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Analysis of institutional authors

Fuentes Prado, MireyaAuthorAbian JAuthorCarrascal MAuthorParadela AAuthor

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December 13, 2021
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Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Publicated to: Journal of Proteomics. 251 104409- - 2022-01-16 251(), DOI: 10.1016/j.jprot.2021.104409

Authors:

Colome, Nuria; Abian, Joaquin; Aloria, Kerman; Arizmendi, Jesus M; Barcelo-Batllori, Silvia; Braga-Lagache, Sophie; Burlet-Schiltz, Odile; Carrascal, Montse; Ignacio Casal, J; Chicano-Galvez, Eduard; Chiva, Cristina; Felipe Clemente, Luis; Elortza, Felix; Estanyol, Josep M; Fernandez-Irigoyen, Joaquin; Fernandez-Puente, Patricia; Jose Fidalgo, Maria; Froment, Carine; Fuentes, Manuel; Fuentes-Almagro, Carlos; Gay, Marina; Hainard, Alexandre; Heller, Manfred; Luisa Hernandez, Maria; Ibarrola, Nieves; Iloro, Ibon; Kieselbach, Thomas; Lario, Antonio; Locard-Paulet, Marie; Marina-Ramirez, Anabel; Martin, Luna; Morato-Lopez, Esperanza; Munoz, Javier; Navajas, Rosana; Odena, M Antonia; Odriozola, Leticia; de Oliveira, Eliandre; Paradela, Alberto; Pasquarello, Carla; de los Rios, Vivian; Ruiz-Romero, Cristina; Sabido, Eduard; Sanchez del Pino, Manuel; Sancho, Jaime; Santamaria, Enrique; Schaeffer-Reiss, Christine; Schneider, Justine; de la Torre, Carolina; Valero, M Luz; Vilaseca, Marta; Wu, Shuai; Wu, Linfeng; Ximenez de Embun, Pilar; Canals, Francesc; Corrales, Fernando J
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Affiliations

