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

• Published in: Journal of proteomics Vol. 152; pp. 138 - 149
• Main Authors: Vialas, Vital, Colomé-Calls, Núria, Abian, Joaquín, Aloria, Kerman, Alvarez-Llamas, Gloria, Antúnez, Oreto, Arizmendi, Jesus M., Azkargorta, Mikel, Barceló-Batllori, Silvia, Barderas, María G., Blanco, Francisco, Casal, J. Ignacio, Casas, Vanessa, de la Torre, Carolina, Chicano-Gálvez, Eduardo, Elortza, Felix, Espadas, Guadalupe, Estanyol, Josep M., Fernandez-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Fuentes, Manuel, Gay, Marina, Gil, Concha, Hainard, Alexandre, Hernaez, Maria Luisa, Ibarrola, Nieves, Kopylov, Arthur T., Lario, Antonio, Lopez, Juan Antonio, López-Lucendo, María, Marcilla, Miguel, Marina-Ramírez, Anabel, Marko-Varga, Gyorgy, Martín, Luna, Mora, Maria I., Morato-López, Esperanza, Muñoz, Javier, Odena, Maria Antonia, de Oliveira, Eliandre, Orera, Irene, Ortea, Ignacio, Pasquarello, Carla, Ray, Kevin B., Rezeli, Melinda, Ruppen, Isabel, Sabidó, Eduard, del Pino, Manuel M. Sanchez, Sancho, Jaime, Santamaría, Enrique, Vazquez, Jesus, Vilaseca, Marta, Vivanco, Fernando, Walters, James J., Zgoda, Victor G., Corrales, Fernando J., Canals, Francesc, Paradela, Alberto
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.01.2017
• Subjects: Basic Medicine; Biomedical Research - methods; Biomedical Research - standards; Cell and Molecular Biology; Cell- och molekylärbiologi; Chromatography, Liquid - methods; Chromatography, Liquid - standards; Inter-laboratory validation; Liquid chromatography; Medical and Health Sciences; Medicin och hälsovetenskap; Medicinska och farmaceutiska grundvetenskaper; Multiple reaction monitoring; Observer Variation; Proteomics; Proteomics - methods; Proteomics - organization & administration; Proteomics - standards; Reference Standards; Reproducibility; Reproducibility of Results; Research - standards; Standardization; Targeted proteomics; Targeted proteomics; Reproducibility; Multiple reaction monitoring; Proteomics; Standardization; Liquid chromatography; Inter-laboratory validation
• ISSN: 1874-3919; 1876-7737
• DOI: 10.1016/j.jprot.2016.10.014

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. 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. [Display omitted] •Dimensionless retention time values (iRT) have been proposed to share retention times across chromatographic set-ups.•We have evaluated (28 laboratories) the suitability of retention time standards to improve targeted proteomic analyses.•We demonstrated that iRTs are a useful tool to transfer and share chromatographic information accrossdifferent set-ups.•Quantitative analyses were highly reproducible despite the variety of experimental strategies and analytical set-ups used.