RT-SVRÂ +Â q: A strategy for post-mascot analysis using retention time and q value metric to improve peptide and protein identifications

► A machine learning approach using retention time based support vector regressor (RT-SVR) is described. ► The application of RT-SVR model on Mascot results increases the accuracy and sensitivity of peptide identifications. ► q Value metric, as a function of ΔRT, is used for the first time to assess the significance of peptide identifications. ► Peptide and protein identifications increase by up to 89.4% and 83.5%, respectively, for NKL cells proteomic analysis. ► A user-friendly Windows-based software is available for free download.