Agilent Technol, Santa Clara, CA 95051 USA - Author
Bellvitge Biomed Res Inst IDIBELL, ProteoRed ISCIII, Barcelona, Spain - Author
BIST Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, ProteoRed ISCIII, Baldiri i Reixac 10, Barcelona 08028, Spain - Author
CBM Severo Ochoa CSIC UAM, ProteoRed ISCIII, Madrid 28049, Spain - Author
CIBERehd, Basque Res & Technol Alliance BRTA, Prote Platform, CIC BioGUNE,ProteoRed ISCIII, Bizkaia Sci & Technol Pk, Derio 48160, Spain - Author
Ctr Genom Regulat, Barcelona Inst Sci & Technol BIST, Prote Unit, Barcelona, Spain - Author
Ctr Invest Biol CSIC, ProteoRed ISCIII, Madrid 28040, Spain - Author
Ctr Nacl Biotecnol CSIC, ProteoRed ISCIII, Madrid 28049, Spain - Author
Ctr Nacl Biotecnol CSIC, Spanish Prote Networked Platform, ProteoRed ISCIII PRB3, Madrid 28049, Spain - Author
Ctr Nacl Biotecnol CSIC, Standardizat Initiat, European Prote Assoc, Madrid 28049, Spain - Author
IIBB CSIC IDIBAPS, Inst Invest Biomed Barcelona, ProteoRed ISCIII, Barcelona 08036, Spain - Author
IMIBIC UCO HURS, Prote Unit, ProteoRed ISCIII, IMIBIC Bldg Fl3, Codroba 14004, Spain - Author
INIBIC Complejo Hosp Univ A Coruna, ProteoRed ISCIII, SERGAS, Unidad Prote,Grp Invest Reumatol GIR, La Coruna, Spain - Author
Inoviem Sci, Bioparc3,850 Blvd Sebastien Brant, F-67400 Illkirch Graffenstaden, France - Author
IPBLN CSIC, ProteoRed ISCIII, Granada 18016, Spain - Author
Prote Platform, ProteoRed ISCIII, Barcelona Sci Pk, Barcelona 08028, Spain - Author
Spanish Natl Canc Res Ctr CNIO, ProteoRed ISCIII, Madrid 28029, Spain - Author
Umea Univ Lib, Sci Commun, S-90174 Umea, Sweden - Author
Umea Univ, Dept Chem, S-90187 Umea, Sweden - Author
Univ A Coruna, Agrupac CICA INIBIC, Grp Invest Reumatol GIR, La Coruna, Spain - Author
Univ Barcelona, Sci & Technol Ctr CCiTUB, ProteoRed ISCIII, Barcelona 08036, Spain - Author
Univ Basque Country UPV EHU, Fac Sci & Technol, Dept Biochem & Mol Biol, Leioa, Spain - Author
Univ Basque Country UPV EHU, Prote Core Facil SGIKER, ProteoRed ISCIII, Leioa, Spain - Author
Univ Bern, Dept BioMed Res DBMR, Prote & Mass Spectrometry Core Facil, CH-3010 Bern, Switzerland - Author
Univ Complutense Madrid, Prote Unit, ProteoRed ISCIII, Madrid 28040, Spain - Author
Univ Cordoba, Prote Unit, SCAI, Ramon y Cajal Bldg,Rabanales Campus, Cordoba 14071, Spain - Author
Univ Geneva, CMU, Prote Core Facil, Geneva, Switzerland - Author
Univ Navarra, CIMA, ProteoRed ISCIII, Pamplona 31008, Spain - Author
Univ Pompeu Fabra, Prote Unit, ProteoRed ISCIII, Barcelona, Spain - Author
Univ Publ Navarra UPNA, Complejo Hosp Navarra CHN, Proteored ISCIII Prote Unit, IdiSNA,Clin Neuroprote Grp, Pamplona 31008, Spain - Author
Univ Salamanca, Canc Res Ctr IBMCC CSIC USAL IBSAL, Dept Med & Gen Cytometry Serv Nucleus, Prote Unit,CIBERONC, Salamanca, Spain - Author
Univ Salamanca, Canc Res Ctr IBMCC CSIC USAL IBSAL, ProteoRed ISCIII, CSIC,Prote Unit, Salamanca, Spain - Author
Univ Strasbourg, CNRS, Lab Spectrometrie Masse BioOrgan, IPHC UMR 7178, F-67000 Strasbourg, France - Author
Univ Toulouse, Prote & Mass Spectrometry Biomol, Prote Infrastruct Toulouse,UPS,CNRS, Prote French Infrastruct,ProFLI Inst Pharmacol &, Toulouse, France - Author
Univ Valencia, Biotechnol & Biomed Interdisciplinary Res Unit ER, Burjassot 46100, Spain - Author
Univ Valencia, Cent Serv Expt Res SCSIE, Prote Unit, ProteoRed ISCIII, Burjassot 46100, Spain - Author
Vall dHebron Inst Oncol VHIO, ProteoRed ISCIII, Barcelona 08035, Spain - Author
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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.Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.
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Keywords

enrichmentArticleBenchmarkingLaboratoriesLaboratoryLaboratory testMass spectrometryNormalitzacióPhosphopeptidePhosphoproteinPhosphoproteinsPhosphoproteomicsPhosphorylationProceduresProtein phosphorylationProteomeProteómicaProteomicsQualitative analysisQuality-controlQuantitative analysisReference standardsReproducibilityReproducibility of resultsStandardStandardizationYeast extract

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Journal of Proteomics due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2022, it was in position 31/77, thus managing to position itself as a Q2 (Segundo Cuartil), in the category Biochemical Research Methods. Notably, the journal is positioned en el Cuartil Q2 para la agencia Scopus (SJR) en la categoría Biophysics.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-05:

  • WoS: 2
  • Scopus: 2
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-05:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 27.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 27 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 5.
  • The number of mentions on the social network X (formerly Twitter): 9 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France; Sweden; Switzerland; United States of America.

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Awards linked to the item

We thank Kevin Ray from MilliporeSigma, Saint Louis, MO, for fruitful discussions on the study design, and MilliporeSigma for kindly providing the Phosphomix standards used in the study. ProteoRed, PRB3 is supported by grant PT17/0019/0001, of the PE I+D+i 2013-2016, funded by ISCIII and ERDF.
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