Peptidomics as a tool for characterizing bioactive milk peptides

Food Chemistry

Volumn 230, Issue , 2017, Pages 91-98

  Giacometti, Jasminka ^a   Buretić Tomljanović, Alena ^b  

^a University of Rijeka   (Croatia)

^b UNIVERSITY OF RIJEKA   (Croatia)

Author keywords

Bioactive milk peptides; Mass spectrometry; Peptidomics

Indexed keywords

FOOD SUPPLY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; SPECTROMETRY;

BIOACTIVE PEPTIDES; BIOLOGICALLY ACTIVE PEPTIDES; CHEMOMETRIC TOOLS; CHROMATOGRAPHIC TECHNIQUES; FERMENTATION PROCESS; HEALTH BENEFITS; HIGH-RESOLUTION TECHNIQUES; PEPTIDOMICS;

PROTEINS;

PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CHEMOMETRICS; CHROMATOGRAPHY; DAIRY PRODUCT; FERMENTATION; FOOD CONTROL; FOOD SAFETY; MASS SPECTROMETRY; MILK; PEPTIDOMICS; PROTEOMICS; ANIMAL; BIOLOGY; CHEMISTRY; FOOD ANALYSIS; PROCEDURES;

ANIMALS; CHROMATOGRAPHY; COMPUTATIONAL BIOLOGY; FOOD ANALYSIS; FOOD SAFETY; MASS SPECTROMETRY; MILK; PEPTIDES; PROTEOMICS;

EID: 85016271181     PISSN: 03088146     EISSN: 18737072     Source Type: Journal    
DOI: 10.1016/j.foodchem.2017.03.016     Document Type: Article

References (89)

