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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant.

James Luke Gallant^1,2, Tiaan Heunis^1,3, Samantha Leigh Sampson¹

¹Division of Molecular Biology and Human Genetics, Department of Biomedical Science, DST/NRF Centre of Excellence in Biomedical TB Research, SA MRC Centre for Tuberculosis Research, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.

Bioinformatics (Oxford, England)

|July 9, 2020

Summary

ProVision simplifies proteomics data analysis for researchers. This free, open-source platform offers user-friendly tools for label-free and TMT-based experiments, enhancing protein expression analysis accessibility.

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Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Proteomics offers powerful protein expression analysis but faces accessibility challenges due to complex data analysis.
Core facilities and collaborations are increasing proteomics availability, yet a bottleneck remains in routine data interpretation.

Purpose of the Study:

To develop ProVision, a free, open-source, web-based analytics platform for proteomics data analysis.
To provide a user-friendly environment for analyzing label-free and Tandem Mass Tag (TMT)-based proteomics experiments.
To facilitate statistical analysis, exploratory data analysis, and downstream bioinformatics tasks.

Main Methods:

Development of a web-based platform, ProVision, accessible online.
Integration of data analysis pipelines for label-free and TMT proteomics workflows.
Inclusion of customizable quality control, differential expression plots, enrichment analysis, and protein-protein interaction prediction.

Main Results:

ProVision offers a user-friendly interface for complex proteomics data analysis.
The platform supports both label-free and TMT-based quantitative proteomics experiments.
Users can perform statistical analysis, generate visualizations, and predict protein interactions in one place.

Conclusions:

ProVision democratizes proteomics data analysis, making advanced techniques more accessible to researchers.
The platform streamlines the interpretation of quantitative proteomics data, accelerating biological discovery.
Open-source availability and comprehensive tutorials enhance ProVision's utility for the scientific community.