Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry.

ABSTRACT: Aim: This study aims to evaluate the impact of experimental workflow on fecal metaproteomic observations, including the recovery of small and antimicrobial proteins often overlooked in metaproteomic studies. The overarching goal is to provide guidance for optimized metaproteomic experimental design, considering the emerging significance of the gut microbiome in human health, disease, and therapeutic interventions. Methods: Mouse feces were utilized as the experimental model. Fecal sample pre-processing methods (differential centrifugation and non-differential centrifugation), protein digestion techniques (in-solution and filter-aided), data acquisition modes (data-dependent and data-independent, or DDA and DIA) when combined with parallel accumulation-serial fragmentation (PA

SUBMITTER: Wang A 

PROVIDER: S-EPMC11480776 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature