Dr. Nuno Bandeira, Ph.D.

The Bandeira laboratory aims to develop novel mass spectrometry algorithms for the discovery and characterization of novel biomarker proteins, post- translational modifications and protein-protein interactions. The research in my lab falls into 5 general areas: (1) De novo sequencing of complete proteins; our Shotgun Protein Sequencing paradigm yields the longest and most accurate de novo sequences, even on mixtures of unknown proteins. (2) Discovery and detailed characterization of post- translational modifications in signaling pathways and health/disease; our Spectral Networks paradigm enables the precise localization of modification sites and reveals novel modifications and highly modified peptides. (3) Sequencing and characterization of non-linear peptidic natural products, including cyclic and branched peptides; (4) Mass spectrometry algorithms for high-throughput analysis of in-vivo structural proteomics and protein-protein interactions; (5) New mass spectrometry approaches to the identification of neuropeptides and other endogenous peptides; biomarker and drug discovery pipelines are severely limited by only identifying 20-30% of all detectable peptide species – new combinations of algorithms and experimental protocols are needed to reveal this proteomics ‘dark matter’. Overall, this research aims to substantially improve the capabilities of proteomics discovery pipelines and could result in the development of novel drug therapeutics.