ARiBo pull-down for riboproteomic studies based on label-free quantitative mass spectrometry

Flowchart for the label-free quantitative MS analysis of the protein interactome for a specific RNA using the ARiBo method. The ARiBo pull-downs are performed with an ARiBo-tagged RNA (sample) and two controls, the ARiBo tag (mock) and an ARiBo-tagged RNA variant (dlet-7g), using the same NT2 whole cell extract (WCE). The tryptic digests of these pull-downs are then analyzed by label-free quantitative LC–MS/MS. The statistical analysis of the MS data from biological triplicates (sample and controls) is performed based on spectral counts using either the mock control or the dlet-7g control.