Proteomics, Bioinformatics, and Infectious Diseases

Geddes-McAlister, Jennifer; Roux-Dalvai, Florence; Droit, Arnaud

doi:10.1016/b978-0-443-28818-0.00024-0

Cited by 2 publications

References 151 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

ProteoPlotter: an executable proteomics visualization tool compatible with Perseus

Olabisi-Adeniyi,

McAlister,

Ferretti

et al. 2024

Preprint

View full text Add to dashboard Cite

Mass spectrometry-based proteomics experiments produce complex datasets 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 datasets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multi-dimensional proteomics data. ProteoPlotter provides 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 towards microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for improved biological characterization. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates a deeper understanding of proteomics data to drive new biological discoveries.

show abstract

ProteoPlotter: an executable proteomics visualization tool compatible with Perseus

Olabisi-Adeniyi,

McAlister,

Ferretti

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Unveiling Novel Insights in Helminth Proteomics: Advancements, Applications, and Implications for Parasitology and Beyond

Soleymani,

Sadr,

Santucciu

et al. 2024

Biologics

View full text Add to dashboard Cite

Helminths have developed intricate mechanisms to survive and evade the host’s immune responses. Hence, understanding the excretory-secretory products (ESPs) by helminths is crucial for developing control tools, including drug targets, vaccines, and potential therapies for inflammatory and metabolic disorders caused by them. Proteomics, the large-scale analysis of proteins, offers a powerful approach to unravel the complex proteomes of helminths and gain insights into their biology. Proteomics, as a science that delves into the functions of proteins, has the potential to revolutionize clinical therapies against parasitic infections that have developed anthelminthic resistance. Proteomic technologies lay a framework for accompanying genomic, reverse genetics, and pharmacokinetic approaches to provide more profound or broader coverage of the cellular mechanisms that underlie the response to anthelmintics. With the development of vaccines against helminth infections, proteomics has brought a major change to parasitology. The proteome of helminths can be analyzed comprehensively, revealing the complex network of proteins that enable parasite survival and pathogenicity. Furthermore, it reveals how parasites interact with hosts’ immune systems. The current article reviews the latest advancements in helminth proteomics and highlights their valuable contributions to the search for anthelminthic vaccines.

show abstract

Proteomics, Bioinformatics, and Infectious Diseases

Cited by 2 publications

References 151 publications

ProteoPlotter: an executable proteomics visualization tool compatible with Perseus

ProteoPlotter: an executable proteomics visualization tool compatible with Perseus

Unveiling Novel Insights in Helminth Proteomics: Advancements, Applications, and Implications for Parasitology and Beyond

Contact Info

Product

Resources

About