Peptide retention prediction in 2D-HPLC as a tool for comparison of MS/MS search engines

摘要

Continued development of our Sequence Specific Retention Calculator (SSRCalc) algorithm provides the opportunity to effectively use retention prediction in 2D RP HPLC for estimating false the positive rates of MS/MS search engines in large-scale bottom-up proteomics experiments. Mascot, Protein Pilot, and X!Tandem (GPM) were compared using the same data sets (analysis of whole NK-type cell lysate, soluble fraction) both in 1D and 2D HPLC (high pH - low pH). A comparison of number of identified peptides and quality of retention time prediction plots indicated high degree of similarity between the three programs. A slightly lower number of peptides with significant deviation from predicted retention was observed for X!Tandem data.