Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes.

ABSTRACT: Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Dat

SUBMITTER: Abele M 

PROVIDER: S-EPMC10407251 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature