Fig. 1.

Outline of the high-throughput immunopurification workflow using a plate format. A, Tissues are first homogenized, lysed with mild detergents and cleared with a centrifugation step. B, To enable sequential loading of the lysates on multiple affinity resins, cleared lysates are loaded on stacked plates containing firstly, Pro-A beads for depletion of tissue endogenous antibodies, then anti-HLA class I and II antibodies cross-linked to Pro-A beads for direct enrichment of HLA class I and II complexes. C, Affinity plates containing the captured HLA complexes are separated, washed individually and stacked on C18 plates. HLA class I and II complexes are then eluted on the C18 plates. Peptide and protein fractions are then recovered separately. Each step is timed with the hourglass symbol that is equivalent to about one hour.