Proteins are highly versatile macromolecules that enact a wide range of biological functions such as catalysis, regulation, communication, mechanical support, movement, and transport. At least several million unique proteins exist in the human body which are, surprisingly, encoded by only fifteen thousand genes. The divergent number of proteins compared to genes is due to protein variants, or "proteoforms", that originate from a single gene as unique combinations of amino acid sequence variations (e.g. alternative splicing or endogenous proteolytical processing) and/or post-translational modifications. It is important to note that out of all possible proteoforms from a single coding gene only one or a few may correlate with (disease) biology.
Established bottom-up proteomics methods are generally used to identify proteins of interest via their proteolytical peptide fragments following tryptic digestion. The tryptic protein digestion step which is at the heart of bottom-up proteomics leads however to issues with protein inference, connectivity, quantitation, and incomplete sequence/modification information. Top-down proteomics is an emerging technique that preserves key biological information by analyzing whole proteins directly by tandem mass spectrometry. Developments in hardware and software advanced top-down proteomics to become an accessible methodology that offers unique possibilities in translational research and patient care. In this webinar we will discuss the importance of proteoforms from a clinical perspective, illustrate the potential of top-down proteomics using real-life examples, and give assistances for implementing top-down proteomics.