemoine J, Musoff C, Bertoncelli C, Rampal V. Surgical treatment of congenital pseudarthrosis of the forearm: Review and quantitative analysis of individual patient data. Hand Surgery and Rehabilitation 2019; 38:233-241. [DOI: 10.1016/j.hansur.2019.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/14/2019] [Accepted: 06/08/2019] [Indexed: 10/26/2022]
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18
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Charnot A, Gouveia D, Ayciriex S, Lemoine J, Armengaud J, Almunia C, Chaumot A, Geffard O, Salvador A. On-Line Solid Phase Extraction Liquid Chromatography-Mass Spectrometry Method for Multiplexed Proteins Quantitation in an Ecotoxicology Test Specie: Gammarus fossarum. J Appl Bioanal 2018. [DOI: 10.17145/jab.18.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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19
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Garcia L, Girod M, Rompais M, Dugourd P, Carapito C, Lemoine J. Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset. Anal Chem 2018; 90:3928-3935. [PMID: 29465226 DOI: 10.1021/acs.analchem.7b04821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Thanks to comprehensive and unbiased sampling of all precursor ions, the interest to move toward bottom-up proteomic with data-independent acquisition (DIA) is continuously growing. DIA offers precision and reproducibility performances comparable to true targeted methods but has the advantage of enabling retrospective data testing with the hypothetical presence of new proteins of interest. Nonetheless, the chimeric nature of DIA MS/MS spectra inherent to concomitant transmission of a multiplicity of precursor ions makes the confident identification of peptides often challenging, even with spectral library-based extraction strategy. The introduction of specificity at the fragmentation step upon ultraviolet or visible laser-induced dissociation (LID) range targeting only the subset of cysteine-containing peptides (Cys-peptide) has been proposed as an option to streamline and reduce the search space. Here, we describe the first coupling between DIA and visible LID at 473 nm to test for the presence of Cys-peptides with a peptide-centric approach. As a test run, a spectral library was built for a pool of Cys-synthetic peptides used as surrogates of human kinases (1 peptide per protein). By extracting ion chromatograms of query standard and kinase peptides spiked at different concentration levels in an Escherichia coli proteome lysate, DIA-LID demonstrates a dynamic range of detection of at least 3 decades and coefficients of precision better than 20%. Finally, the spectral library was used to search for endogenous kinases in human cellular extract.
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Affiliation(s)
- Lény Garcia
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
| | - Marion Girod
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC , Université de Strasbourg, CNRS , UMR 7178, 25 rue Becquerel , 67087 Strasbourg , France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC , Université de Strasbourg, CNRS , UMR 7178, 25 rue Becquerel , 67087 Strasbourg , France
| | - Jérôme Lemoine
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
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20
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Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. J Am Soc Mass Spectrom 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
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21
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Garcia L, Lemoine J, Dugourd P, Girod M. Fragmentation patterns of chromophore-tagged peptides in visible laser induced dissociation. Rapid Commun Mass Spectrom 2017; 31:1985-1992. [PMID: 28884878 DOI: 10.1002/rcm.7984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Tandem mass spectrometry (MS/MS) is the pivotal tool for protein structural characterization and quantification. Identification relies on the fragmentation step of tryptic peptides in bottom-up strategy. Specificity of fragmentation can be obtained using laser-induced dissociation (LID) in the visible range, after tagging of the targeted peptides with an adequate chromophore. Backbone fragmentation is required to obtain specific fragments and confident identification. We present herein a study of fragmentation patterns of chromophore-tagged peptides in LID, showing the potential of LID methodology to provide the maximum number of fragments for further identification and quantification. METHODS A total of 401 cysteine-containing tryptic peptides originating from the human proteome were derivatizated on the thiol group of cysteine with a Dabcyl maleimide chromophore, which has a high photo-absorption cross section at 473 nm. The derivatized peptides were then analyzed by LID at 473 nm on a Q Exactive instrument. RESULTS LID spectra present a characteristic fragment at m/z 252.112 for all precursors. This product ion arises from the internal dissociation of the Dabcyl chromophore. Several peptide-backbone fragment ions are also detected. Results show the quasi absence of fragmentation at the cysteine site. This indicates that part of the energy must be redistributed across the entire system despite excitation initially localized at the chromophore. Indeed, the fragmentation mainly occurs at 3 to 5 amino acids from the derivatized cysteine residue. CONCLUSIONS LID of derivatized cysteine-containing peptides displays the initial fragmentation of the chromophore. As energy is redistributed all along the peptide sequence, fragmentation of the peptide backbone is also observed. Thus, LID of chromophore-tagged peptides produces adequate fragment ions, allowing both good sequence coverage for a greater confidence of identification, and a large choice of transitions for specific quantification.
