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2. About the mechanism of interference of silver staining with peptide mass spectrometry

Author

Richert, Sophie, Luche, Sylvie, Chevallet, Mireille, Van Dorsselaer, Alain, Leize-Wagner, Emmanuelle, and Rabilloud, Thierry

Subjects
Quantitative Biology - Genomics
Abstract

The mechanism by which silver staining of proteins in polyacrylamide gels interferes with mass spectrometry of peptides produced by proteolysis has been investigated. It was demonstrated that this interference increases with time between silver staining and gel processing, although the silver image is constant. This suggested an important role of the formaldehyde used in silver staining development in this interference process. Consequently, a formaldehyde-free staining protocol has been devised, using carbohydrazide as the developing agent. This protocol showed much increased peptide coverage and retained the sensitivity of silver staining. These results were however obtained at the expense of an increased background in the stained gels and of a reduced staining homogeneity.

Published
2012
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3. Power and limitations of electrophoretic separations in proteomics strategies

Author

Rabilloud, Thierry, Vaezzadeh, Ali R, Potier, Noelle, Lelong, Cécile, Leize-Wagner, Emmanuelle, and Chevallet, Mireille

Subjects
Quantitative Biology - Genomics
Abstract

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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4. Oxidative stress response: a proteomic view

Author

Rabilloud, Thierry, Chevallet, Mireille, Luche, Sylvie, and Leize-Wagner, Emmanuelle

Subjects
Quantitative Biology - Genomics
Abstract

The oxidative stress response is characterized by various effects on a range of biologic molecules. When examined at the protein level, both expression levels and protein modifications are altered by oxidative stress. While these effects have been studied in the past by classic biochemical methods, the recent onset of proteomics methods has allowed the oxidative stress response to be studied on a much wider scale. The input of proteomics in the study of oxidative stress response and in the evidence of an oxidative stress component in biologic phenomena is reviewed in this paper.

Published
2008
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5. Improved mass spectrometry compatibility is afforded by ammoniacal silver staining

Author

Chevallet, Mireille, Diemer, Hélène, Luche, Sylvie, van Dorsselaer, Alain, Rabilloud, Thierry, and Leize-Wagner, Emmanuelle

Subjects
Quantitative Biology - Genomics
Abstract

Sequence coverage in MS analysis of protein digestion-derived peptides is a key issue for detailed characterization of proteins or identification at low quantities. In gel-based proteomics studies, the sequence coverage greatly depends on the protein detection method. It is shown here that ammoniacal silver detection methods offer improved sequence coverage over standard silver nitrate methods, while keeping the high sensitivity of silver staining. With the development of 2D-PAGE-based proteomics, another burden is placed on the detection methods used for protein detection on 2-D-gels. Besides the classical requirements of linearity, sensitivity, and homogeneity from one protein to another, detection methods must now take into account another aspect, namely their compatibility with MS. This compatibility is evidenced by two different and complementary aspects, which are (i) the absence of adducts and artefactual modifications on the peptides obtained after protease digestion of a protein detected and digested in - gel, and (ii) the quantitative yield of peptides recovered after digestion and analyzed by the mass spectrometer. While this quantitative yield is not very important per se, it is however a crucial parameter as it strongly influences the S/N of the mass spectrum and thus the number of peptides that can be detected from a given protein input, especially at low protein amounts. This influences in turn the sequence coverage and thus the detail of the analysis provided by the mass spectrometer., Comment: website publisher http://www.interscience.wiley.com

Published
2006
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6. Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view

Author

Chevallet, Mireille, Lescuyer, Pierre, Diemer, Hélène, van Dorsselaer, Alain, Leize-Wagner, Emmanuelle, and Rabilloud, Thierry

