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J Chromatogr B Analyt Technol Biomed Life Sci. 2009 Feb 1;877(4):433-40. doi: 10.1016/j.jchromb.2008.12.047. Epub 2008 Dec 25.

Standardization of retention time data for AMT tag proteomics database generation.

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Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.


The combination of liquid chromatography (LC) with mass spectrometry (MS) has become a mainstream proteome analysis strategy. In LC-MS, measured masses possess their "universal" scale derived from atomic mass tables. In contrast, the observed LC retention times (RT) are not tied to a conventional time scale, and depend on experimental conditions. However, RT data, being explicitly orthogonal to MS, offer relevant information for proteome characterization. We present here a strategy for peptides RT data standardization, based on the generation of a standard scale using retention prediction models, which enables sharing of identification databases in the context of multi-laboratory research.

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