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

Vialas, Vital; Colomé-Calls, Núria; Abian, Joaquín; Aloria, Kerman; Alvarez-Llamas, Gloria; Antúnez, Oreto; Arizmendi, Jesus M.; Azkargorta, Mikel; Barceló-Batllori, Silvia and Barderas, María G., et al. (2017) In Journal of Proteomics2008-01-01+01:00 152. p.138-149
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... (More)

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.

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keywords
Inter-laboratory validation, Liquid chromatography, Multiple reaction monitoring, Proteomics, Reproducibility, Standardization, Targeted proteomics
in
Journal of Proteomics2008-01-01+01:00
volume
152
pages
12 pages
publisher
Elsevier
external identifiers
  • scopus:84994627735
  • wos:000392554900014
ISSN
1874-3919
DOI
10.1016/j.jprot.2016.10.014
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English
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yes
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47fc4f1e-2c18-4477-8507-2504703b8b7e
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2017-03-03 13:42:32
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2018-01-19 12:21:40
@article{47fc4f1e-2c18-4477-8507-2504703b8b7e,
  abstract     = {<p>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.</p>},
  author       = {Vialas, Vital and Colomé-Calls, Núria and Abian, Joaquín and Aloria, Kerman and Alvarez-Llamas, Gloria and Antúnez, Oreto and Arizmendi, Jesus M. and Azkargorta, Mikel and Barceló-Batllori, Silvia and Barderas, María G. and Blanco, Francisco J and Casal, J. Ignacio and Casas, Vanessa and de la Torre, Carolina and Chicano-Gálvez, Eduardo and Elortza, Felix and Espadas, Guadalupe and Estanyol, Josep M. and Fernandez-Irigoyen, Joaquín and Fernandez-Puente, Patricia and Fidalgo, María José and Fuentes, Manuel and Gay, Marina and Gil, Concha and Hainard, Alexandre and Hernaez, Maria Luisa and Ibarrola, Nieves and Kopylov, Arthur T. and Lario, Antonio and Lopez, Juan Antonio and López-Lucendo, María and Marcilla, Miguel and Marina-Ramírez, Anabel and Marko-Varga, Gyorgy and Martín, Luna and Mora, Maria I. and Morato-López, Esperanza and Muñoz, Javier and Odena, Maria Antonia and de Oliveira, Eliandre and Orera, Irene and Ortea, Ignacio and Pasquarello, Carla and Ray, Kevin B. and Rezeli, Melinda and Ruppen, Isabel and Sabidó, Eduard and del Pino, Manuel M Sanchez and Sancho, Jaime and Santamaría, Enrique and Vazquez, Jesus and Vilaseca, Marta and Vivanco, Fernando and Walters, James J. and Zgoda, Victor G. and Corrales, Fernando J. and Canals, Francesc and Paradela, Alberto},
  issn         = {1874-3919},
  keyword      = {Inter-laboratory validation,Liquid chromatography,Multiple reaction monitoring,Proteomics,Reproducibility,Standardization,Targeted proteomics},
  language     = {eng},
  month        = {01},
  pages        = {138--149},
  publisher    = {Elsevier},
  series       = {Journal of Proteomics2008-01-01+01:00},
  title        = {A multicentric study to evaluate the use of relative retention times in targeted proteomics},
  url          = {http://dx.doi.org/10.1016/j.jprot.2016.10.014},
  volume       = {152},
  year         = {2017},
}