Subjects
Quantitative Biology - Genomics
Abstract

The proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the mitochondrial rRNAs and a few tRNAs, we performed a comparative study on the 143B cell line and on its Rho-0 counterpart, i.e., devoid of mitochondrial DNA. Quantitative differences were found, of course in the respiratory complexes subunits, but also in the mitochondrial translation apparatus, mainly mitochondrial ribosomal proteins, and in the ion and protein import system, i.e., including membrane proteins. Various mitochondrial metabolic processes were also altered, especially electron transfer proteins and some dehydrogenases, but quite often on a few proteins for each pathway. This study also showed variations in some hypothetical or poorly characterized proteins, suggesting a mitochondrial localization for these proteins. Examples include a stomatin-like protein and a protein sharing homologies with bacterial proteins implicated in tyrosine catabolism. Proteins involved in apoptosis control are also found modulated in Rho-0 mitochondria., Comment: website publisher: http://www3.interscience.wiley.com/

Published
2006
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7. About thiol derivatization and resolution of basic proteins in two-dimensional electrophoresis

Author

Luche, Sylvie, Diemer, Hélène, Tastet, Chistophe, Chevallet, Mireille, Van Dorsselaer, Alain, Leize-Wagner, Emmanuelle, and Rabilloud, Thierry

Subjects
Quantitative Biology - Genomics
Abstract

The influence of thiol blocking on the resolution of basic proteins by two-dimensional electrophoresis was investigated. Cysteine blocking greatly increased resolution and decreased streaking, especially in the basic region of the gels. Two strategies for cysteine blocking were found to be efficient: classical alkylation with maleimide derivatives and mixed disulfide exchange with an excess of a low molecular weight disulfide. The effect on resolution was significant enough to allow correct resolution of basic proteins with in-gel rehydration on wide gradients (e.g. 3-10 and 4-12), but anodic cup-loading was still required for basic gradients (e.g. 6-12 or 8-12). These results demonstrate that thiol-related problems are not solely responsible for streaking of basic proteins on two-dimensional gels., Comment: web publisher http://www.interscience.wiley.com

Published
2006
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8. Comprehensive multilevel characterization of biologics using sheathless capillary electrophoresis hyphenated to tandem mass spectrometry

Author

Gahoual, Rabah, Biacchi, Michael, Busnel, Jean-Marc, Beck, Alain, Francois, Yannis-Nicolas, and Leize-Wagner, Emmanuelle

Subjects
Biological products -- Research -- Properties, Mass spectrometry -- Usage -- Methods, Electrophoresis -- Research, Chemistry
Abstract

An innovative coupling of capillary electrophoresis and tandem mass spectrometry (CE-MS-MS) provides excellent results for the characterization of the primary structure of biologics. Using a single 200-fmol injection, it is [...]

Published
2015

11. 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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12. 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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13. 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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14. 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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15. 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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16. 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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17. 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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18. 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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19. NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods

