Recently, attempts to reveal the structures of autoantibodies comprehensively using improved proteogenomics technology, have become popular. This technology identifies peptides in highly purified antibodies by using an Orbitrap device to compare spectra from liquid chromatographytandem mass spectrometry against a cDNA database obtained through next-generation sequencing. In this study, we first analyzed granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies in a patient with autoimmune pulmonary alveolar proteinosis, using the trapped ion mobility spectrometry coupled with quadrupole time-of-flight (TIMS-TOF) instrument. The TIMS-TOF instrument identified peptides that partially matched sequences in up to 156 out of 162 cDNA clones. Complementarity-determining region 3 (CDR3) was fully and partially detected in nine and 132 clones, respectively. Moreover, we confirmed one unique framework region 4 (FR4) and at least three unique across CDR3 to FR4 peptides via de novo peptide sequencing. This new technology may thus permit the comprehensive identification of autoantibody structure. Pulmonary alveolar proteinosis (PAP) is a rare lung disorder characterized by the accumulation of surfactant material in the alveoli and terminal bronchioli 1-3. PAP is classified into three different forms: autoimmune, congenital, and secondary 1-3. Autoimmune PAP (aPAP) accounts for 91% of all PAP cases 1-3. It is thought to be caused by granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies (GMAbs), which interfere with alveolar macrophage function and maturation, resulting in impaired surfactant catabolism. However, the mechanism involved in the excessive production of GMAbs remains unclear. According to a previous study, GMAb is a polyclonal antibody with immunoglobulin M (IgM-), IgG-, and IgA-isotypes 4. IgG-GMAb is pathogenic, but IgM-GMAb is thought to be a bystander etiologically, because its binding avidity to GM-CSF is 100-fold lower than that of IgG-GMAb, and its neutralizing capacity is extremely weak, i.e., it has a 20,000-fold higher IC 50 than IgG-GMAb 4. The currently available evidence regarding the effects of IgA-GMAb in the peripheral blood is limited, and its pathogenic role remains unclear. Serum GMAbs are normally present in healthy individuals, although their concentration is much lower than that measured in patients with aPAP 5. Our previous study have reported that circulating GM-CSF autoreactive B cells (GMARBs) producible of GMAb by Epstein-Barr virus transformation are consistently detected in healthy individuals and patients with aPAP 6. These are potential precursor cells for GMAb-producing plasma cells and B cells.