These authors contributed equally to this work.
Using iRT, a normalized retention time for more targeted measurement of peptides
Article first published online: 11 MAY 2012
© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Volume 12, Issue 8, pages 1111–1121, April 2012
How to Cite
Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J., MacCoss, M. J. and Rinner, O. (2012), Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics, 12: 1111–1121. doi: 10.1002/pmic.201100463
- Issue published online: 11 MAY 2012
- Article first published online: 11 MAY 2012
- Manuscript Accepted: 16 JAN 2012
- Manuscript Revised: 6 JAN 2012
- Manuscript Received: 2 SEP 2011
- NIH. Grant Number: P41 RR011823
- Proteomics methods;
- Quantitative analysis;
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.