PXD063844
PXD063844 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Comparing and optimizing protein extraction methods for the analyses of human fecal microbiome via metaproteomics approach |
Description | Metaproteomic 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. |
HostingRepository | iProX |
AnnounceDate | 2025-05-10 |
AnnouncementXML | Submission_2025-05-11_20:30:45.191.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Gordon Zhang |
SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; |
ModificationList | acetylated residue |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2025-05-11 20:30:30 | ID requested | |
⏵ 1 | 2025-05-11 20:30:45 | announced |
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 affiliation | Ohio State University |
contact email | gao.2116@osu.edu |
lab head | |
Gordon Zhang | |
contact affiliation | Ohio State University |
contact email | nzhangwe@outlook.com |
dataset submitter |
Full Dataset Link List
iProX dataset URI |