Label-Free Quantitative Proteomics for Protein Interactions

Digest interaction pulldowns, run LC-MS/MS, normalize intensities, and call specific interactors versus controls using replicate statistics.

Key takeaways

• No labeling step speeds design.
• Requires careful normalization and controls.
• Works with GFP-Trap, antibody IP, or AP-MS.
• Pairs with network annotation.







Related services

Label-free services Label-Free Quantitative Proteomics Service Label-Free Analysis Service 4D Label-Free Quantitative Proteomics Protein Interaction Analysis Service

Interaction workflows Co-Immunoprecipitation Protein Interaction Analysis Service Co-IP/Mass Spectrometry Service Immunoprecipitation Mass Spectrometry Service Protein Interaction Analysis Service

FAQ

How many replicates? Typically ≥3 biological replicates for interaction LFQ.

How control bait specificity? Use empty vector or unrelated GFP fusion controls.

Conclusion

Label-free quant makes interaction proteomics accessible for many bait proteins.