Related Experiment Video
Updated: Jul 4, 2025
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
15.5K
CURTAIN-A unique web-based tool for exploration and sharing of MS-based proteomics data
Toan K Phung1,2, Kerryn Berndsen1,2, Rosamund Shastry1,2
1Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
Summary
New online tools, CURTAIN and CURTAIN-PTM, simplify mass spectrometry proteomics data analysis for non-experts. These platforms enhance data sharing and visualization, enabling deeper insights into protein expression and post-translational modifications.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- Mass spectrometry (MS)-based proteomics generates large datasets requiring specialized analysis.
- Sharing and interactive exploration of proteomics data can be challenging for non-experts.
- Current tools may not fully support comprehensive analysis of protein expression and post-translational modifications (PTMs).
Purpose of the Study:
- To develop user-friendly online tools, CURTAIN and CURTAIN-PTM, for interactive analysis and sharing of MS-based proteomics data.
- To enable non-MS experts to visualize, analyze, and interpret complex proteomics datasets.
- To facilitate the exploration of protein structure, interactions, expression, and disease associations, as well as PTM site analysis.
Main Methods:
- Development of web-based platforms CURTAIN and CURTAIN-PTM with accompanying video tutorials.
- Implementation of interactive visualization features including volcano plots, bar charts, and violin plots.
- Integration of analysis modules for protein domains, predicted structures (AlphaFold), interactors, expression levels, disease links, and PTM site analysis.
- Linking CURTAIN-PTM with a Kinase Library for predicting upstream kinases.
Main Results:
- CURTAIN and CURTAIN-PTM provide accessible interfaces for non-experts to analyze proteomics data.
- Tools enable interactive exploration of volcano plots, primary data deconvolution, and publication-ready data export.
- Analysis of Parkinson's disease-related proteins (PPM1H, LRRK2) and a ubiquitylation dataset (PINK1-Parkin) demonstrated tool utility.
- New biological insights were revealed from reanalyzed datasets, including previously unhighlighted data.
Conclusions:
- CURTAIN and CURTAIN-PTM significantly lower the barrier for MS proteomics data analysis and sharing.
- Open-source nature of the tools promotes data accessibility and collaborative research.
- Advocacy for including shareable CURTAIN weblinks in publications to enhance data reproducibility and exploitation.
Related Concept Videos
01:33Proteomics
7.3K
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...
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...
7.3K
02:26Protein Networks
4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K