Predicting peptide retention times for proteomics.

The vast majority of modern bottom-up proteomic protocols include chromatographic reversed-phase (RP) fractionation of peptides prior to mass-spectrometric analysis. Retention time information can be easily extracted from LC-MS data and it can be used to improve protein identification/characterization procedures. The key to the success of this procedure is the correct retention time prediction based on compositional and structural properties of the separated species. Our Sequence Specific Retention Calculator (SSRCalc) is a Web-based peptide retention prediction that covers the separation selectivity of the most popular RP-HPLC conditions applied in proteomics. Procedures for the application of SSRCalc to proteomic analyses are described in this unit.