ReviewComputational and structural biotechnology journal2022
Considerations for constructing a protein sequence database for metaproteomics.
Review in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Multi-omics insights into bacterial and fungal bioremediation of Potentially Toxic Elements (PTEs): a critical overview of their applications.World journal of microbiology & biotechnology · 2026Review
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Article
- Assessing the diversity and functional profile of the "microbial proteome" in fermented foods.Food & function · 2026Article
- Recent Advancements for Enhanced Biocatalyst and Biotransformation.Molecular biotechnology · 2026Review
- Comprehensive evaluation of statistical approaches for differential metaproteomics.bioRxiv : the preprint server for biology · 2026Article
- Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.Journal of proteomics · 2026Article
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Wastewater metaproteomics: tracking microbial and human protein biomarkers.ISME communications · 2026Article
- Rewiring the proteome of the Euscelidius variegatus holobiont in response to Flavescence dorée phytoplasma.Scientific reports · 2025Article
- Assessing the diversity and functional profile of the "microbial proteome" in fermented foods.bioRxiv : the preprint server for biology · 2025Article
- Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples.Proteomics · 2025Article
- Article
- Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.Proteomics · 2025Article
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.Environmental microbiome · 2025Article
- Dietary protein from different sources escapes host digestion and is differentially modified by gut microbiota.bioRxiv : the preprint server for biology · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.Proteomics · 2025Article
- Metaproteomic Profiling of the Secretome of a Granule-forming Ca. Accumulibacter Enrichment.Proteomics · 2025Article
- Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.Microbiology spectrum · 2025Article
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2 authors.
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Abstract
Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of fragmented peptide ions to a database of protein sequences corresponding to the proteins in the sample. This sequence database determines which protein sequences can be identified from the measurement, and as such the taxonomic and functional information that can be inferred from a metaproteomics measurement. Thus, the construction of the protein sequence database directly impacts the outcome of any metaproteomics study. Several factors, such as source of sequence information and database curation, need to be considered during database construction to maximize accurate protein identifications traceable to the species of origin. In this review, we provide an overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies. Based on this review of the literature and our experience we provide a decision tree and best practices for choosing and implementing database construction strategies.
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