1. Ardö, Y., Lilbæk, H., Kristiansen, K.R., Zakora, M., Otte, J., Identification of large phosphopeptides from β-casein that characteristically accumulate during ripening of the semi-hard cheese Herrgård. International Dairy Journal 17 (2007), 513–524.
2. Aristoteli, L.P., Molloy, M.P., Baker, M.S., Evaluation of endogenous plasma peptide extraction methods for mass spectrometric biomarker discovery. Journal of Proteome Research 6 (2006), 571–581.
3. Aryal, U., Ross, A., Enrichment and analysis of phosphopeptides under different experimental conditions using titanium dioxide affinity chromatography and mass spectrometry. Rapid Communications in Mass Spectrometry: RCM 24 (2010), 219–231.
4. Bargeman, G., Houwing, J., Recio, I., Koops, G.-H., van der Horst, C., Electro-membrane filtration for the selective isolation of bioactive peptides from an αs2-casein hydrolysate. Biotechnology & Bioengineering 80 (2002), 599–609.
5. Bazinet, L., Firaous, L., Separation of bioactive peptides by membrane processes: Technologies and devices. Recent Patents on Biotechnology 7 (2013), 9–27.
6. Bazinet, L., Firdaous, L., Membrane processes and devices for separation of bioactive peptides. Recent Patents on Biotechnology 3 (2009), 61–72.
7. Bernardi, N., Benetti, G., Haouet, N.M., Sergi, M., Grotta, L., Marchetti, S., Martino, G., A rapid high-performance liquid chromatography-tandem mass spectrometry assay for unambiguous detection of different milk species employed in cheese manufacturing. Journal of Dairy Science 98 (2015), 8405–8413.
8. Bolscher, J.G., van der Kraan, M.I., Nazmi, K., Kalay, H., Grün, C.H., Van't, Hof W.,.. Nieuw Amerongen, A.V., A one-enzyme strategy to release an antimicrobial peptide from the LFampin-domain of bovine lactoferrin. Peptides 27 (2006), 1–9.
9. Boutrou, R., Gaudichon, C., Dupont, D., Jardin, J., Airinei, G., Benamouzig, R., Tome, D., Sequential release of milk protein – Derived bioactive peptides. American Journal of Clinical Nutrition 97 (2013), 1314–1323.
10. Brahmachary, M., Krishnan, S.P., Koh, J.L., Khan, A.M., Seah, S.H., Tan, T.W., et al. ANTIMIC: A database of antimicrobial sequences. Nucleic Acids Research 32:Database issue (2004), D586–D589.
11. Callesen, A.K., Madsen, J.S., Vach, W., Kruse, T.A., Mogensen, O., Jensen, O.N., Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool?. Proteomics 9 (2009), 1428–1441.
12. Carrasco-Castilla, J., Hernández-Álvarez, A.J., Jiménez-Martínez, C., Gutiérrez-López, G.F., Dávila-Ortiz, G., Use of proteomics and peptidomics methods in food bioactive peptide science and engineering. Food Engineering Reviews 4 (2012), 224–243.
13. Chianese, L., Calabrese, M.G., Ferranti, P., Mauriello, R., Garro, G., De Simone, C.,.. Ramunno, L., Proteomic characterization of donkey milk “caseome”. Journal of Chromatography A 1217 (2010), 4834–4840.
14. Combes, C., Paterson, E., Amado, R., Isolation and identification of low-molecular-weight peptides from emmentaler cheese. Journal of Food Science 67 (2002), 553–559.
15. Contreras, M.D.M., López-Expósito, I., Hernández-Ledesma, B., Ramos, M., Recio, I., Application of mass spectrometry to the characterization and quantification of food-derived bioactive peptides. Journal of AOAC International 91 (2008), 981–994.
16. Cox, J., Mann, M., Quantitative, high-resolution proteomics for data-driven systems biology. Annual Review of Biochemistry 80 (2011), 273–299.
17. Cuollo, M., Caira, S., Fierro, O., Pinto, G., Picariello, G., Addeo, F., Toward milk speciation through the monitoring of casein proteotypic peptides. Rapid Communications in Mass Spectrometry: RCM 24 (2010), 1687–1696.
18. D'Alessandro, A., Zolla, L., Scaloni, A., The bovine milk proteome: cherishing, nourishing and fostering molecular complexity. An interactomics and functional overview. Molecular Biosystems 7 (2011), 579–597.
