The application of targeted multiplexing using isobaric technology to complex samples remains a challenge. In this ASMS 2016 breakfast workshop, Robert Everley, Harvard Medical School, discusses the challenges for targeted proteomics and the goals his lab sought to accomplish. The first included a dual multiplexing strategy at both the analyte and sample level, which was achieved by monitoring 100 targets across 10 samples in a single injection (1000 quantitation measurements per run). The second goal was to maintain sample data quality without fractionation. In this case, the team found fractionated data (72 hr MS time) could be recapitulated without fractionation (2hr MS time), resulting in a 36-fold reduction in MS time.