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4. Arabidopsis Responds to Alternaria alternata Volatiles by Triggering Plastid Phosphoglucose Isomerase-Independent Mechanisms

Author

Sánchez-López, Ángela María, Bahaji, Abdellatif, De Diego, Nuria, Baslam, Marouane, Li, Jun, Muñoz, Francisco José, Almagro, Goizeder, García-Gómez, Pablo, Ameztoy, Kinia, Ricarte-Bermejo, Adriana, Novák, Ondřej, Humplík, Jan F., Spíchal, Lukáš, Doležal, Karel, Ciordia, Sergio, Mena, María Carmen, Navajas, Rosana, Baroja-Fernández, Edurne, and Pozueta-Romero, Javier

Published
2016

5. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Author

Instituto de Salud Carlos III, Abián, Joaquín [0000-0003-2823-5429], Aloria, Kerman [0000-0001-7268-7700], Arizmendi, Jesús M. [0000-0002-1412-4042], Barceló-Batllori, Silvia [0000-0002-5352-9747], Burlet-Schiltz, Odile [0000-0002-3606-2356], Carrascal, Montserrat [0000-0002-0205-2176], Casal, J. Ignacio [0000-0003-1085-2840], Chicano-Gálvez, Eduardo [0000-0002-9481-9628], Chiva, Cristina [0000-0001-8150-6203], Elortza, Felix [0000-0001-8839-5438], Estanyol, Josep M. [0000-0001-8621-0057], Fernández-Irigoyen, Joaquín [0000-0001-5072-4099], Fernandez-Puente, Patricia [0000-0001-9968-1034], Froment, Carine [0000-0003-3688-5560], Fuentes-Almagro, Carlos [0000-0001-9940-9065], Gay, Marina [0000-0002-8827-7092], Heller, Manfred [0000-0002-6364-7325], Ibarrola, Nieves [0000-0002-9259-5739], Iloro, Ibon [0000-0002-9537-1714], Kieselbach, Thomas [0000-0001-5577-2938], Lario, Antonio [0000-0002-7457-2402], Locard-Paulet, Marie [0000-0003-2879-9224], Morato-López, Esperanza [0000-0003-4768-895X], Muñoz, Javier [0000-0003-3288-3496], Navajas, Rosana [0000-0002-4481-0553], Odena, Maria Antonia [0000-0002-4530-7829], Oliveira, Eliandre [0000-0003-4771-5719], Paradela, Alberto [0000-0001-6837-7056], Ríos, Vivian de los [0000-0001-5582-6879], Ruiz-Romero, Cristina [0000-0001-7649-9803], Sabidó, Eduard 0000-0001-6506-7714], Sánchez del Pino, Manuel M. [0000-0001-9696-7600], Sancho, Jaime [0000-0003-3852-7951], Santamaría, Enrique [0000-0001-8046-8102], Schaeffer-Reiss, Christine [0000-0003-0672-1979], Valero, M. Luz [0000-0002-2082-4600], Vilaseca, Marta [0000-0002-1666-1300], Canals, Francesc [0000-0002-0650-1135], Colomé, Nuria, Abián, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montserrat, Casal, J. Ignacio, Chicano-Gálvez, Eduardo, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernández-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, Maria Antonia, Odriozola, Leticia, Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, Ríos, Vivian de los, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel M., Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, De la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeng, Ximénez de Embún, Pilar, Canals, Francesc, Corrales, Fernando J., ProteoRed-ISCIII, EuPA, Instituto de Salud Carlos III, Abián, Joaquín [0000-0003-2823-5429], Aloria, Kerman [0000-0001-7268-7700], Arizmendi, Jesús M. [0000-0002-1412-4042], Barceló-Batllori, Silvia [0000-0002-5352-9747], Burlet-Schiltz, Odile [0000-0002-3606-2356], Carrascal, Montserrat [0000-0002-0205-2176], Casal, J. Ignacio [0000-0003-1085-2840], Chicano-Gálvez, Eduardo [0000-0002-9481-9628], Chiva, Cristina [0000-0001-8150-6203], Elortza, Felix [0000-0001-8839-5438], Estanyol, Josep M. [0000-0001-8621-0057], Fernández-Irigoyen, Joaquín [0000-0001-5072-4099], Fernandez-Puente, Patricia [0000-0001-9968-1034], Froment, Carine [0000-0003-3688-5560], Fuentes-Almagro, Carlos [0000-0001-9940-9065], Gay, Marina [0000-0002-8827-7092], Heller, Manfred [0000-0002-6364-7325], Ibarrola, Nieves [0000-0002-9259-5739], Iloro, Ibon [0000-0002-9537-1714], Kieselbach, Thomas [0000-0001-5577-2938], Lario, Antonio [0000-0002-7457-2402], Locard-Paulet, Marie [0000-0003-2879-9224], Morato-López, Esperanza [0000-0003-4768-895X], Muñoz, Javier [0000-0003-3288-3496], Navajas, Rosana [0000-0002-4481-0553], Odena, Maria Antonia [0000-0002-4530-7829], Oliveira, Eliandre [0000-0003-4771-5719], Paradela, Alberto [0000-0001-6837-7056], Ríos, Vivian de los [0000-0001-5582-6879], Ruiz-Romero, Cristina [0000-0001-7649-9803], Sabidó, Eduard 0000-0001-6506-7714], Sánchez del Pino, Manuel M. [0000-0001-9696-7600], Sancho, Jaime [0000-0003-3852-7951], Santamaría, Enrique [0000-0001-8046-8102], Schaeffer-Reiss, Christine [0000-0003-0672-1979], Valero, M. Luz [0000-0002-2082-4600], Vilaseca, Marta [0000-0002-1666-1300], Canals, Francesc [0000-0002-0650-1135], Colomé, Nuria, Abián, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montserrat, Casal, J. Ignacio, Chicano-Gálvez, Eduardo, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernández-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, Maria Antonia, Odriozola, Leticia, Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, Ríos, Vivian de los, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel M., Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, De la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeng, Ximénez de Embún, Pilar, Canals, Francesc, Corrales, Fernando J., ProteoRed-ISCIII, and EuPA

