Food science is a complex domain where modern analytical technologies interact with each other. Named as Foodomics, this domain assembles a variety of investigational fields such as genomics, transcriptomics, proteomics, peptidomics, and metabolomics. All these technologies are at the service of several goals that are essentially dictated by fundamental understanding, safety, and consistency. In this report, open questions are summarized around proteins and selected technologies recommended for a proper analytical determination not only of composition, but also considering the low-abundance expressed species difficult to detect for their presence, their function, and their adverse effects such as allergic action. In particular, this review covers the proteome of foodstuff and beverages, as detected via combinatorial peptide ligand libraries, such as: bovine and donkey's milk, egg white, and yolk, white and red wine, beer, and a number of nonalcoholic beverages, such as almond's milk and orgeat syrup, Cola, ginger ale, and vinegar.