19. D'Ambrosio, C., Arena, S., Salzano, A.M., Renzone, G., Ledda, L., Scaloni, A., A proteomic characterization of water buffalo milk fractions describing PTM of major species and the identification of minor components involved in nutrient delivery and defense against pathogens. Proteomics 8 (2008), 3657–3666.
20. Dallas, D.C., Guerrero, A., Khaldi, N., Castillo, P.A., Martin, W.F., Smilowitz, J.T., et al. Extensive in vivo human milk peptidomics reveals specific proteolysis yielding protective antimicrobial peptides. Journal of Proteome Research 12 (2013), 2295–2304.
21. Dallas, D.C., Guerrero, A., Parker, E.A., Robinson, R.C., Gan, J., German, J.B., et al. Current peptidomics: Applications, purification, identification, quantification, and functional analysis. Proteomics 15 (2015), 1026–1038.
22. Doyen, A., Beaulieu, L., Saucier, L., Pouliot, Y., Bazinet, L., Impact of ultrafiltration membrane material on Peptide separation from a snow crab byproduct hydrolysate by electrodialysis with ultrafiltration membranes. Journal of Agricultural and Food Chemistry 59 (2011), 1784–1792.
23. Ebner, J., Arslan, A.A., Fedorova, M., Hoffmann, R., Küçükçetin, A., Pischetsrieder, M., Peptide profiling of bovine kefir reveals 236 unique peptides released from caseins during its production by starter culture or kefir grains. Journal of Proteomics 117 (2015), 41–57.
24. Eisele, T., Stressler, T., Kranz, B., Fischer, L., Quantification of dabsylated di- and tri-peptides in fermented milk. Food Chemistry 135 (2012), 2808–2813.
25. Fernández, A., Suárez, A., Zhu, Y., FitzGerald, R.J., Riera, F., Membrane fractionation of a β-lactoglobulin tryptic digest: Effect of the pH. Journal of Food Engineering 114 (2013), 83–89.
26. Fukao, Y., Yoshida, M., Kurata, R., Kobayashi, M., Nakanishi, M., Fujiwara, M.,.. Ferjani, A., Peptide separation methodologies for in-depth proteomics in Arabidopsis. Plant and Cell Physiology 54 (2013), 808–815.
27. Fukumoto, H., Tokuda, T., Kasai, T., Ishigami, N., Hidaka, H., Kondo, M., et al. High-molecular-weight β-amyloid oligomers are elevated in cerebrospinal fluid of Alzheimer patients. The FASEB Journal 24 (2010), 2716–2726.
28. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., Bairoch, A., Protein identification and analysis tools on the ExPASy server. Walker, J.M., (eds.) The proteomics protocols handbook, 2005, Humana Press Inc, Totowa, NJ, USA, 571–607.
29. Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W., Gygi, S.P., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proceedings of the National Academy of Sciences of the United States of America 100 (2003), 6940–6945.
30. Gong, M., Mohan, A., Gibson, A., Udenigwe, C.C., Mechanisms of plastein formation, and prospective food and nutraceutical applications of the peptide aggregates. Biotechnology Reports 5 (2015), 63–69.
31. Grunert, T., Pock, K., Buchacher, A., Allmaier, G., Selective solid-phase isolation of methionine-containing peptides and subsequent matrix-assisted laser desorption/ionisation mass spectrometric detection of methionine- and of methionine-sulfoxide-containing peptides. Rapid Communications in Mass Spectrometry 17 (2003), 1815–1824.
32. Guarino, C., Fuselli, F., La Mantia, A., Longo, L., Faberi, A., Marianella, R.M., Peptidomic approach, based on liquid chromatography/electrospray ionization tandem mass spectrometry, for detecting sheep's milk in goat's and cow's cheeses. Rapid Communications in Mass Spectrometry: RCM 24 (2010), 3567–3577.
33. Guerrero, A., Dallas, D.C., Contreras, S., Chee, S., Parker, E.A., Sun, X.,.. Lebrilla, C.B., Mechanistic peptidomics: Factors that dictate specificity in the formation of endogenous peptides in human milk. Molecular & Cellular Proteomics 13 (2014), 3343–3351.
34. Guy, P.A., Fenalle, F., Contribution of mass spectrometry to assess quality of milk-based products. Mass Spectrometry Reviews 25 (2006), 290–326.
35. Hepburn, S., Cairns, D., Jackson, D., Craven, R., Riley, B., Hutchinson, M., et al. An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature and proteolysis. Proteomics – Clinical Applications 5–6 (2015), 507–521.
