Using data independent acquisition to model high-responding peptides for targeted proteomics experiments
PREGO is a software tool that predicts high responding peptides for SRM experiments. PREGO predicts peptide responses with an artificial neural network trained using 11 minimally redundant, maximally relevant properties. Crucial to its success, PREGO is trained using fragment ion intensities of equimolar synthetic peptides extracted from data independent acquisition (DIA) experiments.
Our approach is described in this talk from ASMS 2015. PREGO is offered as an external tool for Skyline. PREGO is also offered as a standalone cross platform tool with both graphical and command line interfaces.