ArticleProteomics2013
A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.
Article in Proteomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 1 of them a synthesis that pooled it.
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98 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- Metaproteomic Dataset on Semi-Diurnal Variability of the Bacterioplankton Communities During a Spring Phytoplankton Bloom in the North Sea.Proteomics · 2025Article
- An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.Proteomics · 2025Article
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.Environmental microbiome · 2025Article
- MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.Journal of proteome research · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.Microbiology spectrum · 2025Article
- Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.The ISME journal · 2025Article
- A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting.Computational and structural biotechnology journal · 2025Article
- Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis.Computational and structural biotechnology journal · 2025Article
- Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species.Computational and structural biotechnology journal · 2025Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Activity-based metaproteomics driven discovery and enzymological characterization of potential α-galactosidases in the mouse gut microbiome.Communications chemistry · 2024Article
- Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean.Nature communications · 2024Article
38 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies.
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