36. Hoek, K.S., Milne, J.M., Grieve, P.A., Dionysius, D.A., Smith, R., Antibacterial activity in bovine antibacterial activity of bovine lactoferrin-derived peptides. Antimicrobial Agents and Chemotherapy 41 (1997), 54–59.
37. Holder, A., Birke, A., Eisele, T., Klaiber, I., Fischer, L., Hinrichs, J., Selective isolation of angiotensin I-converting enzyme-inhibitory peptides from micellar casein and β-casein hydrolysates via ultrafiltration. International Dairy Journal 31 (2013), 34–40.
38. Iwaniak, A., Dziuba, J., Niklewicz, M., The BIOPEP database – A tool for the in silico method of classification of food proteins as the source of peptides with antihypertensive activity. Acta Alimentaria 34 (2005), 417–425.
39. John, H., Liquid chromatography-mass spectrometry in peptide drug discovery and development. Analytical and Bioanalytical Chemistry 381 (2005), 51–53.
40. John, H., Walden, M., Schäfer, S., Genz, S., Forssmann, W.G., Analytical procedures for quantification of peptides in pharmaceutical research by liquid chromatography-mass spectrometry. Analytical and Bioanalytical Chemistry 378 (2004), 883–897.
41. Kaji, H., Yamauchi, Y., Takahashi, N., Isobe, T., Mass spectrometric identification of N- linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging. Nature Protocols 1 (2007), 3019–3027.
42. Karametsi, K., Kokkinidou, S., Ronningen, I., Peterson, D.G., Identification of bitter peptides in aged cheddar cheese. Journal of Agricultural and Food Chemistry 62 (2014), 8034–8041.
43. Kawaguchi, S., Higo, Y., Effects of microwave irradiation on nonspecific protein binding in the solid phase coated with bovine serum albumin. Polymer Journal 37 (2005), 109–117.
44. Korhonen, H., Milk-derived bioactive peptides: From science to applications. Journal of Functional Foods 1 (2009), 177–187.
45. Kunda, P.B., Benavente, F., Catala-Clariana, S., Gimenez, E., Barbosa, J., Sanz-Nebot, V., Identification of bioactive peptides in a functional yogurt by micro liquid chromatography time-of-flight mass spectrometry assisted by retention time prediction. Journal of Chromatography A 1229 (2012), 121–128.
46. Kütt, M.L., Malbe, M., Stagsted, J., Nanostructure-assisted laser desorption/ionization (NALDI) for analysis of peptides in milk and colostrum. Agronomy Research 9:Special Issue II (2011), 415–420.
47. Lahrichi, S.L., Affolter, M., Zolezzi, I.S., Panchaud, A., Food Peptidomics: Large scale analysis of small bioactive peptides – A pilot study. Journal of Proteomics 88 (2013), 83–91.
48. Lesur, A., Varesio, E., Domon, B., Hopfgartner, G., Peptides quantification by liquid chromatography with matrix-assisted laser desorption/ionization and selected reaction monitoring detection. Journal of Proteome Research 11 (2012), 4972–4982.
49. Liu, L., Yu, M., Zhang, Y., Wang, C., Lu, H., Hydrazide functionalized core–shell magnetic nanocomposites for highly specific enrichment of N-glycopeptides. ACS Applied Materials & Interfaces 6 (2014), 7823–7832.
50. Mamone, G., Caira, S., Garro, G., Nicolai, A., Ferranti, P., Picariello, G., et al. Casein phosphoproteome: Identification of phosphoproteins by combined mass spectrometry and two-dimensional gel electrophoresis. Electrophoresis 24 (2003), 2824–2837.
51. Mamone, G., Picariello, G., Caira, S., Addeo, F., Ferranti, P., Analysis of food proteins and peptides by mass spectrometry-based techniques. Journal of Chromatography. A 1216 (2009), 7130–7142.
52. Manso, M.A., Léonil, J., Jan, G., Gagnaire, V., Application of proteomics to the chracterization of milk and dairy products. International Dairy Journal 15 (2005), 845–855.
53. Menschaert, G., Vandekerckhove, T.T.M., Baggerman, G., Schoofs, L., Luyten, W., Van Criekinge, W., Peptidomics coming of age: A review of contributions from a bioinformatics angle. Journal of Proteome Research 9 (2010), 2051–2061.
