Implement quantitative epitope binning:
Use AlphaFold-Multimer for structural homology modeling against:
| Nudix Family Member | Sequence Identity |
|---|---|
| NUDT5 | 38-42% |
| NUDT7 | 33-37% |
| CD27 (TNFRSF7) | <15% |
5. Standardized protocols for quantitative comparison across studies:
Establish internal reference standards:
| Material | Storage | Stability Testing |
|---|---|---|
| Lyophilized cell lysate | -80°C | Quarterly WB validation |
| Recombinant protein aliquots | Liquid N2 | Annual MS verification |
7. Systematic approach for reconciling contradictory findings:
| Discrepancy Type | Investigation Protocol |
|---|---|
| Cell-type specific detection | Perform RNA/protein co-expression analysis across 5+ cell lines |
| Subcellular localization mismatch | Conduct fractionation-MS with antibody depletion controls |
| Functional assay divergence | Implement BioLayer interferometry binding-energy calculations |