Standardization of retention time data for AMT tag proteomics database generation

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.