Detection of differential bait proteoforms through IP-mass spec

In an exciting new strategy, Savvas hypothetized that antibody enrichment would enrich modified (PTMs) and mutated bait peptides. Using MSFragger Open Search (Nesvilab) coupled to SAINTexpress, we identify differentially present peptidoforms.

By re-analyzing the publicly available #HRAS WT vs. G12D interactomes, we specifically identify the positive control LVVVGAGGVGK peptidoforms in its mutated and WT state among the most significant hits of our analysis.

Finally, to test our metholodogy against an endogenously expressed bait, we reanalysed #BRD4 IP-MS in 4 leukemia cell lines. Specific phosphorylated peptides were differentially present between these leukemia cell lines suggesting different BRD4 proteoforms in unpertubed cells.

A big thank you to @CRGenomica, @ERC_Research for supporting our work. And a huge Congrats to @Kourtissavvas and the rest of the authors for this intuitive work that will reshape the way we look at IP-MS data!