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Affiliation(s)
- Lény Garcia
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Jérôme Lemoine
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Philippe Dugourd
- Univ de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, VILLEURBANNE, France
| | - Marion Girod
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
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22
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Ahern D, Lemoine J, Walker J, Saucier J. Ethnicity reporting and carrier screening. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Rougemont B, Bontemps Gallo S, Ayciriex S, Carrière R, Hondermarck H, Lacroix JM, Le Blanc JCY, Lemoine J. Scout-MRM: Multiplexed Targeted Mass Spectrometry-Based Assay without Retention Time Scheduling Exemplified by Dickeya dadantii Proteomic Analysis during Plant Infection. Anal Chem 2017; 89:1421-1426. [PMID: 28029036 DOI: 10.1021/acs.analchem.6b03201] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Targeted mass spectrometry of a surrogate peptide panel is a powerful method to study the dynamics of protein networks, but chromatographic time scheduling remains a major limitation for dissemination and implementation of robust and large multiplexed assays. We unveil a Multiple Reaction Monitoring method (Scout-MRM) where the use of spiked scout peptides triggers complex transition lists, regardless of the retention time of targeted surrogate peptides. The interest of Scout-MRM method regarding the retention time independency, multiplexing capability, reproducibility, and putative interest in facilitating method transfer was illustrated by a 782-peptide-plex relative assay targeting 445 proteins of the phytopathogen Dickeya dadantii during plant infection.
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Affiliation(s)
- Blandine Rougemont
- Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , CNRS UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Sébastien Bontemps Gallo
- Université de Lille, CNRS, UMR 8576 , Unité de Glycobiologie Structurale et Fonctionnelle, F 59000 Lille, France
| | - Sophie Ayciriex
- Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , CNRS UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Romain Carrière
- Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , CNRS UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, University of Newcastle , Callaghan, NSW 2308, Australia
| | - Jean Marie Lacroix
- Université de Lille, CNRS, UMR 8576 , Unité de Glycobiologie Structurale et Fonctionnelle, F 59000 Lille, France
| | | | - Jérôme Lemoine
- Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , CNRS UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
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Halim MA, Girod M, MacAleese L, Lemoine J, Antoine R, Dugourd P. Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization. J Am Soc Mass Spectrom 2016; 27:1435-42. [PMID: 27287047 PMCID: PMC5031736 DOI: 10.1007/s13361-016-1419-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 05/10/2023]
Abstract
Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits to promote a comprehensive portrait of protein characterization. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69100, Villeurbanne, France
| | - Luke MacAleese
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69100, Villeurbanne, France
| | - Rodolphe Antoine
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France.
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Gaubert A, Jeudy J, Rougemont B, Bordes C, Lemoine J, Casabianca H, Salvador A. Identification and absolute quantification of enzymes in laundry detergents by liquid chromatography tandem mass spectrometry. Anal Bioanal Chem 2016; 408:4669-81. [PMID: 27098933 DOI: 10.1007/s00216-016-9550-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/24/2016] [Accepted: 04/05/2016] [Indexed: 11/30/2022]
Abstract
In a stricter legislative context, greener detergent formulations are developed. In this way, synthetic surfactants are frequently replaced by bio-sourced surfactants and/or used at lower concentrations in combination with enzymes. In this paper, a LC-MS/MS method was developed for the identification and quantification of enzymes in laundry detergents. Prior to the LC-MS/MS analyses, a specific sample preparation protocol was developed due to matrix complexity (high surfactant percentages). Then for each enzyme family mainly used in detergent formulations (protease, amylase, cellulase, and lipase), specific peptides were identified on a high resolution platform. A LC-MS/MS method was then developed in selected reaction monitoring (SRM) MS mode for the light and corresponding heavy peptides. The method was linear on the peptide concentration ranges 25-1000 ng/mL for protease, lipase, and cellulase; 50-1000 ng/mL for amylase; and 5-1000 ng/mL for cellulase in both water and laundry detergent matrices. The application of the developed analytical strategy to real commercial laundry detergents enabled enzyme identification and absolute quantification. For the first time, identification and absolute quantification of enzymes in laundry detergent was realized by LC-MS/MS in a single run. Graphical Abstract Identification and quantification of enzymes by LC-MS/MS.
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Affiliation(s)
- Alexandra Gaubert
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
| | - Jérémy Jeudy
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Blandine Rougemont
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Claire Bordes
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Hervé Casabianca
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Arnaud Salvador
- Université de Lyon, Institut des Sciences Analytiques UMR 5280 CNRS, Université Claude Bernard Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
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Rougemont B, Fonbonne C, Lemoine J, Bourgeaux V, Salvador A. Liquid chromatography coupled to tandem mass spectrometry for the analysis of inositol hexaphosphate after solid-phase extraction. J LIQ CHROMATOGR R T 2016. [DOI: 10.1080/10826076.2016.1169427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Blandine Rougemont
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France; bERYTECH Pharma, Lyon, France
| | - Catherine Fonbonne
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France; bERYTECH Pharma, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France; bERYTECH Pharma, Lyon, France
| | | | - Arnaud Salvador
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France; bERYTECH Pharma, Lyon, France
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Halim MA, Girod M, MacAleese L, Lemoine J, Antoine R, Dugourd P. 213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns. J Am Soc Mass Spectrom 2016; 27:474-86. [PMID: 26545767 DOI: 10.1007/s13361-015-1297-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 05/25/2023]
Abstract
Characterization of acidic peptides and proteins is greatly hindered due to lack of suitable analytical techniques. Here we present the implementation of 213 nm ultraviolet photodissociation (UVPD) in high-resolution quadrupole-Orbitrap mass spectrometer in negative polarity for peptide anions. Radical-driven backbone fragmentation provides 22 distinctive fragment ion types, achieving the complete sequence coverage for all reported peptides. Hydrogen-deficient radical anion not only promotes the cleavage of Cα-C bond but also stimulates the breaking of N-Cα and C-N bonds. Radical-directed loss of small molecules and specific side chain of amino acids are detected in these experiments. Radical containing side chain of amino acids (Tyr, Ser, Thr, and Asp) may possibly support the N-Cα backbone fragmentation. Proline comprising peptides exhibit the unusual fragment ions similar to reported earlier. Interestingly, basic amino acids such as Arg and Lys also stimulated the formation of abundant b and y ions of the related peptide anions. Loss of hydrogen atom from the charge-reduced radical anion and fragment ions are rationalized by time-dependent density functional theory (TDDFT) calculation, locating the potential energy surface (PES) of ππ* and repulsive πσ* excited states of a model amide system.
