ArticleJournal of proteome research2025
ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus.
Article in Journal of proteome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 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.
The trial behind it
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
5 citing papers in PubMed.
- Article
- Microfluidics-enabled proteomic profiling reveal iron-driven immune evasion by an antimicrobial-resistant pathogen.Cell reports methods · 2026Article
- Lon protease-mediated secretome profiling inMicrobiology resource announcements · 2026Article
- Vibe Coding Omics Data Analysis Applications.Journal of proteome research · 2026Article
- Temporal Wheat Proteome Remodeling by Deoxynivalenol Reveals Novel Detoxification Signatures and Strategies Across Cultivars.Molecular & cellular proteomics : MCP · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mass spectrometry-based proteomics experiments produce complex data sets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly available proteomics data analysis platform, Perseus, is extensively used to perform such tasks, but opportunities to enhance visualization tools and promote accessibility of the data exist. In this study, we developed ProteoPlotter, a user-friendly, executable tool to complement Perseus for visualization of proteomics data sets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multidimensional proteomics data. ProteoPlotter supports mapping of one-dimensional enrichment analyses, enhanced adaptability of volcano plots through incorporation of Gene Ontology terminology, visualization of 95% confidence intervals in principal component analysis plots using data ellipses, and customizable features. ProteoPlotter is designed for intuitive use by biological and computational researchers alike, providing descriptive instructions (i.e., Help Guide) for preparing and uploading Perseus output files. Herein, we demonstrate the application of ProteoPlotter toward microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for enhanced biological insights. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates enhanced visualization of proteomics data to drive new biological discoveries.
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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.