Volume 12, Issue 8 p. 1111-1121
Research Article

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

Claudia Escher

Claudia Escher

Biognosys AG, Schlieren, Switzerland

These authors contributed equally to this work.

Search for more papers by this author
Lukas Reiter

Corresponding Author

Lukas Reiter

Biognosys AG, Schlieren, Switzerland

These authors contributed equally to this work.

Correspondence: Dr. Lukas Reiter, Biognosys, Wagistrasse 25, 8952 Zürich, Switzerland

E-mail: [email protected]Fax: +41-44-738-20-49

Search for more papers by this author
Brendan MacLean

Brendan MacLean

Department of Genome Sciences, University of Washington, Seattle, WA, USA

Search for more papers by this author
Reto Ossola

Reto Ossola

Biognosys AG, Schlieren, Switzerland

Search for more papers by this author
Franz Herzog

Franz Herzog

Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland

Search for more papers by this author
John Chilton

John Chilton

Department of Genome Sciences, University of Washington, Seattle, WA, USA

Search for more papers by this author
Michael J. MacCoss

Michael J. MacCoss

Department of Genome Sciences, University of Washington, Seattle, WA, USA

Search for more papers by this author
Oliver Rinner

Oliver Rinner

Biognosys AG, Schlieren, Switzerland

Search for more papers by this author
First published: 11 May 2012
Citations: 424

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.