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1. Additional file 5 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Abstract

Additional file 5: Figure S5. Amino acid composition across model taxa. (PDF 40 KB)

Published
2021
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2. Additional file 2 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Abstract

Additional file 2: Figure S2. Distribution of complete protein lengths. (PDF 92 KB)

Published
2021
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3. Additional file 10 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Subjects
Data_FILES
Abstract

Authors’ original file for figure 5

Published
2021
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4. Additional file 4 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Abstract

Additional file 4: Figure S4. Example of Alvinella proteins mapped on a KEGG pathway. (PDF 82 KB)

Published
2021
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5. Additional file 1 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Abstract

Additional file 1: Figure S1. Size distributions of contigs in the global assembly. (PDF 99 KB)

Published
2021
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6. Additional file of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Abstract

Additional file of Insights into metazoan evolution from alvinella pompejana cDNAs

Published
2021
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7. Additional file 6 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Subjects
Data_FILES
Abstract

Authors’ original file for figure 1

Published
2021
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8. Additional file 9 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Subjects
Data_FILES
Abstract

Authors’ original file for figure 4

Published
2021
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9. Additional file 7 of Insights into metazoan evolution from alvinella pompejana cDNAs

Author

Gagnière, Nicolas, Jollivet, Didier, Boutet, Isabelle, Brélivet, Yann, Busso, Didier, Da Silva, Corinne, Gaill, Françoise, Higuet, Dominique, Hourdez, Stéphane, Knoops, Bernard, Lallier, François, Leize-Wagner, Emmanuelle, Mary, Jean, Moras, Dino, Perrodou, Emmanuel, Jean-François Rees, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Subjects
Data_FILES
Abstract

Authors’ original file for figure 2

Published
2021
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10. A New Self-Complementary Bis-Acridinium Tweezer

Author

De Rouville, H.-P. J., Zorn, Nathalie, Leize-wagner, Emmanuelle, Heitz, Valerie, Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
010405 organic chemistry, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, 010402 general chemistry, 01 natural sciences, Combinatorial chemistry, 0104 chemical sciences
Published
2018

11. Study of the impact of ion beam analysis on the molecular preservation of mummy hair by a proteomic approach

Author

Charrié-Duhaut, Armelle, Fresnais, Margaux, Richardin, Pascale, Calligaro, Thomas, Lemasson, Quentin, Leize-Wagner, Emmanuelle, Charrié-Duhaut, Armelle, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche et de restauration des musées de France (C2RMF), and Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)

Subjects
[CHIM.ANAL] Chemical Sciences/Analytical chemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

12. Advanced Antibody-Drug Conjugate Structural Characterization by Sheathless Capillary Electrophoresis-Tandem Mass Spectrometry Using Complementary Approaches

Author

Said, Nassur, Giorgetti, Jérémie, Kuhn, Lauriane, Beck, Alain, Leize-Wagner, Emmanuelle, Gahoual, Rabah, Francois, Yannis-Nicolas, Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Plateforme Protéomique Strasbourg - Esplanade (IBMC / CNRS FRC1589 / UNIV Strasbourg), Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Moléculaire et Cellulaire [Strasbourg] (IBMC), Centre d'Immunologie Pierre Fabre (CIPF), PIERRE FABRE, and dhotel, helene

Subjects
[SDV] Life Sciences [q-bio], [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, ComputingMilieux_MISCELLANEOUS, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract

International audience

Published
2017

13. Independent highly sensitive characterization of asparagine deamidation and aspartic acid isomerization by sheathless CZE-ESI-MS/MS

Author

Gahoual, Rabah, Beck, Alain, François, Yannis-Nicolas, Leize-Wagner, Emmanuelle, Laboratoire de Chimie de Coordination Organique, Tectonique Moléculaire du Solide (TMS), Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Laboratoire de Chimie Quantique, and Centre National de la Recherche Scientifique (CNRS)

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry
Abstract

Amino acids residues are commonly submitted to various physicochemical modifications occurring at physiological pH and temperature. Post-translational modifications (PTMs) require comprehensive characterization due to their major influence on protein structure and involvement in numerous in vivo process or signaling. Mass spectrometry (MS) has gradually became an analytical tool of choice to characterize PTMs, however some modifications are still challenging due to sample faint modification levels or difficulty to separate an intact peptide from modified counterparts before their transfer to the ionization source. Here we report the implementation of capillary zone electrophoresis coupled to electrospray ionization tandem mass spectrometry (CZE-ESI-MS/MS) by the intermediate of a sheathless interfacing for independent and highly sensitive characterization of asparagine deamidation (deaN) and aspartic acid isomerization (isoD). CZE selectivity regarding deaN and isoD was studied extensively using different sets of synthetic peptides based on actual tryptic peptides. Results demonstrated CZE ability to separate the unmodified peptide from modified homologous exhibiting deaN, isoD or both independently with a resolution systematically superior to 1.29. Developed CZE-ESI-MS/MS method was applied to the characterization of monoclonal antibodies and complex protein mixture. Conserved CZE selectivity could be demonstrated even for complex samples and foremost results obtained showed that CZE selectivity is similar regardless of the composition of the peptide. Separation of modified peptides prior to the MS analysis allowed to characterize and estimate modification levels of the sample independently for deaN and isoD even for peptides affected by both modifications and as a consequence enables to distinguish the formation of L-aspartic acid or D-aspartic acid generated from deaN. Separation based on peptide modification allowed, supported by the ESI ionization efficiency provided by CZE-ESI-MS properties, enabled to characterize and estimate studied PTMs with an unprecedented sensitivity and proved the relevance of implementing an electrophoretic driven separation for MS based peptide analysis.

