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PXD063844

PXD063844 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleComparing and optimizing protein extraction methods for the analyses of human fecal microbiome via metaproteomics approach
DescriptionMetaproteomic analysis offers critical insights into gut microbiome function; however, efficient microbial protein extraction from fecal samples remains challenging due to the complexity of different types of bacterial cell walls in the microbiome. In this study, we systematically compared three representative detergent-based lysis buffers (SDS_urea, DDM_urea, SDS_DDM_urea) for metaproteomics sample preparation. After multiple levels of analyses, we identified SDS_DDM_urea as the most efficient option for extracting diverse microbial proteins, peptides, and identifying microbial species. Applying this optimized method to samples from a dietary intervention study (Summer Harvest Adventure), we found minimal group-level microbial diversity shifts during this type of intervention, but substantial individual-specific variations reflected by metaproteomics results. Functional analyses also revealed microbial protein changes, especially proteins related to metabolic adaptations, including enhanced carbohydrate metabolism, amino acid biosynthesis, vitamin transport, and increased expression of membrane-associated proteins. Our results highlighted the personalized microbiome response to dietary interventions and underscored the importance of selecting appropriate protein extraction methods to accurately capture microbiome functional dynamics in microbiome analyses via metaproteomics.
HostingRepositoryiProX
AnnounceDate2025-05-10
AnnouncementXMLSubmission_2025-05-11_20:30:45.191.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterGordon Zhang
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListacetylated residue
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02025-05-11 20:30:30ID requested
12025-05-11 20:30:45announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Metaproteomics, Gut microbiota, Protein extraction, Dietary intervention, Microbial diversity, Mass spectrometry, Microbial functional analysis
Contact List
Chris Zhu
contact affiliationOhio State University
contact emailgao.2116@osu.edu
lab head
Gordon Zhang
contact affiliationOhio State University
contact emailnzhangwe@outlook.com
dataset submitter
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