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Affiliation(s)
- Mohammad A Halim
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Marion Girod
- Institut des Sciences Analytiques, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Luke MacAleese
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Rodolphe Antoine
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.
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Rougemont B, Simon R, Carrière R, Biarc J, Fonbonne C, Salvador A, Huillet C, Berard Y, Adam O, Manin C, Lemoine J. Absolute quantification of dengue virus serotype 4 chimera vaccine candidate in Vero cell culture by targeted mass spectrometry. Proteomics 2015. [DOI: 10.1002/pmic.201500101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Blandine Rougemont
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Romain Simon
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Romain Carrière
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Jordane Biarc
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Catherine Fonbonne
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Arnaud Salvador
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Céline Huillet
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Yves Berard
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Olivier Adam
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Catherine Manin
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
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Girod M, Biarc J, Enjalbert Q, Salvador A, Antoine R, Dugourd P, Lemoine J. Implementing visible 473 nm photodissociation in a Q-Exactive mass spectrometer: towards specific detection of cysteine-containing peptides. Analyst 2015; 139:5523-30. [PMID: 25197743 DOI: 10.1039/c4an00956h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Improvement of the fragmentation specificity may streamline data processing of bottom-up proteomic experiments by drastically reducing either the amount of MS/MS data to process in the discovery phase or the detection of interfering signals in targeted quantification. Photodissociation at appropriate wavelengths is a promising alternative technique to the non-discriminating conventional activation mode by collision. Here, we describe the implementation of visible LID at 473 nm in a Q-Exactive-Orbitrap mass spectrometer for the specific detection of cysteine-containing peptides tagged with a Dabcyl group. HCD cell DC offset and irradiation time were optimized to obtain high fragmentation yield and spectra free of contaminating CID product ions, while keeping the irradiation time scale compatible with chromatographic separation. With this optimized experimental set-up, the selective detection of cysteine-containing peptides in a whole tryptic hydrolysate of three combined proteins is demonstrated by comparing all ion fragmentation (AIF) spectra recorded online with and without laser irradiation.
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Jeanne Dit Fouque K, Lavanant H, Zirah S, Lemoine J, Rebuffat S, Tabet JC, Kulesza A, Afonso C, Dugourd P, Chirot F. Gas-phase conformations of capistruin - comparison of lasso, branched-cyclic and linear topologies. Rapid Commun Mass Spectrom 2015; 29:1411-1419. [PMID: 26147481 DOI: 10.1002/rcm.7231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Capistruin is a peptide synthesized by Burkholderia thailandensis E264, which displays a lasso topology. This knot-like structure confers interesting properties to peptides (e.g. antibacterial). Therefore, it is important to evaluate the sensitivity of structural characterization methods to such topological constraints. METHODS Ion mobility mass spectrometry (IMS-MS) experiments, using both drift tube and travelling wave instruments, were performed on lasso capistruin and on peptides with the same sequence, but displaying a branched-cyclic (un-threaded) or linear topology. Molecular dynamics (MD) simulations were then performed to further interpret the IMS results in terms of conformation. RESULTS The collision cross sections (CCSs) measured via IMS for the different forms of capistruin were found to be similar, despite their different topologies for the doubly charged species, but significant differences arise as the charge state is increased. MD simulations for the doubly charged linear peptide were consistent with the hypothesis that salt bridges are present in the gas phase. Moreover, through CCS measurements for peptides with site-specific mutations, the arginine residue at position 11 was found to play a major role in the stabilization of compact structures for the linear peptide. CONCLUSIONS Differences in peptide topologies did not yield marked signatures in their respective IMS spectra. Such signatures were only visible for relatively high charge states, that allow Coulomb repulsion to force unfolding. At low charge states, the topologically unconstrained linear form of capistruin was found to adopt charge solvation-constrained structures, possibly including salt bridges, with CCSs comparable to those measured for the topologically constrained lasso form.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université de Rouen; INSA Rouen; CNRS, IRCOF, 1 Rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Hélène Lavanant
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université de Rouen; INSA Rouen; CNRS, IRCOF, 1 Rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Séverine Zirah
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Sorbonne Universités, Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Jérôme Lemoine
- Université de Lyon, Université Lyon 1, ENS Lyon, CNRS UMR5280, ISA, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Sylvie Rebuffat
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Sorbonne Universités, Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Jean-Claude Tabet
- Institut Parisien de Chimie Moléculaire, UMR 7201, CNRS, Université Pierre et Marie Curie, 4 place Jussieu, 75005, Paris, France
| | - Alexander Kulesza
- Université de Lyon, Université Lyon 1, CNRS UMR5306, ILM, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Carlos Afonso
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université de Rouen; INSA Rouen; CNRS, IRCOF, 1 Rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Philippe Dugourd
- Université de Lyon, Université Lyon 1, CNRS UMR5306, ILM, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Fabien Chirot
- Université de Lyon, Université Lyon 1, ENS Lyon, CNRS UMR5280, ISA, 5 rue de la Doua, 69100, Villeurbanne, France
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Girod M, Sanader Z, Vojkovic M, Antoine R, MacAleese L, Lemoine J, Bonacic-Koutecky V, Dugourd P. UV photodissociation of proline-containing peptide ions: insights from molecular dynamics. J Am Soc Mass Spectrom 2015; 26:432-43. [PMID: 25503080 DOI: 10.1007/s13361-014-1038-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/27/2014] [Accepted: 10/27/2014] [Indexed: 05/16/2023]
Abstract
UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S(2) and S(3), lie close to 213 nm. Non-adiabatic MD simulation starting from S(2) and S(3) shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.
