Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
| Autor: | 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 |
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| Přispěvatelé: | 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, Nafarroako Unibertsitate Publikoa. Osasun Zientziak Saila |
| Rok vydání: | 2021 |
| Předmět: |
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 |
| Zdroj: | Dipòsit Digital de la UB Universidad de Barcelona Addi. Archivo Digital para la Docencia y la Investigación instname Digital.CSIC. Repositorio Institucional del CSIC Scientia 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; ... (2022). Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis. Journal of proteomics, 251, p. 104409. Elsevier 10.1016/j.jprot.2021.104409 Academica-e. Repositorio Institucional de la Universidad Pública de Navarra |
| DOI: | 10.1016/j.jprot.2021.104409 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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