2D-gel electrophoresis
Definition
2D-gel electrophoresis (two-dimensional polyacrylamide gel electrophoresis, or 2D-PAGE) is a classical proteomics technique that separates complex protein mixtures based on two independent properties: isoelectric point (pI) in the first dimension using isoelectric focusing, and molecular weight in the second dimension using SDS-PAGE. This method can resolve thousands of proteins simultaneously, creating a protein map where each spot represents a distinct protein or protein isoform. 2D-gel electrophoresis enables comparative proteomics by revealing differences in protein expression, post-translational modifications, and protein isoforms between samples. Despite being labor-intensive, it remains valuable for detecting protein variants and validating mass spectrometry results, particularly in clinical biomarker discovery and quality control applications.
Visualize 2D-gel electrophoresis in Nodes Bio
Researchers can use Nodes Bio to integrate 2D-gel electrophoresis data with protein-protein interaction networks, mapping differentially expressed protein spots to known pathways and functional modules. By connecting identified proteins to their interaction partners, researchers can visualize how expression changes propagate through biological networks, identify key regulatory hubs, and discover potential biomarkers within connected protein communities that may not be apparent from gel analysis alone.
Visualization Ideas:
- Protein-protein interaction networks highlighting differentially expressed proteins from 2D-gel analysis
- Pathway enrichment maps showing biological processes affected by proteins identified in gel spots
- Multi-omics integration networks connecting 2D-gel proteomics data with transcriptomics and metabolomics datasets
Example Use Case
A cancer research team performs 2D-gel electrophoresis comparing tumor versus normal tissue samples from breast cancer patients. They identify 47 differentially expressed protein spots, which are excised and identified by mass spectrometry. Using Nodes Bio, they map these proteins onto human protein interaction networks and discover that 12 proteins cluster within the PI3K/AKT signaling pathway. This network visualization reveals that several upregulated proteins are direct interaction partners of known drug targets, suggesting potential combination therapy strategies and identifying PTEN as a central node connecting multiple dysregulated proteins.