ArticleJournal of proteome research2016
An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.
Article in Journal of proteome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 52 citations in OpenAlex.
- Metaproteomics uncovers the functional capacity of a soil microbiome.Scientific reports · 2026Article
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model.Nature communications · 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
- Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome.mSystems · 2023Article
- Considerations for constructing a protein sequence database for metaproteomics.Computational and structural biotechnology journal · 2022Review
- Increasing the power of interpretation for soil metaproteomics data.Microbiome · 2021Article
- Development of an Ocean Protein Portal for Interactive Discovery and Education.Journal of proteome research · 2021Article
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification.Protein science : a publication of the Protein Society · 2020Review
- Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes.The ISME journal · 2020Article
- Assessing Protein Sequence Database Suitability UsingMolecular & cellular proteomics : MCP · 2020Article
- Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota.Frontiers in genetics · 2020Review
- A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation.Molecular & cellular proteomics : MCP · 2019Article
- Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.Journal of proteome research · 2019Review
- Article
- Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics.Frontiers in microbiology · 2019Article
- A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer.Frontiers in microbiology · 2019Article
- Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data.Journal of proteome research · 2018Article
- Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.Proteomes · 2018Article
- Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for deriving "metapeptides" (short amino acid sequences that may be represented in multiple organisms) from shotgun metagenomic sequencing of microbiome samples. In two ocean microbiome samples, we constructed site-specific metapeptide databases to detect more than one and a half times as many peptides as by searching against predicted genes from an assembled metagenome and roughly three times as many peptides as by searching against the NCBI environmental proteome database. The increased peptide yield has the potential to enrich the taxonomic and functional characterization of sample metaproteomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.