PXD043890

PXD043890 is an original dataset announced via ProteomeXchange.

Title	High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics
Description	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.
HostingRepository	iProX
AnnounceDate	2023-07-19
AnnouncementXML	Submission_2024-01-16_19:02:07.269.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Enhui Wu
SpeciesList	scientific name: Clostridium butyricum; NCBI TaxID: 1492; scientific name: Enterobacter asburiae; NCBI TaxID: 61645; scientific name: Enterococcus faecalis; NCBI TaxID: 1351; scientific name: feces metagenome; NCBI TaxID: 1861841; scientific name: Lactobacillus acidophilus; NCBI TaxID: 1579; scientific name: Morganella morganii; NCBI TaxID: 582; scientific name: Pseudomonas aeruginosa; NCBI TaxID: 287;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-19 00:13:44	ID requested
⏵ 1	2024-01-16 19:02:08	announced

Wu E, Yang Y, Zhao J, Zheng J, Wang X, Shen C, Qiao L, High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics. Anal Chem, 96(3):1029-1037(2024) [pubmed]

submitter keyword: metaproteomics, data independent acquisition, gut microbiota

Liang Qiao
contact affiliation	Fudan University
contact email	liang_qiao@fudan.edu.cn
lab head
Enhui Wu
contact affiliation	Fudan University
contact email	20110220037@fudan.edu.cn
dataset submitter

iProX dataset URI