We used siRNAs to knockdown PI31 in primary DCs, followed by capturing HLA class I complexes using W6/32-conjugated immunoresin. Acid treatment abolished noncovalent interactions among the complex components. Using reverse-phase HPLC, we separated eluted peptides from the α-chain and β2-microglobulin of the HLA complexes and analysed eluted peptide fractions by LC-MS/MS.