Extended Data Figure 5. Workflow for the SILAC methodology used for identification and quantification of proteins that bind the hexanucleotide repeats in a structurally dependent manner.

HEK293T cells that had complete incorporation of either heavy-, medium-, or lightlabeled isotopes were incubated with either the (GGGGCC)₄ G-quadruplex, the (GGGGCC)₄ hairpin, or the (CCCCGG)₄ hairpin, respectively. The samples were then processed as described in Methods and presented in Figures 3. The final eluted samples were combined and prepared for trypsin digestion using filter-aided sample preparation (FASP). The buffer was exchanged to remove salts and SDS. The sample was then subject to LC-MS/MS analysis as described in the Methods.