Furthermore, instead of a single purified protein as the precursor for generating peptides, food protein sources typically are composed of multiple
constituents, for example, αs1-casein, αs2-casein, β-casein, and κ-casein are all present in sodium caseinate. Thus, the number of unique peptide sequences generated in these protein hydrolysates is usually massive. According to Panchaud et al.  and Lahrichi et al. [29●●], proteomics (for biomarker MK 2206 discovery) and peptidomics (for bioactive peptide discovery) have in common the necessity for identification and validation on the peptide level. However, the majority of peptides generated by specific enzymes such as trypsin in biomarker proteomics analyses fall in the range of 7 to 25 amino acids in length; in contrast the typical length of peptides occurring in protein hydrolysates produced by enzymes for food applications may range from 2 to 100 amino acids, and will vary in properties including charge state and hydrophobicity. Different technological challenges must be considered
Raf inhibitor drugs in the analysis of small (<7 amino acids), medium (7–25 amino acids) and large (>25 amino acids) peptides. Size exclusion chromatography on columns capable of separation in the ∼100 to 10 000 Da range was suggested as a fractionation step prior to mass spectrometry , and the application of LC–MS/MS
with multiple reaction monitoring (MRM) was reported to address challenges of analysis for even very complex peptide sets with large isobaric clusters [29●●]. Promising results were obtained in the analysis IMP dehydrogenase of a set of 117 peptides composed of di-peptides, tri-peptides and tetra-peptides of the three branched chain amino acids (V, L, I) in a model system as well as in a complex matrix (whey protein hydrolysate), by optimizing chromatographic separation followed by LC–MS/MS analysis with MRM scan mode and using a combination of retention time, diagnostic ion as well as ratios of key diagnostic ions [29●●]. Further research is crucial for expansion of this approach to the analysis of other peptide sizes likely to be found in food protein hydrolysates. Picariello et al.  commented that ‘pharmacokinetics’ and ‘pharmacodynamics’, which are integral to understanding drug metabolism, are ‘still elusive for dietary peptides’, with most studies on food-derived bioactive sequences paying little attention to the susceptibility of the peptides to degradation by gastric, pancreatic and small intestinal brush border membrane enzymes, and the likelihood that only nano-molar or even pico-molar concentrations of the original peptide may pass into the systemic circulation.