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Antoine R, Lemoine J, Dugourd P. Electron photodetachment dissociation for structural characterization of synthetic and bio-polymer anions. Mass Spectrom Rev 2014; 33:501-22. [PMID: 24285407 DOI: 10.1002/mas.21402] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 12/21/2012] [Accepted: 01/08/2013] [Indexed: 05/25/2023]
Abstract
Tandem mass spectrometry (MS-MS) is a generic term evoking techniques dedicated to structural analysis, detection or quantification of molecules based on dissociation of a precursor ion into fragments. Searching for the most informative fragmentation patterns has led to the development of a vast array of activation modes that offer complementary ion reactivity and dissociation pathways. Collisional activation of ions using atoms, molecules or surface resulting in unimolecular dissociation of activated ions still plays a key role in tandem mass spectrometry. The discovery of electron capture dissociation (ECD) and then the development of other electron-ion or ion/ion reaction methods, constituted a significant breakthrough, especially for structural analysis of large biomolecules. Similarly, photon activation opened promising new frontiers in ion fragmentation owing to the ability of tightly controlled internal energy deposition and easy implementation on commercial instruments. Ion activation by photons includes slow heating methods such as infrared multiple photon dissociation (IRMPD) and black-body infrared radiative dissociation (BIRD) and higher energy methods like ultra-violet photodissociation (UVPD) and electron photo detachment dissociation (EPD). EPD occurs after UV irradiation of multiply negatively charged ions resulting in the formation of oxidized radical anions. The present paper reviews the hypothesis regarding the mechanisms of electron photo-detachment, radical formation and direct or activated dissociation pathways that support the observation of odd and even electron product ions. Finally, the value of EPD as a complementary structural analysis tool is illustrated through selected examples of synthetic polymers, oligonucleotides, polypeptides, lipids, and polysaccharides.
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Affiliation(s)
- Rodolphe Antoine
- University of Lyon, F-69622, Lyon, France; CNRS et Université Lyon 1, UMR5306, Institut Lumière Matière, Villeurbanne, France
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Biarc J, Gonzalo P, Mikaelian I, Fattet L, Deygas M, Gillet G, Lemoine J, Rimokh R. Combination of a discovery LC–MS/MS analysis and a label-free quantification for the characterization of an epithelial–mesenchymal transition signature. J Proteomics 2014; 110:183-94. [DOI: 10.1016/j.jprot.2014.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/15/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
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Girod M, Enjalbert Q, Brunet C, Antoine R, Lemoine J, Lukac I, Radman M, Krisko A, Dugourd P. Structural basis of protein oxidation resistance: a lysozyme study. PLoS One 2014; 9:e101642. [PMID: 24999730 PMCID: PMC4085010 DOI: 10.1371/journal.pone.0101642] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
Accumulation of oxidative damage in proteins correlates with aging since it can cause irreversible and progressive degeneration of almost all cellular functions. Apparently, native protein structures have evolved intrinsic resistance to oxidation since perfectly folded proteins are, by large most robust. Here we explore the structural basis of protein resistance to radiation-induced oxidation using chicken egg white lysozyme in the native and misfolded form. We study the differential resistance to oxidative damage of six different parts of native and misfolded lysozyme by a targeted tandem/mass spectrometry approach of its tryptic fragments. The decay of the amount of each lysozyme fragment with increasing radiation dose is found to be a two steps process, characterized by a double exponential evolution of their amounts: the first one can be largely attributed to oxidation of specific amino acids, while the second one corresponds to further degradation of the protein. By correlating these results to the structural parameters computed from molecular dynamics (MD) simulations, we find the protein parts with increased root-mean-square deviation (RMSD) to be more susceptible to modifications. In addition, involvement of amino acid side-chains in hydrogen bonds has a protective effect against oxidation Increased exposure to solvent of individual amino acid side chains correlates with high susceptibility to oxidative and other modifications like side chain fragmentation. Generally, while none of the structural parameters alone can account for the fate of peptides during radiation, together they provide an insight into the relationship between protein structure and susceptibility to oxidation.
