Top-Down Proteomic Characterization of Truncated Proteoforms

A top-down proteomic
strategy with semiautomated analysis of data sets has proven successful
for the global identification of truncated proteins without the use
of chemical derivatization, enzymatic manipulation, immunoprecipitation,
or other enrichment. This approach provides the reliable identification
of internal polypeptides formed from precursor gene products by proteolytic
cleavage of both the N- and C-termini, as well as truncated proteoforms
that retain one or the other termini. The strategy has been evaluated
by application to the immunosuppressive extracellular vesicles released
by myeloid-derived suppressor cells. More than 1000 truncated proteoforms
have been identified, from which binding motifs are derived to allow
characterization of the putative proteases responsible for truncation.