title: Mechanistic peptidomics: factors that dictate specificity in the formation of endogenous peptides in human milk.
abstract: An extensive mass spectrometry analysis of the human milk peptidome has revealed almost 700 endogenous peptides from 30 different proteins. Two in-house computational tools were created and used to visualize and interpret the data through both alignment of the peptide quasi-molecular ion intensities and estimation of the differential enzyme participation. These results reveal that the endogenous proteolytic activity in the mammary gland is remarkably specific and well conserved. Certain proteins-not necessarily the most abundant ones-are digested by the proteases present in milk, yielding endogenous peptides from selected regions. Our results strongly suggest that factors such as the presence of specific proteases, the position and concentration of cleavage sites, and, more important, the intrinsic disorder of segments of the protein drive this proteolytic specificity in the mammary gland. As a consequence of this selective hydrolysis, proteins that typically need to be cleaved at specific positions in order to exert their activity are properly digested, and bioactive peptides encoded in certain protein sequences are released. Proteins that must remain intact in order to maintain their activity in the mammary gland or in the neonatal gastrointestinal tract are unaffected by the hydrolytic environment present in milk. These results provide insight into the intrinsic structural mechanisms that facilitate the selectivity of the endogenous milk protease activity and might be useful to those studying the peptidomes of other biofluids.
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616; lebrilla@chem.ucdavis.edu andguerrero@ucdavis.edu.
authors.forename: Andres
authors.initials: A
authors.lastname: Guerrero
authors.affiliation: ¶Department of Food Science, University of California at Davis, One Shields Avenue, Davis, California 95616; ‖Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, California 95616.
authors.forename: David C
authors.initials: DC
authors.lastname: Dallas
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
authors.forename: Stephanie
authors.initials: S
authors.lastname: Contreras
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
authors.forename: Sabrina
authors.initials: S
authors.lastname: Chee
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
authors.forename: Evan A
authors.initials: EA
authors.lastname: Parker
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
authors.forename: Xin
authors.initials: X
authors.lastname: Sun
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616;
authors.forename: Lauren
authors.initials: L
authors.lastname: Dimapasoc
authors.affiliation: ¶Department of Food Science, University of California at Davis, One Shields Avenue, Davis, California 95616; ‖Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, California 95616.
authors.forename: Daniela
authors.initials: D
authors.lastname: Barile
authors.affiliation: ¶Department of Food Science, University of California at Davis, One Shields Avenue, Davis, California 95616; ‖Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, California 95616.
authors.forename: J Bruce
authors.initials: JB
authors.lastname: German
authors.affiliation: From the ‡Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616; lebrilla@chem.ucdavis.edu andguerrero@ucdavis.edu.
authors.forename: Carlito B
authors.initials: CB
authors.lastname: Lebrilla
mesh_terms: D000595:Amino Acid Sequence; D010450:Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D005260:Female; D006801:Humans; D008894:Milk Proteins / Q000737:chemistry* / Q000378:metabolism; D008895:Milk, Human / Q000737:chemistry*; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D010455:Peptides / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D008894:Milk Proteins; D010455:Peptides; D020543:Proteome; D010450:Endopeptidases