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Bioinformatics Advance Access originally published online on May 19, 2008
Bioinformatics 2008 24(14):1590-1595; doi:10.1093/bioinformatics/btn240
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments

Kosaku Shinoda 1,2, Masaru Tomita 1,2 and Yasushi Ishihama 1,3,*

1Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, 2Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052 and 3PRESTO, Japan Science and Technology Agency, Sanbancho Bldg., 5-Sanbancho, Chiyodaku, Tokyo 102-0075, Japan

*To whom correspondence should be addressed.


  Abstract

Motivation: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool in proteomics studies, but when peptide retention information is used for identification purposes, it remains challenging to compare multiple LC-MS/MS runs or to match observed and predicted retention times, because small changes of LC conditions unavoidably lead to variability in retention times. In addition, non-contiguous retention data obtained with different LC-MS instruments or in different laboratories must be aligned to confirm and utilize rapidly accumulating published proteomics data.

Results: We have developed a new alignment method for peptide retention times based on linear solvent strength (LSS) theory. We found that log k0 (logarithm of retention factor for a given organic solvent) in the LSS theory can be utilized as a ‘universal’ retention index of peptides (RIP) that is independent of LC gradients, and depends solely on the constituents of the mobile phase and the stationary phases. We introduced a machine learning-based scheme to optimize the conversion function of gradient retention times (tg) to log k0. Using the optimized function, tg values obtained with different LC-MS systems can be directly compared with each other on the RIP scale. In an examination of Arabidopsis proteomic data, the vast majority of retention time variability was removed, and five datasets obtained with various LC-MS systems were successfully aligned on the RIP scale.

Contact: y-ishi{at}ttck.keio.ac.jp

Associate Editor: David Rocke

Received on February 14, 2008; revised on April 29, 2008; accepted on May 17, 2008

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