ArticlePLoS computational biology2020
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- An electrophysiological and proteomics roadmap for human induced glutamatergic neurons: fine-tuning of culture conditions for pathophysiological studies.Cell death discovery · 2026Article
- MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.Journal of proteome research · 2025Article
- Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota.iScience · 2024Article
- MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.PLoS computational biology · 2023Article
- Mix24X, a Lab-Assembled Reference to Evaluate Interpretation Procedures for Tandem Mass Spectrometry Proteotyping of Complex Samples.International journal of molecular sciences · 2023Article
- Evaluation of the Limit of Detection of Bacteria by Tandem Mass Spectrometry Proteotyping and Phylopeptidomics.Microorganisms · 2023Article
- Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin.Molecular & cellular proteomics : MCP · 2023Article
- Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts.Journal of proteome research · 2022Article
- Panomics to decode virulence and fitness in Gram-negative bacteria.Frontiers in cellular and infection microbiology · 2022Article
- Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics.Computational and structural biotechnology journal · 2022Review
- Multi-omics data integration considerations and study design for biological systems and disease.Molecular omics · 2021Review
- Metaproteomics Analysis of Host-Microbiota Interfaces.Methods in molecular biology (Clifton, N.J.) · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.
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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.