The National Institute of Allergy and Infectious Diseases (NIAID) sponsored Pathogen Functional Genomics Resource Center (PFGRC) at JCVI is pleased to announce the release of the APEX Quantitive Proteomics Tool version 1.1. New features in the APEX Tool include options to perform in silico protein digestions using trypsin, chymotrypsin, or any user defined digestion scheme that matches the lab protocols in use. APEX Tool version 1.1 also includes improved support for the selection of classifier training proteins based on prior LCn-MS/MS results. A new attribute evaluation analysis utility evaluates the power of each reported peptide physicochemical property to predict peptide detection by mass spectrometry. Please visit our APEX page for more information on the new release and to download version 1.1.