Proteomics Primer

Proteomics measures proteins more directly than RNA-seq. In LC-MS/MS experiments, proteins are digested into peptides, measured by mass spectrometry, and inferred back to protein-level abundance.

flowchart LR
    A["Tissue sample"] --> B["Protein extraction"]
    B --> C["Peptide digestion"]
    C --> D["LC-MS/MS"]
    D --> E["Protein quantification"]
    E --> F["Validation overlay"]

Why It Matters Here

RNA evidence alone can over-prioritize genes whose protein products are not changed or detectable. Proteomics adds an orthogonal evidence layer.

Common Pitfalls

• RNA and protein abundance are not always concordant.
• Low-abundance cytokines can be difficult to detect.
• Protein inference can be complicated by shared peptides and isoforms.

Project Guardrail

Weak proteomics support is flagged rather than hidden, especially when RNA evidence is strong.