The unique Top-Down Proteineer (TopPro(TM)) is now available on the apex-Qe(TM) hybrid Q-q-FTMS system launched earlier this year. It combines the analytical power of FTMS equipped with a hybrid ESI-Q-q interface to perform "e;top-down"e; analysis of intact proteins in the FTMS analyzer cell, thus avoiding digestion and additional separation steps. The enormous resolving power of the FTMS is ideal for measuring protein fragment ions generated directly with electron-capture dissociation (ECD) in the FTMS analyzer cell, and can deliver high fidelity long sequence runs, as well as information on the localization of PTMs. Our unique ability for efficient selective ion enrichment using selected ion injection via the analytical quadrupole of the Q-q-FTMS extends the overall systems dynamic range and sensitivity by one to two orders of magnitude. MS Biotools software handles the database searching interface and confirms sequence annotations on the fly.