Using iRT, a normalized retention time for more targeted measurement of peptides.

Proteomics
Claudia EscherOliver Rinner

Abstract

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.

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Citations

Aug 8, 2012·Journal of Proteome Research·Daniel Reker, Lars Malmström
Jul 13, 2012·Science Translational Medicine·Ruth HüttenhainRuedi Aebersold
Nov 28, 2014·Nature·Matthew M GubinRobert D Schreiber
Apr 15, 2014·Nature Biotechnology·Hannes L RöstRuedi Aebersold
Jun 28, 2014·Nature Methods·Jeffrey R WhiteakerAmanda G Paulovich
Aug 26, 2014·Nature Methods·Jonathan D WorboysClaus Jørgensen
Sep 10, 2014·Nature Methods·Martin SostePaola Picotti
Oct 13, 2015·Expert Review of Proteomics·Vendula Pernikářová, Pavel Bouchal
Jul 7, 2015·Expert Review of Proteomics·Olga Kiseleva
Oct 29, 2014·Expert Review of Proteomics·Robert Harlan, Hui Zhang
Jan 19, 2016·Journal of Proteome Research·Stephen W HolmanClaire E Eyers
Jan 23, 2016·Mass Spectrometry Reviews·Luminita Moruz, Lukas Käll
Dec 15, 2015·Journal of Proteome Research·Linda VuorijokiDorota Muth-Pawlak
Nov 13, 2015·Analytical Chemistry·Janice MayneDaniel Figeys
May 15, 2012·Journal of Proteomics·Alessio MaiolicaRuedi Aebersold
Nov 8, 2014·Mass Spectrometry Reviews·Yongsheng Xiao, Yinsheng Wang
Aug 21, 2015·Analytical Chemistry·Jan StanstrupUrška Vrhovšek
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Aug 25, 2015·Journal of Proteome Research·Ying ZhangEmmanuel Varesio
Dec 6, 2014·Environmental Science and Pollution Research International·Florence Arsène-PloetzeChristine Carapito
Jan 28, 2016·International Journal of Cancer. Journal International Du Cancer·Matthew R RussellRobert L J Graham
Sep 3, 2014·Journal of Biochemical and Molecular Toxicology·Melanie M ErzingerShana J Sturla

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