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Affiliation(s)
- Marion Girod
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Quentin Enjalbert
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Brunet
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Iva Lukac
- Mediterranean Institute for Life Sciences, Split, Croatia
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Liverpool, Merseyside, England
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences, Split, Croatia
- INSERM U1001, Faculte de Medecine, Universite R. Descartes Paris-5, Paris, France
| | - Anita Krisko
- Mediterranean Institute for Life Sciences, Split, Croatia
- * E-mail: (PD) (AK); (AK) (PD)
| | - Philippe Dugourd
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail: (PD) (AK); (AK) (PD)
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Simon R, Passeron S, Lemoine J, Salvador A. Hydrophilic interaction liquid chromatography as second dimension in multidimensional chromatography with an anionic trapping strategy: application to prostate-specific antigen quantification. J Chromatogr A 2014; 1354:75-84. [PMID: 24931446 DOI: 10.1016/j.chroma.2014.05.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/22/2014] [Accepted: 05/24/2014] [Indexed: 12/17/2022]
Abstract
Liquid chromatography (LC) coupled with tandem mass spectrometry (MS-MS) in selected reaction monitoring mode (SRM) has become a widely used technique for the quantification of protein biomarkers in plasma and has already proven to give similar results compared to the conventional immunoassays. To improve the lack of insufficient sensitivity for quantification of low abundance protein, we propose a new two dimensional liquid chromatography (2D-LC-SRM) method for the quantitation of prostate specific antigen (PSA) in human plasma. The method centers on anion exchange cartridge between reversed-phase chromatography and hydrophilic interaction liquid chromatography (HILIC) in an on-line arrangement. The use of the anionic cartridge allows an easier online transfer of the analytes between both dimensions. Moreover, it provides an additional selectivity since the more basic peptides are not retained on this support. This setup has been applied to the quantification of prostate specific antigen (PSA) protein in plasma on a previous generation of mass spectrometer, which enabled a limit of quantification (LOQ) of 1ng/mL without any upfront immuno-depletion or intense off-line fractionation before the SRM analysis. The obtained LOQ is compatible with the required sensitivity for the clinically relevant plasma-based PSA tests.
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Affiliation(s)
- Romain Simon
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Sébastien Passeron
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Jérôme Lemoine
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Arnaud Salvador
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France.
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Roland-Lévy C, Lemoine J, Jeoffrion C. Health and well-being at work: The hospital context. European Review of Applied Psychology 2014. [DOI: 10.1016/j.erap.2014.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Brembilla-Perrot B, Moulin-Zinsch A, Sellal JM, Schwartz J, Olivier A, Zinzius PY, De Chillou C, Beurrier D, Rodermann M, Goudote G, Al Amoura H, Terrier de la Chaise A, Lemoine J, Rizk J, Lethor JP, Anne Tisserand JL, Taïhi S, Marçon F. Impact of transesophageal electrophysiologic study to elucidate the mechanism of arrhythmia on children with supraventricular tachycardia and no preexcitation. Pediatr Cardiol 2013; 34:1695-702. [PMID: 23609066 DOI: 10.1007/s00246-013-0703-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/04/2013] [Indexed: 10/26/2022]
Abstract
An electrophysiologic study (EPS) of children and teenagers with paroxysmal supraventricular tachycardia (SVT) and normal electrocardiography (ECG) in sinus rhythm was evaluated. Generally, EPS is performed only before paroxysmal SVT ablation in these patients. In this study, 140 patients (mean age, 15 ± 3 years) with normal ECG in sinus rhythm were studied for SVT by a transesophageal route in baseline state and after isoproterenol. Idiopathic left or right ventricular tachycardia was diagnosed in four patients (3 %). Anterograde conduction over an atrioventricular (AV) left lateral (n = 10) or septal (n = 9) accessory pathway (AP) was noted in 19 patients (13.5 %) at atrial pacing. Orthodromic AV reentrant tachycardia (AVRT) was induced in these children. Five of the patients had a high rate conducted over AP (>240 bpm in baseline state or >290 bpm after isoproterenol). Two of the patients (a 10-year-old girl with well-tolerated SVT and a 17-year-old with syncope-related SVT) had the criteria for a malignant form with the induction of atrial fibrillation conducted over AP at a rate exceeding 290 bpm in baseline state. Of the 140 patients, 74 (53 %) had typical AV node reentrant tachycardia (AVNRT), nine had atypical AVNRT (6 %), 1 had atrial tachycardia (0.7 %), and 33 (23.5 %) had AVRT related to a concealed AP with only retrograde conduction. Electrophysiologic study is recommended for children with paroxysmal SVT and normal ECG in sinus rhythm. The data are helpful for guiding the treatment. Ventricular tachycardia or atrial tachycardia can be misdiagnosed. Masked preexcitation syndrome with anterograde conduction through AP was present in 13.5 % of the patients, and 1.4 % had a malignant preexcitation syndrome.
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Enjalbert Q, Girod M, Jeudy J, Biarc J, Simon R, Antoine R, Dugourd P, Lemoine J, Salvador A. Combined collision-induced dissociation and photo-selected reaction monitoring mass spectrometry modes for simultaneous analysis of coagulation factors and estrogens. J Pharm Anal 2013; 4:183-189. [PMID: 29403881 PMCID: PMC5761116 DOI: 10.1016/j.jpha.2013.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/10/2013] [Indexed: 11/16/2022] Open
Abstract
Oral estrogens are directly associated with changes in plasma levels of coagulation proteins. Thus, the detection of any variation in protein concentrations due to estrogen contraceptives, by a simultaneous analysis of both coagulation proteins and estrogens, would be a very informative tool. In the present study, the merit of photo-selected reaction monitoring (SRM), a new analytical tool, was evaluated towards estrogens detection in plasma. Then, SRM and photo-SRM detection modes were combined for the simultaneous analysis of estrogen molecules together with heparin co-factor and factor XIIa, two proteins involved in the coagulation cascade. This study shows that photo-SRM could open new multiplexed analytical routes.
