CCMS Project

Shotgun Protein Sequencing

Full-length de-novo protein sequencing of proteins from organisms with unsequenced genomes and recombinant proteins from model organisms (eg. monoclonal antibodies) remains a challenging open problem. While complete ion series are needed to accurately sequence proteins, this is rarely observed. Thus conventional de-novo methods using only one fragmentation method and not taking advantage of spectra from overlapping peptides achieve sub-optimal sequencing accuracy and coverage. In contrast with current approaches, our method jointly sequences spectra from overlapping peptides while using multi-spectrum acquisition of CID, HCD, and ETD spectra from the same precursor. We show that our method can assemble protein sequences up to 145 amino acids long at 99% sequencing accuracy without requiring a database.