Abstract

Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.

Published
2022

7. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Author

Colomé, Nuria, Abián, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montserrat, Casal, J. Ignacio, Chicano-Gálvez, Eduardo, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernández-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, Maria Antonia, Odriozola, Leticia, Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, Ríos, Vivian de los, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel M., Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, De la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeng, Ximénez de Embún, Pilar, Canals, Francesc, Corrales, Fernando J., ProteoRed-ISCIII, EuPA, Instituto de Salud Carlos III, Abián, Joaquín [0000-0003-2823-5429], Aloria, Kerman [0000-0001-7268-7700], Arizmendi, Jesús M. [0000-0002-1412-4042], Barceló-Batllori, Silvia [0000-0002-5352-9747], Burlet-Schiltz, Odile [0000-0002-3606-2356], Carrascal, Montserrat [0000-0002-0205-2176], Casal, J. Ignacio [0000-0003-1085-2840], Chicano-Gálvez, Eduardo [0000-0002-9481-9628], Chiva, Cristina [0000-0001-8150-6203], Elortza, Felix [0000-0001-8839-5438], Estanyol, Josep M. [0000-0001-8621-0057], Fernández-Irigoyen, Joaquín [0000-0001-5072-4099], Fernandez-Puente, Patricia [0000-0001-9968-1034], Froment, Carine [0000-0003-3688-5560], Fuentes-Almagro, Carlos [0000-0001-9940-9065], Gay, Marina [0000-0002-8827-7092], Heller, Manfred [0000-0002-6364-7325], Ibarrola, Nieves [0000-0002-9259-5739], Iloro, Ibon [0000-0002-9537-1714], Kieselbach, Thomas [0000-0001-5577-2938], Lario, Antonio [0000-0002-7457-2402], Locard-Paulet, Marie [0000-0003-2879-9224], Morato-López, Esperanza [0000-0003-4768-895X], Muñoz, Javier [0000-0003-3288-3496], Navajas, Rosana [0000-0002-4481-0553], Odena, Maria Antonia [0000-0002-4530-7829], Oliveira, Eliandre [0000-0003-4771-5719], Paradela, Alberto [0000-0001-6837-7056], Ríos, Vivian de los [0000-0001-5582-6879], Ruiz-Romero, Cristina [0000-0001-7649-9803], Sabidó, Eduard 0000-0001-6506-7714], Sánchez del Pino, Manuel M. [0000-0001-9696-7600], Sancho, Jaime [0000-0003-3852-7951], Santamaría, Enrique [0000-0001-8046-8102], Schaeffer-Reiss, Christine [0000-0003-0672-1979], Valero, M. Luz [0000-0002-2082-4600], Vilaseca, Marta [0000-0002-1666-1300], Canals, Francesc [0000-0002-0650-1135], Institut Català de la Salut, [Colomé N, Martín L, Canals F] ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Abian J] ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona, Spain. [Aloria K] ProteoRed-ISCIII, Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain. [Arizmendi JM] Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain. [Barceló-Batllori S] ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain. [Braga-Lagache S] Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, Bern, Switzerland, Vall d'Hebron Barcelona Hospital Campus, Abián, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Burlet-Schiltz, Odile, Carrascal, Montserrat, Casal, J. Ignacio, Chicano-Gálvez, Eduardo, Chiva, Cristina, Elortza, Felix, Estanyol, Josep M., Fernández-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Froment, Carine, Fuentes-Almagro, Carlos, Gay, Marina, Heller, Manfred, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, Maria Antonia, Oliveira, Eliandre, Paradela, Alberto, Ríos, Vivian de los, Ruiz-Romero, Cristina, Sánchez del Pino, Manuel M., Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Valero, M. Luz, Vilaseca, Marta, Canals, Francesc, Universidad Pública de Navarra. Departamento de Ciencias de la Salud, and Nafarroako Unibertsitate Publikoa. Osasun Zientziak Saila