Published
2016

15. Chemical cross-linking and mass spectrometry to determine the subunit interaction network in a recombinant human SAGA HAT subcomplex

Author

Nguyen-Huynh, Nha-Thi, Sharov, Grigory, Potel, Clément, Fichter, Pélagie, Trowitzsch, Simon, Berger, Imre, Lamour, Valérie, Schultz, Patrick, Potier, Noëlle, Leize-Wagner, Emmanuelle, Chimie de la matière complexe (CMC), and Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Protein Conformation, Molecular Sequence Data, Succinimides, Articles, Recombinant Proteins, Protein Subunits, Cross-Linking Reagents, Acetyltransferases, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Multiprotein Complexes, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Protein Interaction Mapping, Humans, p300-CBP Transcription Factors, Amino Acid Sequence, Protein Interaction Maps, Protein Multimerization, ComputingMilieux_MISCELLANEOUS, Adaptor Proteins, Signal Transducing, Transcription Factors
Abstract

Understanding the way how proteins interact with each other to form transient or stable protein complexes is a key aspect in structural biology. In this study, we combined chemical cross-linking with mass spectrometry to determine the binding stoichiometry and map the protein-protein interaction network of a human SAGA HAT subcomplex. MALDI-MS equipped with high mass detection was used to follow the cross-linking reaction using bis[sulfosuccinimidyl] suberate (BS3) and confirm the heterotetrameric stoichiometry of the specific stabilized subcomplex. Cross-linking with isotopically labeled BS3 d0-d4 followed by trypsin digestion allowed the identification of intra- and intercross-linked peptides using two dedicated search engines: pLink and xQuest. The identified interlinked peptides suggest a strong network of interaction between GCN5, ADA2B and ADA3 subunits; SGF29 is interacting with GCN5 and ADA3 but not with ADA2B. These restraint data were combined to molecular modeling and a low-resolution interacting model for the human SAGA HAT subcomplex could be proposed, illustrating the potential of an integrative strategy using cross-linking and mass spectrometry for addressing the structural architecture of multiprotein complexes.

Published
2015

17. Analysis of monoclonal antibody by a novel CE-UV/MALDI-MS interface

Author

Biacchi, Michael, Bhajun, Ricky, Saïd, Nassur, Beck, Alain, Francois, Yannis Nicolas, Leize-Wagner, Emmanuelle, Tectonique Moléculaire du Solide (TMS), Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination Organique, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Laboratoire de Chimie Quantique, and Centre National de la Recherche Scientifique (CNRS)

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry
Abstract

Monoclonal antibodies (mAb) are highly complex proteins that advertise a wide range of microheterogeneity that requires multiple analytical methods for full structure assessment and quality control. As a consequence, the characterization of mAbs on different levels is particularly product - and time - consuming. Capillary Electrophoresis-Mass Spectrometry (CE-MS) couplings, especially to matrix-assisted laser desorption/ionization (MALDI) appear really attractive methods for the characterization of biological samples. In this work, we report on the last instrumental development and performance of the first totally automated off-line CE-UV/MALDI-MS/MS. This interface is based on the removal of the original UV cell of the CE apparatus, the modification of the spotting device geometry and the creation of an integrated delivery matrix system. The performance of the method was evaluated with separations of 5 intact proteins and a tryptic digest mixture of 9 proteins. Intact proteins application shows the acquisition of electropherograms with high resolution and high repeatability. In the peptide mapping approach, a total number of 154 unique identified peptides were characterized using MS/MS spectra corresponding to average sequence coverage of 64.1%. Comparison with NanoLC/MALDI-MS/MS showed complementarity at the peptide level with an increase by 42% when using CE/MALDI-MS coupling. Finally, this work represents the first analysis of intact mAb charge variants by capillary zone electrophoresis using a MS detection. Moreover, using a peptide mapping approach CE-UV/MALDI-MS/MS fragmentation allowed 100% sequence coverage of the light chain and 92 % on the heavy chain and the separation of the 4 major glycosylated peptides and their structural characterization

Published
2014

18. Power and limitations of electrophoretic separations in proteomics strategies

Author

Rabilloud, Thierry, Vaezzadeh, Ali R, Potier, Noelle, Lelong, Cécile, Leize-Wagner, Emmanuelle, Chevallet, Mireille, Biochimie et biophysique des systèmes intégrés (BBSI), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), Laboratoire de Protéomique Clinique, Service de Médecine de Laboratoire, HCUG, Hôpital Universitaire de Genève, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG)

Subjects
Genomics (q-bio.GN), Electrophoresis, Proteomics, MESH: Mass Spectrometry, MESH: Humans, Proteome, MESH: Peptides, MESH: Proteomics, MESH: Research Design, Proteins, MESH: Electrophoresis, Mass Spectrometry, MESH: Proteome, Research Design, FOS: Biological sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, Quantitative Biology - Genomics, MESH: Animals, MESH: Proteins, Peptides
Abstract

International audience; Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.

Published
2009

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