New Application Note: The Importance of Hydrophobic Peptides for T cell Activation 

Why Hydrophobic Sequences Matter for T-Cell Epitope Coverage 

Peptide pools are critical for monitoring and studying antigen-specific T-cell responses. But here’s the problem: peptide pools from some manufacturers miss hydrophobic peptides due to synthesis challenges - leading to incomplete T-cell activation. 

At JPT Peptide Technologies, we don’t skip the hard parts. With 20 years of expertise and advanced synthesis protocols, we ensure full sequence coverage, including the most hydrophobic peptides. We analyzed the whole human proteome (approx. 30 mio overlapping peptides) to shed light on this topic. To predict the hydrophobicity of these peptides we calculated their GRAVY (grand average of hydropathy) score. The GRAVY score is widely used to estimate the hydrophobicity of peptides and ranges from ‑4.5 to +4.5 with higher values representing higher hydrophobicity. The results of this analysis have now been published: 

“The Importance of Hydrophobic Peptides in Peptide Pools for T-Cell Activation”
Pfeil et al., Application Note (2025) 

Read the full Text.

A short summary of the results: 

Why Hydrophobic Peptides Matter More Than You Think 

Hydrophobic peptides aren’t just tough to synthesize—they’re biologically essential. 

• T-cell epitopes are often hydrophobic—especially those binding to HLA-A*02:01 
• Using GRAVY scores, our analysis of IEDB data shows: 
  -T-cell epitopes: mean score = 0.04
  -Average human peptides: mean score = – 0.41 
• The trend holds across viral proteomes like SARS-CoV-2, EBV, and HCMV. 

Hydrophobicity Enhances MHC Binding 

• In EBV’s LMP1 protein, known T-cell epitopes cluster in hydrophobic regions. 
• NetMHCpan analysis shows strong correlations between peptide hydrophobicity and MHC binding affinity:
  -HLA-A*02:01 → r² = 0.61
  -HLA-A*03:01 → r² = 0.58
  -HLA-A*24:02 → r² = 0.41 

Hydrophobic peptides don’tjust bind—they bind better. 

Full Coverage. Better Activation. Accurate Monitoring. 

It can be concluded that special attention must be paid to the successful chemical synthesis of hydrophobic peptides, because their inclusion in protein-spanning peptide pools is essential for complete epitope coverage. Hydrophobic peptides are vital for complete epitope coverage and effective immune stimulation. 

JPT’s Expertise = No Peptide Left Behind 

Other manufacturers may skip difficult peptides. Not us. 

• Our optimized protocols and solubility-enhancing techniques allow us to include even the most hydrophobic sequences. 
• Example: The top four most published viral epitopes in IEDB - all with GRAVY scores >1.5 - are synthesized at high purity by JPT in overlapping peptide pools.