Proteogenomic analysis of granulocyte macrophage colony- stimulating factor autoantibodies in the blood of a patient with autoimmune pulmonary alveolar proteinosis
peer-reviewed · Scientific Reports · 2020
| Date | 2020-03-18 |
| Type | peer-reviewed |
| Venue | Scientific Reports |
| Publisher | Springer Science and Business Media LLC |
| Contribution | downstream-application |
| DOI | 10.1038/s41598-020-61934-y |
| Citations (OpenAlex) | 3 |
| Venue 2-year citedness | 5.08 |
Abstract
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 chromatography-tandem 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.
Methods and tools
- GM-CSF autoantibody proteogenomics: Analyses GM-CSF autoantibodies from an autoimmune alveolar proteinosis patient by TIMS-TOF proteogenomics, confirming CDR3 to FR4 peptides by de novo sequencing.
Methods it uses
- PEAKS: Commercial DP-based de novo