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Peptidomics pp 223-240 | Cite as

Milk Peptidomics to Identify Functional Peptides and for Quality Control of Dairy Products

  • David DallasEmail author
  • Søren Drud Nielsen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1719)

Abstract

Human milk and dairy products are important parts of human nutrition. In addition to supplying nutrients, milk proteins contain fragments—peptides—with important biological functions that are released during processing or digestion. Besides their potential functional relevance, peptides released during processing can be used as markers of ripening stage or product deterioration. Hence, identification and quantification of peptides in milk can be used to assay potential health benefits or product quality. This chapter describes how to extract, identify, and analyze peptides within breast milk, dairy products, and dairy digestive samples. We describe how to analyze extracted peptides with liquid chromatography-mass spectrometry, to use software to identify peptides based on database searching, and to extract peak areas for relative quantification of each peptide. We describe methods for data analysis, including predicting which enzymes are responsible for protein cleavage, identifying the site specificity of protein breakdown, mapping identified peptides to known bioactive peptides, and applying models to predict novel functional peptides.

Key words

Peptidomics Milk Mass spectrometry Peptide Bioactive Identification Quantification X! Tandem Skyline Proteome Discoverer 

Notes

Acknowledgments

The authors thank C. J. Dillard for editing this manuscript. The authors gratefully acknowledge funding from the National Institutes of Health, Eunice Kennedy Shriver Institute of Child Health and Development (4R00HD079561) R00 Pathway to Independence Career Award.

