PXD040947 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Expanding the Characterization of Microbial Ecosystems using DIA-PASEF Metaproteomics |
Description | Metaproteomics is gaining momentum in microbiome research due to the multi-dimensional information it provides. However, current approaches have reached their detection limits. We present a highly-sensitive metaproteomic workflow using the extra information captured by Parallel Accumulation-Serial Fragmentation (PASEF) technology. The comparison of different acquisition modes and data analysis software packages showed that DIA-PASEF and DIA-NN doubled protein identifications in the mouse gut microbiota and, importantly, also in the host proteome compared to DDA-PASEF. DIA-PASEF significantly improved peptide detection reproducibility and quantification accuracy, which resulted in more than twofold identified taxa, reaching depths comparable to metagenomic studies. Consequently, DIA-PASEF exhibited improved coverage of functional networks revealing 131 additional pathways compared to DDA-PASEF. We applied our optimized workflow to a pre-clinical mouse model of chronic pain, in which we deciphered novel host-microbiome interactions. In summary, we present here a metaproteomic approach that paves the way for increasing the functional characterization of microbiome ecosystems and is applicable to diverse fields of biological research. |
HostingRepository | PRIDE |
AnnounceDate | 2023-05-04 |
AnnouncementXML | Submission_2023-05-04_01:51:42.605.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | FengXian |
SpeciesList | scientific name: Microbiota; NCBI TaxID: 13613; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-03-17 09:22:41 | ID requested | |
⏵ 1 | 2023-05-04 01:51:42 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Metaproteomics, DIA-PASEF, Mouse, Chronic pain, Gut microbiome |
Contact List
ManuelaSchmidt |
contact affiliation | Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Vienna |
contact email | manuela_schmidt@univie.ac.at |
lab head | |
FengXian |
contact affiliation | Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna |
contact email | feng.xian@univie.ac.at |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD040947
- Label: PRIDE project
- Name: Expanding the Characterization of Microbial Ecosystems using DIA-PASEF Metaproteomics