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Affiliation(s)
- Quentin Enjalbert
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut Lumière Matière, UMR5306, France
- Institut des Sciences Analytiques, UMR 5280, France
| | - Marion Girod
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut des Sciences Analytiques, UMR 5280, France
| | - Jérémy Jeudy
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut des Sciences Analytiques, UMR 5280, France
| | - Jordane Biarc
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut des Sciences Analytiques, UMR 5280, France
| | - Romain Simon
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut des Sciences Analytiques, UMR 5280, France
| | - Rodolphe Antoine
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut Lumière Matière, UMR5306, France
| | - Philippe Dugourd
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut Lumière Matière, UMR5306, France
| | - Jérôme Lemoine
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut des Sciences Analytiques, UMR 5280, France
| | - Arnaud Salvador
- Université Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
- Institut des Sciences Analytiques, UMR 5280, France
- Corresponding author at: Institut des Sciences Analytiques, UMR 5280, France. Tel.: +33 4 37 42 35 49; fax: +33 4 37 42 37 00.
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Pailleux F, Vachon P, Lemoine J, Beaudry F. Targeted liquid chromatography quadrupole ion trap mass spectrometry analysis of tachykinin related peptides reveals significant expression differences in a rat model of neuropathic pain. Neuropeptides 2013; 47:261-71. [PMID: 23490005 DOI: 10.1016/j.npep.2013.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 12/26/2022]
Abstract
Animal models are widely used to perform basic scientific research in pain. The rodent chronic constriction injury (CCI) model is widely used to study neuropathic pain. Animals were tested prior and after CCI surgery using behavioral tests (von Frey filaments and Hargreaves test) to evaluate pain. The brain and the lumbar enlargement of the spinal cord were collected from neuropathic and normal animals. Tachykinin related peptides were analyzed by high performance liquid chromatography quadrupole ion trap mass spectrometry. Our results reveal that the β-tachykinin₅₈₋₇₁, SP and SP₃₋₁₁ up-regulation are closely related to pain behavior. The spinal β-tachykinin₅₈₋₇₁, SP and SP₃₋₁₁ concentrations were significantly up-regulated in neuropathic animals compared with normal animals (p<0.001; p<0.001 and p<0.05, respectively). In contrast, the spinal SP5₅₋₁₁ concentration in neuropathic animals revealed a significant down-regulation compared with normal animals (p<0.05). The brain β-tachykinin₅₈₋₇₁ and SP concentrations were significantly up-regulated (p<0.05 and p<0.001, respectively). Interestingly, no significant concentration differences were observed in the spinal cord and brain for NKA, β-tachykinin₅₈₋₇₁, SP₁₋₇ and SP₆₋₁₁ (p>0.05). The β-tachykinin₅₈₋₇₁, SP and C-terminal SP metabolites could potentially serve as biomarkers in early drug discovery.
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Affiliation(s)
- Floriane Pailleux
- Groupe de Recherche en Pharmacologie Animal du Québec-GREPAQ, Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
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Enjalbert Q, Brunet C, Vernier A, Allouche AR, Antoine R, Dugourd P, Lemoine J, Giuliani A, Nahon L. Vacuum ultraviolet action spectroscopy of polysaccharides. J Am Soc Mass Spectrom 2013; 24:1271-1279. [PMID: 23722725 DOI: 10.1007/s13361-013-0657-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 06/02/2023]
Abstract
We studied the optical properties of gas-phase polysaccharides (maltose, maltotetraose, and maltohexaose) ions by action spectroscopy using the coupling between a quadrupole ion trap and a vacuum ultraviolet (VUV) beamline at the SOLEIL synchrotron radiation facility (France) in the 7 to 18 eV range. The spectra provide unique benchmarks for evaluation of theoretical data on electronic transitions of model carbohydrates in the VUV range. The effects of the nature of the charge held by polysaccharide ions on the relaxation processes were also explored. Finally the effect of isomerization of polysaccharides (with melezitose and raffinose) on their photofragmentation with VUV photons is presented.
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Affiliation(s)
- Quentin Enjalbert
- Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
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41
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Enjalbert Q, Girod M, Simon R, Jeudy J, Chirot F, Salvador A, Antoine R, Dugourd P, Lemoine J. Improved detection specificity for plasma proteins by targeting cysteine-containing peptides with photo-SRM. Anal Bioanal Chem 2013; 405:2321-31. [PMID: 23325399 DOI: 10.1007/s00216-012-6603-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/16/2012] [Accepted: 11/23/2012] [Indexed: 01/05/2023]
Abstract
Targeted mass spectrometry using selected reaction monitoring (SRM) has emerged as an alternative to immunoassays for protein quantification owing to faster development time and higher multiplexing capability. However, the SRM strategy is faced with the high complexity of peptide mixtures after trypsin digestion of whole plasma or the cellular proteome that most of the time causes contamination, irremediably, by interfering compounds in the transition channels monitored. This problem becomes increasingly acute when the targeted protein is present at a low concentration. In this work, the merit of laser-induced photo-dissociation in the visible region at 473 nm implemented in an hybrid quadrupole linear ion-trap mass spectrometer (photo-SRM) was evaluated for detection specificity of cysteine-containing peptides in a group of plasma proteins after tagging with a dabcyl chromophore. Compared with conventional SRM, photo-SRM chromatograms have improved detection specificity for most of peptides monitored. Comparison of the signals obtained for the best proteotypic peptides in SRM mode and those recorded by photo-SRM of cysteine-containing peptides for the same proteins reveals either increased (up to 10-fold) or similar signal to photo-SRM detection. Finally, photo-SRM has extended response linearity across a calibration plot obtained by diluting human plasma in rat plasma, down to the lowest concentrations. Hence, photo-SRM may advantageously complement conventional SRM in assay of proteins in complex biological matrices.
