High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics

ABSTRACT: Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge in metaproteomics is the construction of a suitable protein sequence database to interpret the highly complex metaproteomic data, especially in the absence of metagenomic sequencing data. Herein, we present a high-abundance protein-guided hybrid spectral library strategy for in-depth data independent acquisition (DIA) metaproteomic analysis (HAPs-hyblibDIA). A dedicated high-abundance protein database of gut microbial species is constructed and used to mine the strains information of microbiota samples by directDIA. Then, sample-specific protein sequence database is built based on the strains information using Uniprot protein sequence for subsequent analysis of DIA data using directDIA or hybrid spectral library-based DIA analysis strategies. We evaluated the accuracy and sensitivity of the method using synthetic microbial community samples and human gut microbiome samples. It was demonstrated that the strategy can successfully identify species in microbiota samples, and that the peptides identified by HAPs-hyblibDIA shared a great common part with the peptides identified using metagenomic sequencing-derived database. At the peptide and species level, our results can serve as a complement to the results obtained by metagenomic sequencing-derived database. Furthermore, we validated the applicability of the HAPs-hyblibDIA strategy in a cohort of human gut microbiota samples of colorectal cancer patients and control, highlighting its usability in biomedical research.

ORGANISM(S): Morganella Morganii Clostridium Butyricum Lactobacillus Acidophilus Enterococcus Faecalis Feces Metagenome Enterobacter Asburiae Pseudomonas Aeruginosa

SUBMITTER: Liang Qiao  

PROVIDER: PXD043890 | iProX | Wed Jul 19 00:00:00 BST 2023

REPOSITORIES: iProX