There are a number of elements to consider when designing individual peptides, specifically amino acid composition, length, solubility and the application in which the peptides are to be used. Acinopeptide can provide the designing of large numbers of peptides in sets for high throughput synthesis.

As the length of the peptide increases, so the proportion of full-length peptide obtained from the synthesis will decrease. Optimal synthesis results are achieved for peptides up to 15 amino acids, and peptides 10-15 amino acids long are recommended for generation of peptide antisera.

The amino acid content strongly influences the purification of the peptide and the resulting solubility. The ratio of charged amino acids to uncharged and hydrophobic residues is critical in determining the ease of solubility of a peptide, and therefore its usefulness in the downstream application.

A high content of hydrophobic residues will reduce the solubility of a peptide in aqueous solution. A design with at least one charged residue every five amino acids is recommended, otherwise it is recommended to replace hydrophobic amino acids with charged or polar residues where possible. If determination of peptide concentration is critical, the addition of a Tyrosine residue at the N- and C- terminus of the peptide is recommended if the peptide does not already contain Tyrosine or Tryptophan.