Author

De Leoz, Maria Lorna A., Duewer, David L, Fung, Adam, Liu, Lily, Kei Yau, Hoi, Potter, Oscar, Staples, Gregory O, Furuki, Kenichiro, Frenkel, Ruth, Hu, Yunli, Socic, Zoran, Zhang, Peiqing, Altmann, Friedrich, Grunwald-Grube, Clemens, Shao, Chun, Zaia, Joseph, Evers, Waltraud, Pengelley, Stuart, Detlev, Suckau, Wiechmann, Anja, Resemann, Anja, Jabs, Wolfgang, Beck, Alain, Froehlich, John W, Huang, Chuncui, Yan, Li, Yaming, Liu, Sun, Shiwei, Wang, Yaojun, Seo, Youngsuk, An, Hyun Joo, Reichardt, Niels-Christian, Ruiz, Juan Echevarria, Archer-Hartmann, Stephanie, Azadi, Parastoo, Bell, Len, Lakos, Zsuzsanna, An, Yanming, Cipollo, John F, Pucic-Bakovic, Maja, Stambuk, Jerko, Lauc, Gordan, Li, Xu, Wang, Peng George, Bock, Andreas, Hennig, Rene, Rapp, Erdmann, Creskey, Marybeth, Cyr, Terry D, Nakano, Miyako, Sugiyama, Taiki, Leung, Pui-King Amy, Link-Lenczowski, Pawel, Jaworek, Jolanta, Yoo, Jong Shin, Kim, Sa-Rang, Suh, Soo-Kyung, de Haan, Noortje, Falck, David, Lageveen-Kammeijer, Guinevere S. M., Wuhrer, Manfred, Emery, Robert J, Liew, Li Phing, Royle, Louise, Urbanowicz, Paulina A, Packer, Nicolle H, Song, Xiaomin, Everest-Dass, Arun, Lattova, Erika, Cajic, Samanta, Alagesan, Kathirvel, Kolarich, Daniel, Kasali, Toyin, Lindo, Viv, Chen, Yuetian, Goswami, Kudrat, Gau, Brian, Amunugama, Ravi, Jones, Richard, Stroop, Corné J M, Kato, Koichi, Yagi, Hirokazu, Kondo, Sachiko, Yuen, C T, Harazono, Akira, Shi, Xiafeng, Magnelli, Paula, Kasper, Brian T, Mahai, Lara, Harvey, David J, O'Flaherty, Roisin, Rudd, Pauline M., Saldova, Radka, Hecht, Elizabeth S, Muddiman, David C, Kang, Jichao, Bhoskar, Prachi, Menard, Daniele, Saati, Andrew, Merle, Christine, Mast, Steven, Tep, Sam, Truong, Jennie, Nishikaze, Takashi, Sekiya, Sadanori, Shafer, Aaron, Funaoka, Sohei, Toyoda, Masaaki, de Vreugd, Peter, Caron, Cassie, Pradhan, Pralima, Tan, Niclas Chiang, Mechref, Yehia, Patil, Sachin, Rohrer, Jeffrey S, Chakrabarti, Ranjan, Dadke, Disha, Lahori, Mohammedazam, Zou, Chunxia, Cairo, Christopher, Reiz, Béla, Whittal, Randy M, Lebrilla, Carlito B, Wu, Lauren, Guttman, Andras, Szigeti, Marton, Kremkow, Benjamin G, Lee, Kevin H, Sihlbom, Carina, Adamczyk, Barbara, Jin, Chunsheng, Karlsson, Niclas G, Omros, Jessica, Larson, Goran, Nilsson, Jonas, Meyer, Bernd, Alena, Wiegandt, Komatsu, Emy, Perreault, Helene, Bodnar, Edward D, Said, Nassur, Francois, Yannis-Nicolas, Leize-Wagner, Emmanuelle, Maier, Sandra, Zeck, Anne, Heck, Albert J R, Yang, Yang, Haselberg, Rob, Qing Yu, Ying, Alley, William, Leone, Joseph W, Yuan, Hua, Stein, Stephen