Decoding Human Milk Lactoprotein Heterogeneity: From Genetic Variation to Proteoforms and Peptidoforms in a Comparative Mammalian Context

Human milk proteins exhibit extensive molecular heterogeneity arising from genetic variation, transcript diversity, post-translational modifications, and proteolytic processing. This review integrates evidence on major human milk caseins and selected whey proteins within a genome–transcript–proteoform–peptidoform framework, incorporating comparative mammalian data where relevant. Particular emphasis is placed on distinguishing predicted molecular consequences, relationships supported by indirect evidence, and experimentally demonstrated molecular entities and transitions. Genomic variation and alternative RNA processing provide potential sources of primary-sequence diversity, whereas phosphorylation, glycosylation, and proteolysis further expand protein and peptide heterogeneity. Human β-casein provides a particularly informative example, with experimentally characterized phosphorylation- and glycosylation-defined proteoforms and corresponding modification-resolved peptidoforms. However, evidence remains uneven across molecular levels, and direct tracing from maternal genotype to expressed transcripts, secreted proteoforms, and downstream peptidoforms within the same individual remains limited. By identifying experimentally established relationships and unresolved molecular connections, this review provides an evidence-based framework for interpreting human milk lactoprotein heterogeneity and guiding future integrated proteogenomic investigations.