References

  1. 1.
    Migliore-Samour D, Floch F, Jollès P (1989) Biologically-active casein peptides implicated in immunomodulation. J Dairy Res 56:357–362CrossRefPubMedGoogle Scholar
  2. 2.
    Jørgensen ALW, Juul-Madsen HR, Stagsted J (2010) Colostrum and bioactive, colostral peptides differentially modulate the innate immune response of intestinal epithelial cells. J Pept Sci 16:21–30CrossRefPubMedGoogle Scholar
  3. 3.
    Brantl V (1984) Novel opioid peptides derived from human beta-casein: human beta-casomorphins. Eur J Pharmacol 106:213–214CrossRefPubMedGoogle Scholar
  4. 4.
    Kampa M, Loukas S, Hatzoglou A et al (1996) Identification of a novel opioid peptide (Tyr-Val-Pro-Phe-Pro) derived from human alpha S1 casein (alpha S1-casomorphin, and alpha S1-casomorphin amide). Biochem J 319:903–908CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Aniansson G, Andersson B, Lindstedt R, Svanborg C (1990) Antiadhesive activity of human casein against Streptococcus pneumoniae and Haemophilus influenzae. Microb Pathog 8:315–323CrossRefPubMedGoogle Scholar
  6. 6.
    Stromqvist M, Falk P, Bergstrom S et al (1995) Human-milk k-casein and inhibition of Helicobacter pylori adhesion to human gastric mucosa. J Pediatr Gastroenterol Nutr 21:288–296CrossRefPubMedGoogle Scholar
  7. 7.
    Liepke C, Zucht H-D, Forssmann W-G, Ständker L (2001) Purification of novel peptide antibiotics from human milk. J Chromatogr B Analyt Technol Biomed Life Sci 752:369–377CrossRefGoogle Scholar
  8. 8.
    Yamada A, Sakurai T, Ochi D et al (2015) Antihypertensive effect of the bovine casein-derived peptide Met-Lys-Pro. Food Chem 172:441–446CrossRefPubMedGoogle Scholar
  9. 9.
    Suetsuna K, Ukeda H, Ochi H (2000) Isolation and characterization of free radical scavenging activities peptides derived from casein. J Nutr Biochem 11:128–131CrossRefPubMedGoogle Scholar
  10. 10.
    Dallas DC, Guerrero A, Khaldi N et al (2013) Extensive in vivo human milk peptidomics reveals specific proteolysis yielding protective antimicrobial peptides. J Proteome Res 12:2295–2304CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Guerrero A, Dallas DC, Contreras S et al (2014) Mechanistic peptidomics: factors that dictate the specificity on the formation of endogenous peptides in human milk. Mol Cell Proteomics 13:3343–3351CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Dallas DC, Guerrero A, Khaldi N et al (2014) A peptidomic analysis of human milk digestion in the infant stomach reveals protein-specific degradation patterns. J Nutr 144:815–820CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Combes C, Paterson E, Amadò R (2002) Isolation and identification of low-molecular-weight peptides from Emmentaler cheese. J Food Sci 67:553–559CrossRefGoogle Scholar
  14. 14.
    Toelstede S, Hofmann T (2008) Sensomics mapping and identification of the key bitter metabolites in Gouda cheese. J Agric Food Chem 56:2795–2804CrossRefPubMedGoogle Scholar
  15. 15.
    Gupta A, Mann B, Kumar R, Sangwan RB (2010) Identification of antioxidant peptides in cheddar cheese made with adjunct culture Lactobacillus casei ssp. casei 300. Milchwissenschaft 65:396–399Google Scholar
  16. 16.
    Sforza S, Cavatorta V, Lambertini F et al (2012) Cheese peptidomics: a detailed study on the evolution of the oligopeptide fraction in Parmigiano-Reggiano cheese from curd to 24 months of aging. J Dairy Sci 95:3514–3526CrossRefPubMedGoogle Scholar
  17. 17.
    Miclo L, Roux E, Genay M et al (2012) Variability of hydrolysis of β-, αs1-, and αs2-caseins by 10 strains of Streptococcus thermophilus and resulting bioactive peptides. J Agric Food Chem 60:554–565CrossRefPubMedGoogle Scholar
  18. 18.
    Dallas DC, Citerne F, Tian T et al (2016) Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins. Food Chem 197:273–284CrossRefPubMedGoogle Scholar
  19. 19.
    Rauh VM, Johansen LB, Ipsen R et al (2014) Plasmin activity in UHT milk: relationship between proteolysis, age gelation, and bitterness. J Agric Food Chem 62:6852–6860CrossRefPubMedGoogle Scholar
  20. 20.
    Jensen S, Sidsel J, Therese J et al (2015) Storage-induced changes in the sensory characteristics and volatiles of conventional and lactose-hydrolyzed UHT processed milk. Eur Food Res Technol 240:1247–1257CrossRefGoogle Scholar
  21. 21.
    Nielsen SD, Jansson T, Le TT et al (2017) Correlation between sensory properties and peptides derived from lactose-hydrolyzed UHT milk during storage. Int Dairy J 68:1–108CrossRefGoogle Scholar
  22. 22.
    Dallas DC, Guerrero A, Parker EA et al (2013) Peptidomic profile of milk of Holstein cows at peak lactation. J Agric Food Chem 62:58–65CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Guerrero A, Dallas DC, Contreras S et al (2014) Peptidomic analysis of healthy and subclinically mastitic bovine milk. Int Dairy J 46:46–52CrossRefPubMedCentralGoogle Scholar
  24. 24.
    Dallas DC, Guerrero A, Parker EA et al (2015) Current peptidomics: applications, purification, identification, quantification and functional analysis. Proteomics 15:1026–1038CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Schilling B, Rardin MJ, MacLean BX et al (2012) Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in Skyline application to protein acetylation and phosphorylation. Mol Cell Proteomics 11:202–214CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Vijayakumar V, Guerrero AN, Davey N et al (2012) EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. J Proteome Res 11:6056–6065CrossRefPubMedGoogle Scholar
  27. 27.
    Waghu FH, Barai RS, Gurung P, Idicula-Thomas S (2016) CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res 44:D1094–D1097CrossRefPubMedGoogle Scholar
  28. 28.
    Vizcaíno JA, Côté RG, Csordas A et al (2013) The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41:D1063–D1069CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.College of Public Health and Human SciencesOregon State UniversityCorvallisUSA

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