MetaPep: A core peptide database for faster human gut metaproteomics database searches

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Sun, Zhongzhi, Ning, Zhibin, Cheng, Kai, Duan, Haonan, Wu, Qing, Mayne, Janice and Figeys, Daniel (2023) MetaPep: A core peptide database for faster human gut metaproteomics database searches. Computational and Structural Biotechnology Journal, 21. pp. 4228-4237. ISSN 2001-0370

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Abstract

Metaproteomics has increasingly been applied to study functional changes in the human gut microbiome. Peptide identification is an important step in metaproteomics research, with sequence database search (SDS) and spectral library search (SLS) as the two main methods to identify peptides. However, the large search space in metaproteomics studies causes significant challenges for both identification methods. Moreover, with the development of mass spectrometry, it is now feasible to perform metaproteomic projects involving 100–1000 individual microbiomes. These large-scale projects create a conundrum for searching large databases. In this study, we constructed MetaPep, a core peptide database (including both collections of peptide sequences and tandem MS spectra) greatly accelerating the peptide identifications. Raw files from fifteen metaproteomics projects were re-analyzed and the identified peptide-spectrum matches (PSMs) were used to construct the MetaPep database. The constructed MetaPep database achieved rapid and accurate identification of peptides for human gut metaproteomics. MetaPep has a large collection of peptides and spectra that have been identified in published human gut metaproteomics datasets. MetaPep database can be used as an important resource in the current stage of human gut metaproteomics research. This study showed the possibility of applying a core peptide database as a generic metaproteomics workflow. MetaPep could also be an important resource for future human gut metaproteomics research, such as DIA (data-independent acquisition) analysis.

Item Type: Article
Additional Information: Scripts applied for the construction of MetaPep spectral library have been shared on GitHub Gist at: https://gist.github.com/starsunstar/d0af1ef047bff3bff5edffd5819f5313. Both the MetaPep peptide sequence database and the MetaPep spectral library have been uploaded to the open dataset repository, Zenodo (https://zenodo.org/), with DOI: 10.5281/zenodo.8101702.
Uncontrolled Keywords: database search,dia (data-independent acquisition),gut microbiome,metaproteomics,spectral library,biotechnology,biophysics,structural biology,biochemistry,genetics,computer science applications ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
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Depositing User: LivePure Connector
Date Deposited: 06 Mar 2026 16:30
Last Modified: 09 Mar 2026 16:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/102247
DOI: 10.1016/j.csbj.2023.08.025

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