ArticleMicrobiome2021
Increasing the power of interpretation for soil metaproteomics data.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Enhanced phosphorus availability and uptake in Salvia miltiorrhiza associated with humic-induced changes in soil phosphorus fractions.Scientific reports · 2026Article
- The Peptonizer2000: Bringing Confidence to Metaproteomics.Journal of proteome research · 2026Article
- Diagnosing soil bioremediation failure: evidence-weighted pathways from mechanism to field closure.Frontiers in bioengineering and biotechnology · 2026Review
- An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.Proteomics · 2025Article
- Impact of moisture on microbial decomposition phenotypes and enzyme dynamics.The ISME journal · 2025Article
- FISH-FACS proteomics: enhanced label-free quantitative proteome analysis from low cell numbers of uncultured environmental microorganisms.ISME communications · 2025Article
- The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.Genome biology · 2024Article
- [Microbial metaproteomics--From sample processing to data acquisition and analysis].Se pu = Chinese journal of chromatography · 2024Review
- Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics.Microbiome · 2024Article
- Life at the borderlands: microbiomes of interfaces critical to One Health.FEMS microbiology reviews · 2024Review
- Article
- Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis.Microbiology and molecular biology reviews : MMBR · 2023Review
- Human gut microbiome and metabolite dynamics under simulated microgravity.Gut microbes · 2023Article
- GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry.International journal of molecular sciences · 2023Article
- Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing.ISME communications · 2023Article
- Short-term effects of etifoxine on human gut microbiome in healthy men.Frontiers in neuroscience · 2023Article
- Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool.Frontiers in microbiology · 2023Article
- Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future.Environmental microbiology · 2023Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSoil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples.
resultsThe number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases.
conclusionsA two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information. Video abstract.
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