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PXD051104-1

PXD051104 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlemetaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis
DescriptionAnalysis of large-scale data-independent acquisition mass spectrometry (DIA-MS) metaproteomics data remains a computational challenge. Here, we present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS (DDA-MS), protein identification and quantification using DIA-MS, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap and timsTOF MS instruments. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples indicated that metaExpertPro quantified an average of 45,000 peptides in a 60-minute diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual false discovery rate (FDR) of approximately 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67–0.90) in genus diversity and showed a high correlation (rSpearman = 0.73–0.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia (DLP) patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.
HostingRepositoryPRIDE
AnnounceDate2024-09-28
AnnouncementXMLSubmission_2024-09-28_08:28:49.136.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTiannan Guo
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmethylthiolated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF Pro; Orbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-03-31 11:06:41ID requested
12024-09-28 08:28:49announced
Publication List
10.1016/J.MCPRO.2024.100840;
Keyword List
submitter keyword: computational workflow, data-independent acquisition mass spectrometry, metaproteomics
Contact List
Tiannan Guo
contact affiliation1, Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China 2, School of Medicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China 3, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
contact emailguotiannan@westlake.edu.cn
lab head
Tiannan Guo
contact affiliationWestlake University
contact emailguotiannan@westlake.edu.cn
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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