Spectral entropy as a measure of the metaproteome complexity

Duan, Haonan, Ning, Zhibin, Zhang, Ailing and Figeys, Daniel (2024) Spectral entropy as a measure of the metaproteome complexity. Proteomics, 24 (16). ISSN 1615-9853

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Abstract

The diversity and complexity of the microbiome's genomic landscape are not always mirrored in its proteomic profile. Despite the anticipated proteomic diversity, observed complexities of microbiome samples are often lower than expected. Two main factors contribute to this discrepancy: limitations in mass spectrometry's detection sensitivity and bioinformatics challenges in metaproteomics identification. This study introduces a novel approach to evaluating sample complexity directly at the full mass spectrum (MS1) level rather than relying on peptide identifications. When analyzing under identical mass spectrometry conditions, microbiome samples displayed significantly higher complexity, as evidenced by the spectral entropy and peptide candidate entropy, compared to single-species samples. The research provides solid evidence for the complexity of microbiome in proteomics indicating the optimization potential of the bioinformatics workflow.

Item Type:	Article
Additional Information:	DATA AVAILABILITY STATEMENT The code and Spectral Entropy Calculator are available at: https://github.com/northomics/spectra_entropy. The raw data and searching results can be found at ProteomeXchange Consortium (dataset identifier: PXD050781).
Uncontrolled Keywords:	bioinformatics,metaproteomics,spectral entropy,biochemistry,molecular biology ,/dk/atira/pure/subjectarea/asjc/1300/1303
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	20 Mar 2026 11:30
Last Modified:	20 Mar 2026 11:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102504
DOI:	10.1002/pmic.202300570

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