Subjects
Proteomics, enrichment, Standardization, Proteome, Computer science, Cellbiologi, Mass-spectrometry, Biophysics, 610 Medicine & health, Computational biology, Bioinformatik och systembiologi, Proteòmica, Chemical Phenomena::Biochemical Phenomena::Phosphorylation [PHENOMENA AND PROCESSES], Biochemistry, Experiment, Fosforilació, Natural Science Disciplines::Biological Science Disciplines::Biochemistry::Proteomics [DISCIPLINES AND OCCUPATIONS], Investigative Techniques::Epidemiologic Methods::Epidemiologic Research Design::Reproducibility of Results [ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT], Inter-laboratory, Phosphorylation, quality control, Epidemiologia, Bioinformatics and Systems Biology, Fosfoproteïnes, fenómenos químicos::fenómenos bioquímicos::fosforilación [FENÓMENOS Y PROCESOS], disciplinas de las ciencias naturales::disciplinas de las ciencias biológicas::bioquímica::proteómica [DISCIPLINAS Y OCUPACIONES], Phosphoproteomics, Biochemistry and Molecular Biology, Reproducibility of Results, Cell Biology, Reference Standards, técnicas de investigación::métodos epidemiológicos::diseño de la investigación epidemiológica::reproducibilidad de los resultados [TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS], Normalització, Phosphoproteins, Reference sample, Phosphoproteome, Laboratory experiment, Laboratories, Biokemi och molekylärbiologi
Abstract

6 p.-2 fig.-2 tab., Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance., ProteoRed, PRB3 is supported by grant PT17/0019/0001, of the PE I+D+i 2013-2016, funded by ISCIII and ERDF.

Published
2021
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9. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Author

Colomé, Núria, Abian, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montse, Casal, J. Ignacio, Chicano-Gálvez, Eduard, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernandez-Irigoyen, Joaquín, Fernández-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina-Ramírez, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, M. Antonia, Odriozola, Leticia, de Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, de los Rios, Vivian, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel, Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, de la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeg, de Embún, Pilar Ximénez, Canals, Francesc, Corrales, Fernando J., Colomé, Núria, Abian, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montse, Casal, J. Ignacio, Chicano-Gálvez, Eduard, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernandez-Irigoyen, Joaquín, Fernández-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina-Ramírez, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, M. Antonia, Odriozola, Leticia, de Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, de los Rios, Vivian, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel, Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, de la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeg, de Embún, Pilar Ximénez, Canals, Francesc, and Corrales, Fernando J.

Abstract

Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.

Published
2022
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11. Additional file 1 of Quantitative proteomic analysis of serum-purified exosomes identifies putative pre-eclampsia-associated biomarkers

Author

Navajas, Rosana, Ramos-Fernandez, Antonio, Herraiz, Ignacio, Galindo, Alberto, Bartha, Jos�� Luis, Corrales, Fernando, and Paradela, Alberto

Abstract

Additional file 1: Figure S1. Scheme of the experimental flow used in the proteomic analysis of exosomes purified from clinical serum samples (control / EOPE).

Published
2022
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12. Additional file 2 of Quantitative proteomic analysis of serum-purified exosomes identifies putative pre-eclampsia-associated biomarkers

Author

Navajas, Rosana, Ramos-Fernandez, Antonio, Herraiz, Ignacio, Galindo, Alberto, Bartha, Jos�� Luis, Corrales, Fernando, and Paradela, Alberto

Abstract

Additional file 2: Figure S2a���c. Boxplots of differences in estimated abundance in pre-eclampsia (PE) and control (C) samples. Only proteins with q C or PE

Published
2022
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15. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Author

