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Milk is an excellent source of bioactive peptides. However, the composition of the native milk peptidome has only been partially elucidated. The present study applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) directly or after prefractionation of the milk peptides by reverse-phase high-performance liquid chromatography (RP-HPLC) or OFFGEL fractionation for the comprehensive analysis of the peptide profile of raw milk. The peptide sequences were determined by MALDI-TOF/TOF or nano-ultra-performance liquid chromatography-nanoelectrospray ionization-LTQ-Orbitrap-MS. Direct MALDI-TOF-MS analysis led to the assignment of 57 peptides. Prefractionation by both complementary methods led to the assignment of another 191 peptides. Most peptides originate from α(S1)-casein, followed by β-casein, and α(S2)-casein. κ-Casein and whey proteins seem to play only a minor role as peptide precursors. The formation of many, but not all, peptides could be explained by the activity of the endogenous peptidases, plasmin or cathepsin D, B, and G. Database searches revealed the presence of 22 peptides with established physiological function, including those with angiotensin-converting-enzyme (ACE) inhibitory, immunomodulating, or antimicrobial activity.

Multiphosphorylated peptides endogenously present in milk exert anticariogenic activity due to their calcium binding capacity. This study performed comprehensive analysis of multiphosphorylated peptides in raw milk using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Since phosphopeptides are often negatively discriminated during ionization, putative phosphopeptides were identified by three different methods: (i) selective detection in 4-chloro-α-cyanocinnamic acid MALDI matrix compared to α-cyano-4-hydroxycinnamic acid; (ii) higher relative signal intensity in negative compared to positive ionization mode; and (iii) detection of signal pairs with mass differences of -80 Da or multiples thereof before and after enzymatic dephosphorylation. Thus, 18 putative phosphopeptides from raw milk were annotated. Peptide structures were then determined by product ion spectra from targeted liquid chromatography electrospray ionization tandem-MS analysis. Thus, β-casein33-48, β-casein29-48, β-casein1-21, β-casein2-25, β-casein1-25, β-casein1-27, β-casein1-28, β-casein1-29, β-casein1-32, αS2-casein1-21, and αS2-casein1-24 were revealed as major peptides with one or four phosphorylation sites in raw milk.

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