54. Minkiewicz, P., Dziuba, J., Dziuba, M., Nal, D., Food peptidomics. Food Technology & Biotechnology 46 (2008), 1–10.
55. Morifuji, M., Koga, J., Kawanaka, K., Higuchi, M., Branched-chain amino acid-containing dipeptides, identified from whey protein hydrolysates, stimulate glucose uptake rate in L6 myotubes and isolated skeletal muscles. Journal of Nutritional Science and Vitaminology 55 (2009), 81–86.
56. Neue, K., Mormann, M., Peter- Katalinić, J., Pohlentz, G., Elucidation of glycoprotein structures by unspecific proteolysis and direct nanoESI mass spectrometric analysis of ZIC- HILIC-enriched glycopeptides. Journal of Proteome Research 10 (2011), 2248–2260.
57. Norbeck, A.D., Monroe, M.E., Adkins, J.N., Smith, R.D., The utility of accurate mass and LC elution time information in the analysis of complex proteomes. Journal of the American Society for Mass Spectrometry 16 (2005), 1239–1249.
58. Orr, V., Zhong, L., Moo-Young, M., Chou, C.P., Recent advances in bioprocessing application of membrane chromatography. Biotechnology Advance 31 (2013), 450–465.
59. Paizs, B., Suhai, S., Fragmentation pathways of protonated peptides. Mass Spectrometry Reviews 24 (2005), 508–548.
60. Panchaud, A., Affolter, M., Kussmann, M., Mass spectrometry for nutritional peptidomics: How to analyze food bioactives and their health effects. Journal of Proteomics 75 (2012), 3546–3559.
61. Paul, M., Nuñez, A., Van Hekken, D., The effect of milling on proteins in model Queso Fresco cheeses. Advances in Bioscience and Biotechnology 3 (2012), 1–6.
62. Petritis, K., Kangas, L.J., Yan, B., Monroe, M.E., Strittmatter, E.F., Qian, W., Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Analytical Chemistry 78 (2006), 5026–5039.
63. Pierri, G., Kotoni, D., Simone, P., Villani, C., Pepe, G., Campiglia, P.,.. Gasparrini, F., Analysis of bovine milk caseins on organic monolithic columns: An integrated capillary liquid chromatography-high resolution mass spectrometry approach for the study of time-dependent casein degradation. Journal of Chromatography A 1313 (2013), 259–269.
64. Piovesana, S., Capriotti, A.L., Cavaliere, C., La Barbera, G., Samperi, R., Zenezini Chiozzi, R., Laganà, A., Peptidome characterization and bioactivity analysis of donkey milk. Journal of Proteomics 119 (2015), 21–29.
65. Polson, C., Sarkar, P., Incledon, B., Raguvaran, V., Grant, R., Optimization of protein precipitation based upon effectiveness of protein removal and ionization effect in liquid chromatography–tandem mass spectrometry. Journal of Chromatography B 785 (2003), 263–275.
66. Pouliot, Y., Gauthier, S.F., Groleau, P.E., Membrane-based fractionation and purification strategies for bioactive peptides. Mine, Y., Shahidi, F., (eds.) Nutraceutical proteins and peptides in health and disease, 2006, CRC Press Taylor & Francis Group, Boca Raton, FL, 639–658.
67. Raikos, V., Dassios, T., Health-promoting properties of bioactive peptides derived from milk proteins in infant food: A review. Dairy Science and Technology 94 (2014), 91–101.
68. Saavedra, L., Hebert, E.M., Minahk, C., Ferranti, P., An overview of “omic” analytical methods applied in bioactive peptide studies. Food Research International 54 (2013), 925–934.
69. Sánchez-Rivera, L., Diezhandino, I., Gómez-Ruiz, J.Á., Fresno, J.M., Miralles, B., Recio, I., Peptidomic study of Spanish blue cheese (Valdeón) and changes after simulated gastrointestinal digestion. Electrophoresis 35 (2014), 1627–1636.
70. Sánchez-Rivera, L., Martínez-Maqueda, D., Cruz-Huerta, E., Miralles, B., Recio, I., Peptidomics for discovery, bioavailability and monitoring of dairy bioactive peptides. Food Research International 63 (2014), 170–181.
71. Schuchard, M.D., Mehigh, R.J., Cockrill, S.L., Lipscomb, G.T., Stephan, J.D., Wildsmith, J.,.. Scott, G.B., Artifactual isoform profile modification following treatment of human plasma or serum with protease inhibitor, monitored by 2-dimensional electrophoresis and mass spectrometry. Biotechniques 39 (2005), 239–247.
