HA-Flag-SHFL was expressed in HEK293 cells in a doxycycline-inducible manner. The cell lysates were first treated with the nuclease benzonase to disrupt RNA- or DNA-mediated protein-protein interactions. The proteins were sequentially purified with anti-HA and anti-Flag conjugated beads. Purified proteins was subjected to Mass spectrometry analysis combined with label-free quantification.