Colomé, Núria, primary, Abian, Joaquín, additional, Aloria, Kerman, additional, Arizmendi, Jesús M., additional, Barceló-Batllori, Silvia, additional, Braga-Lagache, Sophie, additional, Burlet-Schiltz, Odile, additional, Carrascal, Montse, additional, Casal, J. Ignacio, additional, Chicano-Gálvez, Eduard, additional, Chiva, Cristina, additional, Clemente, Luis Felipe, additional, Elortza, Felix, additional, Estanyol, Josep M., additional, Fernandez-Irigoyen, Joaquín, additional, Fernández-Puente, Patricia, additional, Fidalgo, María José, additional, Froment, Carine, additional, Fuentes, Manuel, additional, Fuentes-Almagro, Carlos, additional, Gay, Marina, additional, Hainard, Alexandre, additional, Heller, Manfred, additional, Hernández, María Luisa, additional, Ibarrola, Nieves, additional, Iloro, Ibon, additional, Kieselbach, Thomas, additional, Lario, Antonio, additional, Locard-Paulet, Marie, additional, Marina-Ramírez, Anabel, additional, Martín, Luna, additional, Morato-López, Esperanza, additional, Muñoz, Javier, additional, Navajas, Rosana, additional, Odena, M. Antonia, additional, Odriozola, Leticia, additional, de Oliveira, Eliandre, additional, Paradela, Alberto, additional, Mosimann, Carla Pasquarello, additional, de los Rios, Vivian, additional, Ruiz-Romero, Cristina, additional, Sabidó, Eduard, additional, del Pino, Manuel Sánchez, additional, Sancho, Jaime, additional, Santamaría, Enrique, additional, Schaeffer-Reiss, Christine, additional, Schneider, Justine, additional, de la Torre, Carolina, additional, Valero, M. Luz, additional, Vilaseca, Marta, additional, Wu, Shuai, additional, Wu, Linfeng, additional, de Embún, Pilar Ximénez, additional, Canals, Francesc, additional, and Corrales, Fernando, additional

Published
2021
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22. Phosphorylation-related crosstalk between distant regions of the core region of the coat protein contributes to virion assembly of plum pox virus

Author

Ministerio de Economía y Competitividad (España), Hervás, Marta, Navajas, Rosana, Chagoyen, Mónica, García, Juan Antonio, Martínez-Turiño, Sandra, Ministerio de Economía y Competitividad (España), Hervás, Marta, Navajas, Rosana, Chagoyen, Mónica, García, Juan Antonio, and Martínez-Turiño, Sandra

Abstract

Eukaryotic proteins are often targets of posttranslational modifications (PTMs). Capsid protein (CP) of plum pox virus (PPV), a member of genus Potyvirus, has been reported to be prone to phosphorylation in four serines at the N-terminal region. CP phosphorylation has been proposed to influence PPV infection by regulating CP accumulation in coordination with a second PTM, O-GlcNAcylation. In this study, a further proteomic characterization of PPV CP phosphorylation revealed additional phospho-targets, thus evidencing even greater complexity of the network of PTMs affecting this protein. In particular, two new phosphorylation targets, T254 and T313, at protein distal core, appear to be highly relevant for infection. Although abolishing phosphorylation at these positions does not have a severe effect on infectivity or viral accumulation, phospho-mimicking at either of these targets disrupts cell-to-cell movement. Strand-specific reverse transcription-quantitative PCR analysis and fractionation by centrifugation in a continuous sucrose gradient enabled us to conclude that such a deleterious effect is not related to failures in replication but is a consequence of inaccurate virion assembly. The analysis of spontaneous compensatory mutations at the CP core identified in a multiple phospho-mimicking mutant disclosed a functional dialogue between distant phospho-targets, which was further supported by an in silico PPV virion model, built on the watermelon mosaic virus atomic structure. Therefore, whereas joint and opposite action of O-GlcNAcylation and phosphorylation at the N-terminal disordered protrusion of CP appears to regulate protein stability, we propose that phosphorylations at the core region control assembly and disassembly of viral particles.

Published
2020

23. Common and Strain-Specific Post-Translational Modifications of the Potyvirus Plum pox virus Coat Protein in Different Hosts

Author

Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Hervás, Marta, Ciordia, Sergio, Navajas, Rosana, García, Juan Antonio, Martínez-Turiño, Sandra, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Hervás, Marta, Ciordia, Sergio, Navajas, Rosana, García, Juan Antonio, and Martínez-Turiño, Sandra

Abstract

Phosphorylation and O-GlcNAcylation are widespread post-translational modifications (PTMs), often sharing protein targets. Numerous studies have reported the phosphorylation of plant viral proteins. In plants, research on O-GlcNAcylation lags behind that of other eukaryotes, and information about O-GlcNAcylated plant viral proteins is extremely scarce. The potyvirus Plum pox virus (PPV) causes sharka disease in Prunus trees and also infects a wide range of experimental hosts. Capsid protein (CP) from virions of PPV-R isolate purified from herbaceous plants can be extensively modified by O-GlcNAcylation and phosphorylation. In this study, a combination of proteomics and biochemical approaches was employed to broaden knowledge of PPV CP PTMs. CP proved to be modified regardless of whether or not it was assembled into mature particles. PTMs of CP occurred in the natural host Prunus persica, similarly to what happens in herbaceous plants. Additionally, we observed that O-GlcNAcylation and phosphorylation were general features of different PPV strains, suggesting that these modifications contribute to general strategies deployed during plant-virus interactions. Interestingly, phosphorylation at a casein kinase II motif conserved among potyviral CPs exhibited strain specificity in PPV; however, it did not display the critical role attributed to the same modification in the CP of another potyvirus, Potato virus A.