72. Schulz-Knappe, P., Zucht, H.D., Heine, G., Jurgens, M., Hess, R., Schrader, M., Peptidomics: The comprehensive analysis of peptides in complex biological mixtures. Combinatorial Chemistry & High Throughput Screening 4 (2001), 207–217.
73. Sforza, S., Cavatorta, V., Lambertini, F., Galaverna, G., Dossena, A., Marchelli, R., Cheese peptidomics: A detailed study on the evolution of the oligopeptide fraction in Parmigiano-Reggiano cheese from curd to 24 months of aging. Journal of Dairy Science 95 (2012), 3514–3526.
74. Shtatland, T., Guettler, D., Kossodo, M., Pivovarov, M., Weissleder, R., PepBank – A database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics, 8, 2007, 280.
75. Silva, R.A., Bezerra, V.S., Pimentel, M.C., Porto, A.L., Cavalcanti, M.T., Filho, J.L., Proteomic and peptidomic profiling of Brazilian artisanal “Coalho” cheese. Journal of the Science of Food and Agriculture, 2016, 10.1002/jsfa.7640 in press.
76. Singh, T.K., Fox, P.F., Healy, A., Isolation and identification of further peptides in the diafiltration retentate of the water-soluble fraction of Cheddar cheese. The Journal of Dairy Research 64 (1997), 433–443.
77. Sommella, E., Pepe, G., Ventre, G., Pagano, F., Manfra, M., Pierri, G.,.. Campiglia, P., Evaluation of two sub-2μm stationary phases, core-shell and totally porous monodisperse, in the second dimension of on-line comprehensive two dimensional liquid chromatography, a case study: Separation of milk peptides after expiration date. Journal of Chromatography A 1375 (2015), 54–61.
78. Toelstede, S., Hofmann, T., Sensomics mapping and identification of the key bitter metabolites in Gouda cheese. Journal of Agricultural and Food Chemistry 56 (2008), 2795–2804.
79. Vaast, A., Tyteca, E., Desmet, G., Schoenmakers, P.J., Eeltink, S., Gradient-elution parameters in capillary liquid chromatography for high-speed separations of peptides and intact proteins. Journal of Chromatography A 1355 (2014), 149–157.
80. Villanueva, J., Carrascal, M., Abian, J., Isotope dilution mass spectrometry for absolute quantification in proteomics: Concepts and strategies. Journal of Proteomics 96 (2014), 184–199.
81. Vitorino, R., Barros, A.S., Caseiro, A., Ferreira, R., Amado, F., Evaluation of different extraction procedures for salivary peptide analysis. Talanta 94 (2012), 209–215.
82. Vogel, C., Marcotte, E.M., Label-free protein quantitation using weighted spectral counting. Methods in Molecular Biology 893 (2012), 321–341.
83. Wada, Y., Tajiri, M., Yoshidas, S., Hydrophilic affinity isolation and MALDI multiple- stage tandem mass spectrometry of glycopeptides for glycoproteomics. Analytical Chemistry 76 (2004), 6560–6565.
84. Wang, G., Li, X., Wang, Z., APD2: The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research 37 (2009), D933–D937.
85. Wu, S., Qi, W., Li, T., Lu, D., Su, R., He, Z., Simultaneous production of multi-functional peptides by pancreatic hydrolysis of bovine casein in an enzymatic membrane reactor via combinational chromatography. Food Chemistry 141 (2013), 2944–2951.
86. Xu, Y., Cao, Q., Svec, F., Fréchet, J.M.J., Porous polymer monolithic column with surface-bound gold nanoparticles for the capture and separation of cysteine-containing peptides. Analytical Chemistry 82 (2010), 3352–3358.
87. Yu, L., Li, X., Guo, Z., Zhang, X., Liang, X., Hydrophilic interaction chromatography based enrichment of glycopeptides by using Click maltose: A matrix with high selectivity and glycosylation heterogeneity coverage. Chemistry 15 (2009), 12618–12626.
88. Zamyatnin, A.A., Fragmentomics of proteins and natural oligopeptides. Biofizika 53 (2008), 725–733.
89. Zhang, L., Zhao, Q., Liang, Z., Yang, K., Sun, L., Zhang, L., Zhang, Y., Synthesis of adenosine functionalized metal immobilized magnetic nanoparticles for highly selective and sensitive enrichment of phosphopeptides. Chemical Communications 48 (2012), 6274–6276.