Summary Primary biliary cholangitis (PBC) is characterized by the presence of serum anti‐mitochondrial autoantibodies (AMAs). To date, four antigens among the 2‐oxo‐acid dehydrogenase complex family, which commonly have lipoyl domains as an epitope, have been identified as AMA‐corresponding antigens (AMA‐antigens). It has recently been reported that AMAs react more strongly with certain chemically modified mimics than with the native lipoyl domains in AMA‐antigens. Moreover, high concentrations of circulating immune complexes (ICs) in PBC patients have been reported. However, the existence of ICs formed by AMAs and their antigens has not been reported to date. We hypothesized that AMAs and their antigens formed ICs in PBC sera, and analyzed sera of PBC and four autoimmune diseases (Sjögren's syndrome, systemic lupus erythematosus, systemic scleroderma, and rheumatoid arthritis) using immune complexome analysis, in which ICs are separated from serum and are identified by nano‐liquid chromatography‐tandem mass spectrometry. To correctly assign MS/MS spectra to peptide sequences, we used a protein‐search algorithm that including lipoylation and certain xenobiotic modifications. We found three AMA‐antigens, the E2 subunit of the pyruvate dehydrogenase complex (PDC‐E2), the E2 subunit of the 2‐oxo‐glutarate dehydrogenase complex (OGDC‐E2) and dihydrolipoamide dehydrogenase binding protein (E3BP), by detecting peptides containing lipoylation and xenobiotic modifications from PBC sera. Although the lipoylated sites of these peptides were different from the well‐known sites, abnormal lipoylation and xenobiotic modification may lead to production of AMAs and the formation ICs. Further investigation of the lipoylated sites, xenobiotic modifications, and IC formation will lead to deepen our understanding of PBC pathogenesis. Primary biliary cholangitis (PBC) is characterized by the presence of serum anti‐mitochondrial autoantibodies (AMAs) against the 2‐oxo‐acid dehydrogenase complex family; however, the immune complexes (ICs) formed by AMAs and the antigens has not been reported to date and their in vivo antigenicity is not fully clear. Immune complexome analysis identified three AMA‐antigens to be incorporated into ICs from PBC sera, the E2 subunit of the pyruvate dehydrogenase complex (PDC‐E2), the E2 subunit of the 2‐oxo‐glutarate dehydrogenase complex (OGDC‐E2), and dihydrolipoamide dehydrogenase binding protein (E3BP), by detecting peptides containing lipoylation or xenobiotic modifications. The lipoylated sites of these peptides were different from the well‐known sites; therefore, abnormal lipoylation and xenobiotic modification may lead to production of AMAs and the formation ICs