Peptide array technology, also referred to as scanning peptide array or microarray technology, may offer a relatively cost-effective approach to generate an array of longer peptide sequences that can be probed on the array support, and used to investigate interactions of the peptides with physiologically relevant proteins or other molecules, for example,

peptide–protein interactions involved in allergenic epitope analysis, enzyme–substrate, and enzyme–inhibitor investigations 26 and 27. Peptide array technology may thus offer a high throughput approach as a complement to classical and bioinformatics-driven approaches to select peptide sequences for further investigation ( Figure 1). In the end, both the traditional (empirical) and newer (bioinformatics PD 332991 driven) approaches converge at a common point (Figure 1), namely the need to test the activity of specific peptide sequences that have either been identified by the experimental data or suggested by in silico high throughput screening compounds analysis, and then to verify that these sequences are actually released

and exist in the end-products, whether the latter be unfractionated protein hydrolysates containing bioactive properties, or else partially purified fractions with enriched concentrations of the bioactive sequences. Compared to synthetic small-molecule drugs, which are single identifiable entities, in most cases, the target end product for bioactive peptides derived from food is not usually a single peptide with 99% purity — not only due to the unacceptable high cost and low yield that would be involved, but also because products containing only single peptide entities would ignore any additive, old synergistic

or antagonistic effects among peptides. Moreover, peptides possessing bioactivity are often hydrophobic in nature and exhibit poor aqueous solubility at high concentrations. Formulating products with several peptides each at lower concentration can ameliorate the solubility problem while conferring the same level of bioactivity. Thus, the minimum level of information for quality assurance should include not only verification of specific peptide sequences in the complex matrix that are associated with the activity but also the bioactivity of peptide mixtures under standard conditions. Mass spectrometry, or more specifically liquid chromatography tandem mass spectrometry (LC–MS/MS) is recognized as the primary tool for sequencing peptides and identifying proteins, but requires particular paradigms for the analysis of bioactive peptides derived from food.