Source: Nucleic Acids Res. 2022, 50, D526. License: CC-BY-NC
Proteoforms are the specific form of proteins after considering all possible variations that can occur via gene mutation, alternative splicing, and post-translational modification (PTM). These are the molecular entities that interact with other proteins and ligand, propagate signals, and ultimately carry out biological processes.
The widely practiced bottom-up approach (A) is a powerful technique for determining protein abundance. By digesting proteins into peptides, however, linkage of individual modification sites is broken. Despite its strengths in sensitivity and depth of protein coverage, the bottom-up approach struggles to capture PTM stoichiometry and combination. The top-down approach, in which intact proteins are ionized and then fragmented in the gas phase, can provide the overall extent and location of modifications.