Published
2020

24. Serum Exosome Isolation by Size-Exclusion Chromatography for the Discovery and Validation of Preeclampsia-Associated Biomarkers

Author

Instituto de Salud Carlos III, European Commission, Navajas, Rosana, Corrales, Fernando J., Paradela, Alberto, Instituto de Salud Carlos III, European Commission, Navajas, Rosana, Corrales, Fernando J., and Paradela, Alberto

Abstract

Exosomes are extracellular nanovesicles of complex and heterogeneous composition that are released in biofluids such as blood. The interest in the characterization of exosomal biochemistry has increased over the last few years as they convey cellular proteins, lipids, and RNA that might reflect the biological or pathological condition of the source cell. In particular, association of changes of exosome proteins with specific pathogenic processes arises as a promising method to identify disease biomarkers as for the pregnancy-related preeclampsia. However, the overlapping physicochemical and structural characteristics of different types of extracellular vesicles have hindered the consolidation of universally accepted and standardized purification or enrichment protocols. Thus, it has been recently demonstrated that the exosomal protein profile resulting from in-depth proteomics analyses is highly dependent on the preparation protocol used, which will determine the particle type specificity and the presence/absence of contaminating proteins. In this chapter, an isolation method of serum exosomes based on size-exclusion chromatography (SEC) using qEV columns (Izon) is described. We show that this method is fast and reliable, as the population of exosomes isolated is homogeneous in terms of size, morphology, and protein composition. This exosome enrichment method is compatible with downstream qualitative and quantitative proteomic analysis of the samples.

Published
2019

26. PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets

Author

Martínez-Bartolomé, Salvador, primary, Medina-Aunon, J. Alberto, additional, López-García, Miguel Ángel, additional, González-Tejedo, Carmen, additional, Prieto, Gorka, additional, Navajas, Rosana, additional, Salazar-Donate, Emilio, additional, Fernández-Costa, Carolina, additional, Yates, John R., additional, and Albar, Juan Pablo, additional

Published
2018
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27. In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets

Author

Segura, Víctor, primary, Valero, M., additional, Cantero, Laura, additional, Muñoz, Javier, additional, Zarzuela, Eduardo, additional, García, Fernando, additional, Aloria, Kerman, additional, Beaskoetxea, Javier, additional, Arizmendi, Jesús, additional, Navajas, Rosana, additional, Paradela, Alberto, additional, Díez, Paula, additional, Dégano, Rosa, additional, Fuentes, Manuel, additional, Orfao, Alberto, additional, García Montero, Andrés, additional, Garin-Muga, Alba, additional, Corrales, Fernando, additional, and Sánchez del Pino, Manuel, additional

Published
2018
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28. In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets

Author

Bioquímica y biología molecular, Biokimika eta biologia molekularra, Segura, Victor, Valero, M. Luz, Cantero, Laura, Muñoz, Javier, Zarzuela, Eduardo, García, Fernando, Aloria Escolastico, Kerman, Beaskoetxea Lejarzegi, Javier, Arizmendi Bastarrika, Jesús María, Navajas, Rosana, Paradela, Alberto, Díez, Paula, Degano, Rosa M., Fuentes, Manuel, Orfao, Alberto, García Montero, Andrés, Garin-Muga, Alba, Corrales, Fernando J., Sánchez del Pino, Manuel M., Bioquímica y biología molecular, Biokimika eta biologia molekularra, Segura, Victor, Valero, M. Luz, Cantero, Laura, Muñoz, Javier, Zarzuela, Eduardo, García, Fernando, Aloria Escolastico, Kerman, Beaskoetxea Lejarzegi, Javier, Arizmendi Bastarrika, Jesús María, Navajas, Rosana, Paradela, Alberto, Díez, Paula, Degano, Rosa M., Fuentes, Manuel, Orfao, Alberto, García Montero, Andrés, Garin-Muga, Alba, Corrales, Fernando J., and Sánchez del Pino, Manuel M.

Abstract

Monocytes are bone marrow-derived leukocytes that are part of the innate immune system. Monocytes are divided into three subsets: classical, intermediate and non-classical, which can be differentiated by their expression of some surface antigens, mainly CD14 and CD16. These cells are key players in the inflammation process underlying the mechanism of many diseases. Thus, the molecular characterization of these cells may provide very useful information for understanding their biology in health and disease. We performed a multicentric proteomic study with pure classical and non-classical populations derived from 12 healthy donors. The robust workflow used provided reproducible results among the five participating laboratories. Over 5000 proteins were identified, and about half of them were quantified using a spectral counting approach. The results represent the protein abundance catalogue of pure classical and enriched non-classical blood peripheral monocytes, and could serve as a reference dataset of the healthy population. The functional analysis of the differences between cell subsets supports the consensus roles assigned to human monocytes.

