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A multicentric study to evaluate the use of relative retention times in targeted proteomics

By Vital Vialas, Núria Colomé-Calls, Joaquín Abian, Kerman Aloria, Gloria Alvarez-Llamas, Oreto Antúnez, Jesus M. Arizmendi, Mikel Azkargorta, Silvia Barceló-Batllori, María G. Barderas, Francisco J Blanco, J. Ignacio Casal, Vanessa Casas, Carolina de la Torre, Eduardo Chicano-Gálvez, Felix Elortza, Guadalupe Espadas, Josep M. Estanyol, Joaquín Fernandez-Irigoyen, Patricia Fernandez-Puente, María José Fidalgo, Manuel Fuentes, Marina Gay, Concha Gil, Alexandre Hainard, Maria Luisa Hernaez, Nieves Ibarrola, Arthur T. Kopylov, Antonio Lario, Juan Antonio Lopez, María López-Lucendo, Miguel Marcilla, Anabel Marina-Ramírez, Gyorgy Marko-Varga, Luna Martín, Maria I. Mora, Esperanza Morato-López, Javier Muñoz, Maria Antonia Odena, Eliandre de Oliveira, Irene Orera, Ignacio Ortea, Carla Pasquarello, Kevin B. Ray, Melinda Rezeli, Isabel Ruppen, Eduard Sabidó, Manuel M Sanchez del Pino, Jaime Sancho, Enrique Santamaría, Jesus Vazquez, Marta Vilaseca, Fernando Vivanco, James J. Walters, Victor G. Zgoda, Fernando J. Corrales, Francesc Canals and Alberto Paradela

Abstract

Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. Biological significance From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups

Topics: Cell and Molecular Biology, Inter-laboratory validation, Liquid chromatography, Multiple reaction monitoring, Proteomics, Reproducibility, Standardization, Targeted proteomics
Publisher: 'Elsevier BV'
Year: 2017
DOI identifier: 10.1016/j.jprot.2016.10.014
OAI identifier: oai:lup.lub.lu.se:47fc4f1e-2c18-4477-8507-2504703b8b7e
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