E, De Leoz, Maria Lorna A., Duewer, David L, Fung, Adam, Liu, Lily, Kei Yau, Hoi, Potter, Oscar, Staples, Gregory O, Furuki, Kenichiro, Frenkel, Ruth, Hu, Yunli, Socic, Zoran, Zhang, Peiqing, Altmann, Friedrich, Grunwald-Grube, Clemens, Shao, Chun, Zaia, Joseph, Evers, Waltraud, Pengelley, Stuart, Detlev, Suckau, Wiechmann, Anja, Resemann, Anja, Jabs, Wolfgang, Beck, Alain, Froehlich, John W, Huang, Chuncui, Yan, Li, Yaming, Liu, Sun, Shiwei, Wang, Yaojun, Seo, Youngsuk, An, Hyun Joo, Reichardt, Niels-Christian, Ruiz, Juan Echevarria, Archer-Hartmann, Stephanie, Azadi, Parastoo, Bell, Len, Lakos, Zsuzsanna, An, Yanming, Cipollo, John F, Pucic-Bakovic, Maja, Stambuk, Jerko, Lauc, Gordan, Li, Xu, Wang, Peng George, Bock, Andreas, Hennig, Rene, Rapp, Erdmann, Creskey, Marybeth, Cyr, Terry D, Nakano, Miyako, Sugiyama, Taiki, Leung, Pui-King Amy, Link-Lenczowski, Pawel, Jaworek, Jolanta, Yoo, Jong Shin, Kim, Sa-Rang, Suh, Soo-Kyung, de Haan, Noortje, Falck, David, Lageveen-Kammeijer, Guinevere S. M., Wuhrer, Manfred, Emery, Robert J, Liew, Li Phing, Royle, Louise, Urbanowicz, Paulina A, Packer, Nicolle H, Song, Xiaomin, Everest-Dass, Arun, Lattova, Erika, Cajic, Samanta, Alagesan, Kathirvel, Kolarich, Daniel, Kasali, Toyin, Lindo, Viv, Chen, Yuetian, Goswami, Kudrat, Gau, Brian, Amunugama, Ravi, Jones, Richard, Stroop, Corné J M, Kato, Koichi, Yagi, Hirokazu, Kondo, Sachiko, Yuen, C T, Harazono, Akira, Shi, Xiafeng, Magnelli, Paula, Kasper, Brian T, Mahai, Lara, Harvey, David J, O'Flaherty, Roisin, Rudd, Pauline M., Saldova, Radka, Hecht, Elizabeth S, Muddiman, David C, Kang, Jichao, Bhoskar, Prachi, Menard, Daniele, Saati, Andrew, Merle, Christine, Mast, Steven, Tep, Sam, Truong, Jennie, Nishikaze, Takashi, Sekiya, Sadanori, Shafer, Aaron, Funaoka, Sohei, Toyoda, Masaaki, de Vreugd, Peter, Caron, Cassie, Pradhan, Pralima, Tan, Niclas Chiang, Mechref, Yehia, Patil, Sachin, Rohrer, Jeffrey S, Chakrabarti, Ranjan, Dadke, Disha, Lahori, Mohammedazam, Zou, Chunxia, Cairo, Christopher, Reiz, Béla, Whittal, Randy M, Lebrilla, Carlito B, Wu, Lauren, Guttman, Andras, Szigeti, Marton, Kremkow, Benjamin G, Lee, Kevin H, Sihlbom, Carina, Adamczyk, Barbara, Jin, Chunsheng, Karlsson, Niclas G, Omros, Jessica, Larson, Goran, Nilsson, Jonas, Meyer, Bernd, Alena, Wiegandt, Komatsu, Emy, Perreault, Helene, Bodnar, Edward D, Said, Nassur, Francois, Yannis-Nicolas, Leize-Wagner, Emmanuelle, Maier, Sandra, Zeck, Anne, Heck, Albert J R, Yang, Yang, Haselberg, Rob, Qing Yu, Ying, Alley, William, Leone, Joseph W, Yuan, Hua, and Stein, Stephen E

