Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques.

ABSTRACT: The polyclonal repertoire of circulating antibodies potentially holds valuable information about an individual's humoral immune state. While bottom-up proteomics is well suited for serum proteomics, the vast number of antibodies and dynamic range of serum challenge this analysis. To acquire the serum proteome more comprehensively, we incorporated high-field asymmetric waveform ion-mobility spectrometry (FAIMS) or two-dimensional chromatography into standard trypsin-based bottom-up proteomics. Thereby, the number of variable region (VR)-related spectra increased 1.7-fold with FAIMS and 10-fold with chromatography fractionation. To match antibody VRs to spectra, we combined de novo searching and BLAST alignment. Validation of this approach showed that, as peptide length increased, the de nov

SUBMITTER: Stingl C 

PROVIDER: S-EPMC11228375 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature