During fermentation of milk, many bioactive compounds are released. Some of these compounds are oxidized and may dimerize the peptides, thereby decreasing their activity and reproducibility. In addition, frequent freezing and thawing can also cause degradation of the peptides. Therefore, storing the peptides in refrigerated conditions is necessary.
Peptides in solution form should be stored at -20 degC and kept away from light. This will help to reduce the risk of degradation and thwart reproducibility.
To study the intramolecular folding of peptides, we developed a 20-amino acid peptide, Max-1. In this peptide, the amino acids are arranged in an amphiphilic b-hairpin conformation. This conformation allows the peptide to self-assemble into a network of fibrils. The peptide can be used to study peptide intramolecular folding and its influence on environmental changes.
For analysis, we analyzed the peptides using polyacrylamide gel electrophoresis. We found that cells expressing similar alleles had more peptides than cells expressing different alleles. However, there was no correlation between the number of HLA complexes and the immunogenicity of a peptide.
The peptides were then screened for co-eluting species using MS2. This approach resulted in a chromatogram of all fragments present in the full mass range of MS2. The intensity threshold was determined by the maximum injection time. This threshold was set to 120 ms.
Then, the final score of the peptide was computed by summing the logarithm of the corresponding PWM entries. The peptide score was then compared with the distribution of scores from randomly selected peptides in the human proteome.