ArticleJournal of proteome research2019
ComPIL 2.0: An Updated Comprehensive Metaproteomics Database.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Exogenous prion-like proteins and their potential to trigger cognitive dysfunction.Molecular systems biology · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
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- Spectra without stories: reporting 94% dark and unidentified ancient proteomes.Open research Europe · 2024Article
- The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).Journal of biomolecular techniques : JBT · 2023Article
- Uncovering Hidden Members and Functions of the Soil Microbiome UsingJournal of proteome research · 2022Article
- Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics.Computational and structural biotechnology journal · 2022Review
- Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.Nature communications · 2021Article
- Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review.Biotechnology for biofuels · 2021Review
- Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.Journal of proteome research · 2021Article
- Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat AgentsFrontiers in immunology · 2021Article
- A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.Nature protocols · 2020Article
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Authors and funding
6 authors.
Funding
Abstract
We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex metasamples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 113 million protein records and roughly 4.8 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a data set collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.
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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.