Abstract

Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.

Published
2020

21. NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods

Author

De Leoz, Maria Lorna A., primary, Duewer, David L., additional, Fung, Adam, additional, Liu, Lily, additional, Yau, Hoi Kei, additional, Potter, Oscar, additional, Staples, Gregory O., additional, Furuki, Kenichiro, additional, Frenkel, Ruth, additional, Hu, Yunli, additional, Sosic, Zoran, additional, Zhang, Peiqing, additional, Altmann, Friedrich, additional, Grunwald-Grube, Clemens, additional, Shao, Chun, additional, Zaia, Joseph, additional, Evers, Waltraud, additional, Pengelley, Stuart, additional, Suckau, Detlev, additional, Wiechmann, Anja, additional, Resemann, Anja, additional, Jabs, Wolfgang, additional, Beck, Alain, additional, Froehlich, John W., additional, Huang, Chuncui, additional, Li, Yan, additional, Liu, Yaming, additional, Sun, Shiwei, additional, Wang, Yaojun, additional, Seo, Youngsuk, additional, An, Hyun Joo, additional, Reichardt, Niels-Christian, additional, Ruiz, Juan Echevarria, additional, Archer-Hartmann, Stephanie, additional, Azadi, Parastoo, additional, Bell, Len, additional, Lakos, Zsuzsanna, additional, An, Yanming, additional, Cipollo, John F., additional, Pucic-Bakovic, Maja, additional, Štambuk, Jerko, additional, Lauc, Gordan, additional, Li, Xu, additional, Wang, Peng George, additional, Bock, Andreas, additional, Hennig, René, additional, Rapp, Erdmann, additional, Creskey, Marybeth, additional, Cyr, Terry D., additional, Nakano, Miyako, additional, Sugiyama, Taiki, additional, Leung, Pui-King Amy, additional, Link-Lenczowski, Paweł, additional, Jaworek, Jolanta, additional, Yang, Shuang, additional, Zhang, Hui, additional, Kelly, Tim, additional, Klapoetke, Song, additional, Cao, Rui, additional, Kim, Jin Young, additional, Lee, Hyun Kyoung, additional, Lee, Ju Yeon, additional, Yoo, Jong Shin, additional, Kim, Sa-Rang, additional, Suh, Soo-Kyung, additional, de Haan, Noortje, additional, Falck, David, additional, Lageveen-Kammeijer, Guinevere S.M., additional, Wuhrer, Manfred, additional, Emery, Robert J., additional, Kozak, Radoslaw P., additional, Liew, Li Phing, additional, Royle, Louise, additional, Urbanowicz, Paulina A., additional, Packer, Nicolle H., additional, Song, Xiaomin, additional, Everest-Dass, Arun, additional, Lattová, Erika, additional, Cajic, Samanta, additional, Alagesan, Kathirvel, additional, Kolarich, Daniel, additional, Kasali, Toyin, additional, Lindo, Viv, additional, Chen, Yuetian, additional, Goswami, Kudrat, additional, Gau, Brian, additional, Amunugama, Ravi, additional, Jones, Richard, additional, Stroop, Corné J.M., additional, Kato, Koichi, additional, Yagi, Hirokazu, additional, Kondo, Sachiko, additional, Yuen, C.T., additional, Harazono, Akira, additional, Shi, Xiaofeng, additional, Magnelli, Paula E., additional, Kasper, Brian T., additional, Mahal, Lara, additional, Harvey, David J., additional, O'Flaherty, Roisin, additional, Rudd, Pauline M., additional, Saldova, Radka, additional, Hecht, Elizabeth S., additional, Muddiman, David C., additional, Kang, Jichao, additional, Bhoskar, Prachi, additional, Menard, Daniele, additional, Saati, Andrew, additional, Merle, Christine, additional, Mast, Steven, additional, Tep, Sam, additional, Truong, Jennie, additional, Nishikaze, Takashi, additional, Sekiya, Sadanori, additional, Shafer, Aaron, additional, Funaoka, Sohei, additional, Toyoda, Masaaki, additional, de Vreugd, Peter, additional, Caron, Cassie, additional, Pradhan, Pralima, additional, Tan, Niclas Chiang, additional, Mechref, Yehia, additional, Patil, Sachin, additional, Rohrer, Jeffrey S., additional, Chakrabarti, Ranjan, additional, Dadke, Disha, additional, Lahori, Mohammedazam, additional, Zou, Chunxia, additional, Cairo, Christopher, additional, Reiz, Béla, additional, Whittal, Randy M., additional, Lebrilla, Carlito B., additional, Wu, Lauren, additional, Guttman, Andras, additional, Szigeti, Marton, additional, Kremkow, Benjamin G., additional, Lee, Kelvin H., additional, Sihlbom, Carina, additional, Adamczyk, Barbara, additional, Jin, Chunsheng, additional, Karlsson, Niclas G., additional, Örnros, Jessica, additional, Larson, Göran, additional, Nilsson, Jonas, additional, Meyer, Bernd, additional, Wiegandt, Alena, additional, Komatsu, Emy, additional, Perreault, Helene, additional, Bodnar, Edward D., additional, Said, Nassur, additional, Francois, Yannis-Nicolas, additional, Leize-Wagner, Emmanuelle, additional, Maier, Sandra, additional, Zeck, Anne, additional, Heck, Albert J.R., additional, Yang, Yang, additional, Haselberg, Rob, additional, Yu, Ying Qing, additional, Alley, William, additional, Leone, Joseph W., additional, Yuan, Hua, additional, and Stein, Stephen E., additional

Published
2020
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23. 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, Rees, Jean-François, Segurens, Béatrice, Shillito, Bruce, Tanguy, Arnaud, Thierry, Jean-Claude, Weissenbach, Jean, Wincker, Patrick, Zal, Franck, Poch, Olivier, and Lecompte, Odile

Published
2010
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24. 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

25. Insights into metazoan evolution from alvinella pompejana cDNAs

Author

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

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C). This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures. Results We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity. Conclusions Our study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates.

