Standardization of retention time data for AMT tag proteomics database generation

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.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Chromatography, High Pressure Liquid / methods
  • Databases, Protein*
  • Mass Spectrometry / methods
  • Molecular Sequence Data
  • Proteins / chemistry
  • Proteomics*

Substances

  • Proteins