Published
2018

29. In-depth proteomic characterization of classical and non-classical monocyte subsets

Author

European Commission, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia e Innovación (España), Segura, Víctor, Valero, M. Luz, Cantero, Laura, Muñoz, Javier, Zarzuela, Eduardo, García, Fernando, Aloria, Kerman, Beaskoetxea, Javier, Arizmendi, Jesús M., Navajas, Rosana, Paradela, Alberto, Díez, Paula, Dégano, Rosa M., Fuentes, Manuel, Orfao, Alberto, García-Montero, Andrés, Garin-Muga, Alba, Corrales, Fernando J., Sánchez del Pino, Manuel M., European Commission, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia e Innovación (España), Segura, Víctor, Valero, M. Luz, Cantero, Laura, Muñoz, Javier, Zarzuela, Eduardo, García, Fernando, Aloria, Kerman, Beaskoetxea, Javier, Arizmendi, Jesús M., Navajas, Rosana, Paradela, Alberto, Díez, Paula, Dégano, Rosa M., Fuentes, Manuel, Orfao, Alberto, García-Montero, Andrés, Garin-Muga, Alba, Corrales, Fernando J., and Sánchez del Pino, Manuel M.

Abstract

Monocytes are bone marrow-derived leukocytes that are part of the innate immune system. Monocytes are divided into three subsets: classical, intermediate and non-classical, which can be differentiated by their expression of some surface antigens, mainly CD14 and CD16. These cells are key players in the inflammation process underlying the mechanism of many diseases. Thus, the molecular characterization of these cells may provide very useful information for understanding their biology in health and disease. We performed a multicentric proteomic study with pure classical and non-classical populations derived from 12 healthy donors. The robust workflow used provided reproducible results among the five participating laboratories. Over 5000 proteins were identified, and about half of them were quantified using a spectral counting approach. The results represent the protein abundance catalogue of pure classical and enriched non-classical blood peripheral monocytes, and could serve as a reference dataset of the healthy population. The functional analysis of the differences between cell subsets supports the consensus roles assigned to human monocytes.

Published
2018

31. Arabidopsis responds to Alternaria alternata volatiles by triggering pPG-independent mechanisms

Author

Sánchez López, Ángela María, Bahaji, Abdellatif, Diego, Nuria de, Baslam, Marouane, Li, Jun, Muñoz Pérez, Francisco José, Almagro Zabalza, Goizeder, García Gómez, Pablo, Ameztoy del Amo, Kinia, Ricarte Bermejo, Adriana, Novák, Ondrej, Humplik, Jan F., Spíchal, Lukás, Dolezal, Karel, Ciordia, Sergio, Mena, María Carmen, Navajas, Rosana, Baroja Fernández, Edurne, Pozueta Romero, Javier, IdAB – Instituto de Agrobiotecnología / Agrobioteknologiako Institutua, Gobierno de Navarra / Nafarroako Gobernua (IIM010491.RI1), and Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa

Subjects
Cytokinins, fungi, Arabidopsis, Volatile compounds, food and beverages, Alternaria alternata, Phosphoglucose isomerase
Abstract

Incluye material complementario Volatile compounds (VCs) emitted by phylogenetically diverse microorganisms (including plant pathogens and microbes that do not normally interact mutualistically with plants) promote photosynthesis, growth, and the accumulation of high levels of starch in leaves through cytokinin (CK)-regulated processes. In Arabidopsis (Arabidopsis thaliana) plants not exposed to VCs, plastidic phosphoglucose isomerase (pPGI) acts as an important determinant of photosynthesis and growth, likely as a consequence of its involvement in the synthesis of plastidic CKs in roots. Moreover, this enzyme plays an important role in connecting the Calvin- Benson cycle with the starch biosynthetic pathway in leaves. To elucidate the mechanisms involved in the responses of plants to microbial VCs and to investigate the extent of pPGI involvement, we characterized pPGI-null pgi1-2 Arabidopsis plants cultured in the presence or absence of VCs emitted by Alternaria alternata. We found that volatile emissions from this fungal phytopathogen promote growth, photosynthesis, and the accumulation of plastidic CKs in pgi1-2 leaves. Notably, the mesophyll cells of pgi1-2 leaves accumulated exceptionally high levels of starch following VC exposure. Proteomic analyses revealed that VCs promote global changes in the expression of proteins involved in photosynthesis, starch metabolism, and growth that can account for the observed responses in pgi1-2 plants. The overall data show that Arabidopsis plants can respond to VCs emitted by phytopathogenic microorganisms by triggering pPGI-independent mechanisms. This work was supported by the Comisión Interministerial de Ciencia y Tecnología and Fondo Europeo de Desarrollo Regional, Spain (grant nos. BIO2010–18239 and BIO2013–49125–C2–1–P), by the Government of Navarra (grant no. IIM010491.RI1), by the I-Link0939 project from the Ministerio de Economía y Competitividad, by the Ministry of Education, Youth, and Sports of the Czech Republic (grant no. LO1204 from the National Program of Sustainability), by Palacky University institutional support, by predoctoral fellowships from the Spanish Ministry of Science and Innovation (to A.M.S.-L. and P.G.-G.), and by postdoctoral fellowships from the Public University of Navarra (to M.B. and G.A.).

