LC-MS/MS
Definition
LC-MS/MS (Liquid Chromatography-Tandem Mass Spectrometry) is an analytical technique combining liquid chromatography separation with tandem mass spectrometry detection for identifying and quantifying proteins, peptides, and post-translational modifications in complex biological samples. The LC component separates peptides by physicochemical properties, while the first MS stage measures mass-to-charge ratios and the second MS stage fragments selected ions for structural identification. This bottom-up proteomics approach enables comprehensive protein profiling, differential expression analysis, and discovery of disease biomarkers. LC-MS/MS provides high sensitivity, specificity, and throughput, making it the gold standard for quantitative proteomics in systems biology, drug development, and clinical research.
Visualize LC-MS/MS in Nodes Bio
Researchers can visualize LC-MS/MS proteomics data as protein-protein interaction networks, where nodes represent identified proteins and edges show functional relationships or co-expression patterns. Nodes Bio enables integration of quantitative abundance data with pathway annotations, allowing users to map differentially expressed proteins onto biological networks, identify dysregulated pathways, and discover novel protein complexes or signaling cascades relevant to disease mechanisms.
Visualization Ideas:
- Protein-protein interaction networks colored by LC-MS/MS abundance ratios
- Pathway enrichment maps showing dysregulated protein complexes from quantitative proteomics
- Time-course networks tracking protein expression dynamics across experimental conditions
Example Use Case
A cancer research team uses LC-MS/MS to profile protein expression in drug-resistant versus drug-sensitive tumor cells. They identify 2,500 proteins with 300 showing significant differential expression. By importing this data into Nodes Bio, they visualize how upregulated proteins cluster within specific signaling pathways, revealing that resistance involves coordinated changes in autophagy and metabolic networks. This network view helps identify combination therapy targets by highlighting key regulatory nodes connecting multiple dysregulated pathways.