Proteomics 101 (cancer)
Proteomics measures proteins and their modifications (e.g. phosphorylation, ubiquitination). It sits close to phenotype: what the cell is actually doing, not only what it is transcribing.
Typical technologies
- Mass spectrometry (LC-MS/MS) for discovery and targeted panels
- Antibody-based multiplex assays (e.g. Olink, reverse-phase protein arrays in research)
Why it matters in oncology
- Drug targets and pathway activation (kinase signaling)
- Resistance mechanisms that may not show up cleanly in RNA
- Immunotherapy context (e.g. checkpoint expression at protein level, though often IHC is used clinically)
Integration
RNA and protein are correlated but not identical (translation, turnover, PTMs). Multi-layer models often combine transcript and protein; see Multi‑omics integration.