Published
2016

32. Guidelines for reporting quantitative mass spectrometry based experiments in proteomics

Author

Martínez-Bartolomé, Salvador, Deutsch, Eric W., Binz, Pierre-Alain, Jones, Andrew R., Eisenacher, Martin, Mayer, Gerhard, Campos, Alex, Canals, Francesc, Bech-Serra, Joan-Josep, Carrascal, Montserrat, Gay, Marina, Paradela, Alberto, Navajas, Rosana, Marcilla, Miguel, Hernáez, María Luisa, Gutiérrez-Blázquez, María Dolores, Velarde, Luis Felipe Clemente, Aloria, Kerman, Beaskoetxea, Jabier, Medina-Aunon, J. Alberto, and Albar, Juan P.

Published
2013
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33. Arabidopsis responds to Alternaria alternata volatiles by triggering plastid phosphoglucose isomerase-independent mechanisms

Author

Comisión Interministerial de Ciencia y Tecnología, CICYT (España), European Commission, Nafarroako Gobernua, Ministerio de Economía y Competitividad (España), Ministry of Education, Youth and Sports (Czech Republic), Palacky University, Ministerio de Ciencia e Innovación (España), Universidad Pública de Navarra, Sánchez-López, Ángela María, Bahaji, Abdellatif, Diego, Nuria de, Muñoz Pérez, Francisco José, Almagro, Goizeder, Ricarte-Bermejo, Adriana, Ciordia, Sergio, Mena Valverde, Mª Carmen, Navajas, Rosana, Baroja-Fernández, Edurne, Pozueta Romero, Javier, Comisión Interministerial de Ciencia y Tecnología, CICYT (España), European Commission, Nafarroako Gobernua, Ministerio de Economía y Competitividad (España), Ministry of Education, Youth and Sports (Czech Republic), Palacky University, Ministerio de Ciencia e Innovación (España), Universidad Pública de Navarra, Sánchez-López, Ángela María, Bahaji, Abdellatif, Diego, Nuria de, Muñoz Pérez, Francisco José, Almagro, Goizeder, Ricarte-Bermejo, Adriana, Ciordia, Sergio, Mena Valverde, Mª Carmen, Navajas, Rosana, Baroja-Fernández, Edurne, and Pozueta Romero, Javier

Abstract

Volatile compounds (VCs) emitted by phylogenetically diverse microorganisms (including plant pathogens and microbes that do not normally interact mutualistically with plants) promote photosynthesis, growth, and the accumulation of high levels of starch in leaves through cytokinin (CK)-regulated processes. In Arabidopsis (Arabidopsis thaliana) plants not exposed to VCs, plastidic phosphoglucose isomerase (pPGI) acts as an important determinant of photosynthesis and growth, likely as a consequence of its involvement in the synthesis of plastidic CKs in roots. Moreover, this enzyme plays an important role in connecting the Calvin-Benson cycle with the starch biosynthetic pathway in leaves. To elucidate the mechanisms involved in the responses of plants to microbial VCs and to investigate the extent of pPGI involvement, we characterized pPGI-null pgi1-2 Arabidopsis plants cultured in the presence or absence of VCs emitted by Alternaria alternata. We found that volatile emissions from this fungal phytopathogen promote growth, photosynthesis, and the accumulation of plastidic CKs in pgi1-2 leaves. Notably, the mesophyll cells of pgi1-2 leaves accumulated exceptionally high levels of starch following VC exposure. Proteomic analyses revealed that VCs promote global changes in the expression of proteins involved in photosynthesis, starch metabolism, and growth that can account for the observed responses in pgi1-2 plants. The overall data show that Arabidopsis plants can respond to VCs emitted by phytopathogenic microorganisms by triggering pPGI-independent mechanisms.

Published
2016

34. Phosphorylation coexists with <italic>O</italic>‐GlcNAcylation in a plant virus protein and influences viral infection.