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Affiliation(s)
- Quentin Enjalbert
- Université Lyon, 43 Boulevard du 11 Novembre 1918, 69622 Lyon, France
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Pérot-Taillandier M, Zirah S, Enjalbert Q, Antoine R, Lemoine J, Dugourd P, Rebuffat S, Tabet JC, Afonso C. Prompt and Slow Electron-Detachment-Dissociation/Electron-Photodetachment-Dissociation of a 21-Mer Peptide. Chemistry 2013. [DOI: 10.1002/chem.201202578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Simon R, Enjalbert Q, Biarc J, Lemoine J, Salvador A. Evaluation of hydrophilic interaction chromatography (HILIC) versus C₁₈ reversed-phase chromatography for targeted quantification of peptides by mass spectrometry. J Chromatogr A 2012; 1264:31-9. [PMID: 23073287 DOI: 10.1016/j.chroma.2012.09.059] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 10/27/2022]
Abstract
Hydrophilic-interaction liquid chromatography (HILIC) is a widely used technique for small polar molecule analysis and offers the advantage of improved sensitivity in mass spectrometry. Although HILIC is today frequently employed as an orthogonal fractionation method for peptides during the proteomic discovery phase, it is still seldom considered for quantification. In this study, the performances in terms of peak capacity and sensitivity of 3 HILIC columns were compared to traditional reversed phase liquid C(18) column in the context of targeted quantification of proteotypic peptides using selected reaction monitoring mode (SRM). The results showed that the maximum sensitivity in HILIC chromatography was achieved by using an amide column without salt buffer and that the signal increased compared to classic reversed phase chromatography. However, the intensity improvement is quite low compared to the one obtained for small molecules. This is due on one hand to a higher matrix effect in HILIC and on the other hand to a change of charge states of peptides in organic solvent (doubly charged to monocharged). The doubly charged ions can be more readily dissociated than singly charged ions, making them ideal for SRM peptide quantification. As a result "supercharging" reagents are added to the mobile phase to shift from predominant singly charged ions to the more favorable doubly charged species. Using such optimized conditions, peptide signal is improved by a factor of between two and ten for 88% of the peptides of the 81 peptides investigated.
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Affiliation(s)
- Romain Simon
- UMR 5280, Institut des Sciences Analytiques, Université de Lyon, Lyon 1, France
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Lemoine J, Fortin T, Salvador A, Jaffuel A, Charrier JP, Choquet-Kastylevsky G. The current status of clinical proteomics and the use of MRM and MRM(3) for biomarker validation. Expert Rev Mol Diagn 2012; 12:333-42. [PMID: 22616699 DOI: 10.1586/erm.12.32] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The transfer of biomarkers from the discovery field to clinical use is still, despite progress, on a road filled with pitfalls. Since the emergence of proteomics, thousands of putative biomarkers have been published, often with overlapping diagnostic capacities. The strengthening of the robustness of discovery technologies, particularly in mass spectrometry, has been followed by intense discussions on establishing well-defined evaluation procedures for the identified targets to ultimately allow the clinical validation and then the clinical use of some of these biomarkers. Some of the obstacles to the evaluation process have been the lack of the availability of quick and easy-to-develop, easy-to-use, robust, specific and sensitive alternative quantitative methods when immunoaffinity-based tests are unavailable. Multiple reaction monitoring (MRM; also called selected reaction monitoring) is currently proving its capabilities as a complementary or alternative technique to ELISA for large biomarker panel evaluation. Here, we present how MRM(3) can overcome the lack of specificity and sensitivity often encountered by MRM when tracking minor proteins diluted by complex biological matrices.