Published
2010
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26. 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

29. Structural characterization of hemoglobins from Monilifera and Frenulata tubeworms (Siboglinids): First discovery of giant hexagonal-bilayer hemoglobin in the former “Pogonophora” group

Author

Meunier, Cédric, Andersen, Ann C., Bruneaux, Matthieu, Le Guen, Dominique, Terrier, Peran, Leize-Wagner, Emmanuelle, Zal, Franck, Meunier, Cédric, Andersen, Ann C., Bruneaux, Matthieu, Le Guen, Dominique, Terrier, Peran, Leize-Wagner, Emmanuelle, and Zal, Franck

Abstract

Siboglinids are symbiotic polychete annelids having hemoglobins as essential oxygen- and sulfide-carriers for their endosymbiotic bacteria. We analyzed the structure of the hemoglobins from two species of siboglinids: the monilifera Sclerolinum contortum and the frenulata Oligobrachia webbi (i.e. haakonmosbiensis) from Norwegian cold seeps. Measured by Multi-Angle Laser Light Scattering (MALLS), Sclerolinum shows a 3190 ± 50 kDa hexagonal bilayer hemoglobin (HBL-Hb) and a 461 ± 46 kDa ring-Hb, just as vestimentifera, whereas Oligobrachia has a 409 ± 3.7 kDa ring-Hb only. Electrospray Ionization-Mass Spectrometry (ESI-MS) showed Sclerolinum HBL-Hb composed of seven monomeric globins (15–16 kDa), three disulfide-bonded globin heterodimers and three linkers. The heterodimers always contain globin-b (15814.4 ± 1.5 Da). Sclerolinum ring-Hb is composed of globins and dimers with identical masses as its HBL-Hb, but lacks linkers. Oligobrachia ring-Hb has three globin monomers (14–15 kDa) only, with no disulfide-bonded dimers. Comparison of Sclerolinum hemoglobins between Storegga and Haakon Mosby Mud Volcano, using the normalized height of deconvoluted ESI-MS peaks, shows differences in globin monomers abundances that could reflect genetic differences or differential gene expression between distinct seep populations. The discovery of HBL-Hb in Sclerolinum is a new element supporting the hypothesis of monilifera being phylogenetically more closely related to vestimentifera, than to frenulata.

Published
2010

36. Omics for Precious Rare Biosamples: Characterization of Ancient Human Hair by a Proteomic Approach.

Author

Fresnais M, Richardin P, Sepúlveda M, Leize-Wagner E, and Charrié-Duhaut A

Subjects
Humans, Keratins analysis, Mass Spectrometry, Tandem Mass Spectrometry, Hair chemistry, Keratins chemistry, Proteomics methods
Abstract

Omics technologies have far-reaching applications beyond clinical medicine. A case in point is the analysis of ancient hair samples. Indeed, hair is an important biological indicator that has become a material of choice in archeometry to study the ancient civilizations and their environment. Current characterization of ancient hair is based on elemental and structural analyses, but only few studies have focused on the molecular aspects of ancient hair proteins-keratins-and their conservation state. In such cases, applied extraction protocols require large amounts of raw hair, from 30 to 100 mg. In the present study, we report an optimized new proteomic approach to accurately identify archeological hair proteins, and assess their preservation state, while using a minimum of raw material. Testing and adaptation of three protocols and of nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) parameters were performed on modern hair. On the basis of mass spectrometry data quality, and of the required initial sample amount, the most promising workflow was selected and applied to an ancient archeological sample, dated to about 3880 years before present. Finally, and importantly, we were able to identify 11 ancient hair proteins and to visualize the preservation state of mummy's hair from only 500 μg of raw material. The results presented here pave the way for new insights into the understanding of hair protein alteration processes such as those due to aging and ecological exposures. This work could enable omics scientists to apply a proteomic approach to precious and rare samples, not only in the context of archeometrical studies but also for future applications that would require the use of very small amounts of sample.

Published
2017
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