Author

Martínez‐Turiño, Sandra, Pérez, José De Jesús, Hervás, Marta, Navajas, Rosana, Ciordia, Sergio, Udeshi, Namrata D., Shabanowitz, Jeffrey, Hunt, Donald F., and García, Juan Antonio

Subjects
PHOSPHORYLATION, PLANT virus proteins, VIRUS diseases of plants, PLUM pox virus, POTYVIRUSES
Abstract

Summary: Phosphorylation and O‐GlcNAcylation are two widespread post‐translational modifications (PTMs), often affecting the same eukaryotic target protein. Plum pox virus (PPV) is a member of the genus Potyvirus which infects a wide range of plant species. O‐GlcNAcylation of the capsid protein (CP) of PPV has been studied extensively, and some evidence of CP phosphorylation has also been reported. Here, we use proteomics analyses to demonstrate that PPV CP is phosphorylated in vivo at the N‐terminus and the beginning of the core region. In contrast with the ‘yin–yang’ mechanism that applies to some mammalian proteins, PPV CP phosphorylation affects residues different from those that are O‐GlcNAcylated (serines Ser‐25, Ser‐81, Ser‐101 and Ser‐118). Our findings show that PPV CP can be concurrently phosphorylated and O‐GlcNAcylated at nearby residues. However, an analysis using a differential proteomics strategy based on iTRAQ (isobaric tags for relative and absolute quantitation) showed a significant enhancement of phosphorylation at Ser‐25 in virions recovered from O‐GlcNAcylation‐deficient plants, suggesting that crosstalk between O‐GlcNAcylation and phosphorylation in PPV CP takes place. Although the preclusion of phosphorylation at the four identified phosphotarget sites only had a limited impact on viral infection, the mimicking of phosphorylation prevents PPV infection in Prunus persica and weakens infection in Nicotiana benthamiana and other herbaceous hosts, prompting the emergence of potentially compensatory second mutations. We postulate that the joint action of phosphorylation and O‐GlcNAcylation in the N‐proximal segment of CP allows a fine‐tuning of protein stability, providing the amount of CP required in each step of viral infection. [ABSTRACT FROM AUTHOR]

Published
2018
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43. Serum Exosome Isolation by Size-Exclusion Chromatography for the Discovery and Validation of Preeclampsia-Associated Biomarkers.

Author

Navajas R, Corrales FJ, and Paradela A

Subjects
Chromatography, Liquid, Exosomes ultrastructure, Extracellular Vesicles metabolism, Extracellular Vesicles ultrastructure, Female, Humans, Pre-Eclampsia diagnosis, Pregnancy, Proteomics methods, Reproducibility of Results, Tandem Mass Spectrometry, Workflow, Biomarkers, Chromatography, Gel instrumentation, Chromatography, Gel methods, Chromatography, Gel standards, Exosomes metabolism, Pre-Eclampsia blood
Abstract

Exosomes are extracellular nanovesicles of complex and heterogeneous composition that are released in biofluids such as blood. The interest in the characterization of exosomal biochemistry has increased over the last few years as they convey cellular proteins, lipids, and RNA that might reflect the biological or pathological condition of the source cell. In particular, association of changes of exosome proteins with specific pathogenic processes arises as a promising method to identify disease biomarkers as for the pregnancy-related preeclampsia. However, the overlapping physicochemical and structural characteristics of different types of extracellular vesicles have hindered the consolidation of universally accepted and standardized purification or enrichment protocols. Thus, it has been recently demonstrated that the exosomal protein profile resulting from in-depth proteomics analyses is highly dependent on the preparation protocol used, which will determine the particle type specificity and the presence/absence of contaminating proteins.In this chapter, an isolation method of serum exosomes based on size-exclusion chromatography (SEC) using qEV columns (Izon) is described. We show that this method is fast and reliable, as the population of exosomes isolated is homogeneous in terms of size, morphology, and protein composition. This exosome enrichment method is compatible with downstream qualitative and quantitative proteomic analysis of the samples.

Published
2019
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44. Immobilized metal affinity chromatography/reversed-phase enrichment of phosphopeptides and analysis by CID/ETD tandem mass spectrometry.

Author

Navajas R, Paradela A, and Albar JP

Subjects
Amino Acid Sequence, Analytic Sample Preparation Methods, Animals, Databases, Protein, Electron Transport, Humans, Immobilized Proteins chemistry, Immobilized Proteins metabolism, Phosphopeptides chemistry, Phosphopeptides metabolism, Chromatography, Affinity methods, Immobilized Proteins analysis, Immobilized Proteins isolation & purification, Metals chemistry, Phosphopeptides analysis, Phosphopeptides isolation & purification, Tandem Mass Spectrometry methods
Abstract

Major difficulties in phosphoprotein analysis relate to the presence of a huge number of nonphosphorylated proteins and to the wide concentration dynamic range among them. In order to overcome the analysis complexity, specific clean-up and highly efficient enrichment procedures are mandatory prior to the -chromatographic separation and identification by tandem mass spectrometry. In this chapter, a procedure based on immobilized metal affinity chromatography (IMAC)/reversed-phase phosphopeptide purification and analysis by nanoHPLC-ESI-MS/MS with ion trap is described in detail. CID (collision-induced -dissociation) and ETD (electron-transfer dissociation) fragmentation techniques are used in combination to specifically determine phosphorylation sites inside the peptide sequences, through the analysis of MS/MS spectra.

Published
2011
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