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Affiliation(s)
- Jérôme Lemoine
- UMR 5280 CNRS Université Lyon 1, Institut des Sciences Analytiques, Université de Lyon, 69622 Villeurbanne cedex, France
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Simon R, Girod M, Fonbonne C, Salvador A, Clément Y, Lantéri P, Amouyel P, Lambert JC, Lemoine J. Total ApoE and ApoE4 isoform assays in an Alzheimer's disease case-control study by targeted mass spectrometry (n=669): a pilot assay for methionine-containing proteotypic peptides. Mol Cell Proteomics 2012; 11:1389-403. [PMID: 22918225 DOI: 10.1074/mcp.m112.018861] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allelic polymorphism of the apolipoprotein E (ApoE) gene (ApoE ε2, ApoE ε3 and ApoE ε4 alleles) gives rise to three protein isoforms (ApoE2, ApoE3 and ApoE4) that differ by 1 or 2 amino acids. Inheritance of the ApoE ε4 allele is a risk factor for developing Alzheimer's disease (AD). The potential diagnostic value of ApoE protein levels in biological fluids (i.e. cerebrospinal fluid, plasma and serum) for distinguishing between AD patients and healthy elderly subjects is subject to great controversy. Although a recent study reported subnormal total ApoE and ApoE4 levels in the plasma of AD patients, other studies have found normal or even elevated protein levels (versus controls). Because all previously reported assays were based on immunoenzymatic techniques, we decided to develop an orthogonal assay based on targeted mass spectrometry by tracking (i) a proteotypic peptide common to all ApoE isoforms and (ii) a peptide that is specific for the ε4 allele. After trypsin digestion, the ApoE4-specific peptide contains an oxidation-prone methionine residue. The endogenous methionine oxidation level was evaluated in a small cohort (n=68) of heterozygous ε3ε4 carriers containing both healthy controls and AD patients. As expected, the proportion of oxidized residues varied from 0 to 10%, with an average of 5%. We therefore developed a standardized strategy for the unbiased, absolute quantification of ApoE4, based on performic acid oxidization of methionine. Once the sample workflow had been thoroughly validated, it was applied to the concomitant quantification of total ApoE and ApoE4 isoform in a large case-control study (n=669). The final measurements were consistent with most previously reported ApoE concentration values and confirm the influence of the different alleles on the protein expression level. Our results illustrate (i) the reliability of selected reaction monitoring-based assays and (ii) the value of the oxidization step for unbiased monitoring of methionine-containing proteotypic peptides. Furthermore, a statistical analysis indicated that neither total ApoE and ApoE4 levels nor the ApoE/ApoE4 ratio correlated with the diagnosis of AD. These findings reinforce the conclusions of previous studies in which plasma ApoE levels had no obvious clinical significance.
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Affiliation(s)
- Romain Simon
- Institut des Sciences Analytiques, UMR n° 5280 CNRS Université Lyon 1, Université de Lyon, France
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Pailleux F, Lemoine J, Beaudry F. Quantitative Mass Spectrometry Analysis Reveals that Deletion of the TRPV1 Receptor in Mice Alters Substance P and Neurokinin A Expression in the Central Nervous System. Neurochem Res 2012; 37:2678-85. [DOI: 10.1007/s11064-012-0856-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/04/2012] [Accepted: 07/26/2012] [Indexed: 11/28/2022]
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Calvo F, Chirot F, Albrieux F, Lemoine J, Tsybin YO, Pernot P, Dugourd P. Statistical analysis of ion mobility spectrometry. II. Adaptively biased methods and shape correlations. J Am Soc Mass Spectrom 2012; 23:1279-1288. [PMID: 22573497 DOI: 10.1007/s13361-012-0391-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 05/31/2023]
Abstract
Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptively biased molecular dynamics (ABMD) simulations are used to sample the configuration space and to achieve flat-histogram sampling along the reaction coordinates of the first two moments of the gyration tensor. The method is tested and compared with replica-exchange simulations on triply-protonated bradykinin and on a larger 25-residue peptide. It is found to have a much higher efficiency for producing large sets of conformations in a broad range of diffusion cross-sections, whereas it does not compete with conventional replica-exchange molecular dynamics in locating the lowest-energy structure. Nevertheless, the broad sampling obtained from the ABMD method allows to quantitatively correlate the diffusion cross-section Ω with other geometric order parameters that have simpler interpretation. The strong correlations found between the diffusion cross-section and the radius of gyration, the surface area and the volume of the convex hull suggest an optimal template for accurately mimicking the variations of Ω in a broad range of conformations, using only geometrical information and doing so at a very moderate computational cost. The existence of such a correlation is confirmed on the much larger protein α-lactalbumin.
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Affiliation(s)
- Florent Calvo
- Université de Lyon, Université Lyon 1, Villeurbanne, 69622, France
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Dupery M, Lescaut V, Lenglet A, Lemoine J, Petit N, Poncelet A, Tranchet E. Des outils pour la prévention des risques professionnels chez les caristes. ARCH MAL PROF ENVIRO 2012. [DOI: 10.1016/j.admp.2012.03.575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Pailleux F, Lemoine J, Beaudry F. Investigation of the metabolic biotransformation of substance P in liver microsomes by liquid chromatography quadrupole ion trap mass spectrometry. Biomed Chromatogr 2012; 27:39-47. [DOI: 10.1002/bmc.2746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 11/11/2022]
Affiliation(s)
| | - Jérôme Lemoine
- UMR 5280 CNRS Université de Lyon 1, Institut des Sciences Analytiques; Université de Lyon; 69622; Villeurbanne cedex; France
| | - Francis Beaudry
- Groupe de Recherche en Pharmacologie Animal du Québec (GREPAQ), Département de biomedicine vétérinaire, Faculté de Médecine Vétérinaire; Université de Montréal; Saint-Hyacinthe; Québec; Canada
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Aravind G, Klærke B, Rajput J, Toker Y, Andersen LH, Bochenkova AV, Antoine R, Lemoine J, Racaud A, Dugourd P. Photodissociation pathways and lifetimes of protonated peptides and their dimers. J Chem Phys 2012; 136:014307. [PMID: 22239781 DOI: 10.1063/1.3671943] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photodissociation lifetimes and fragment channels of gas-phase, protonated YA(n) (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ~2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.
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Affiliation(s)
- G Aravind
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
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