Uniquome: Construction and decoding of a novel proteomic atlas that contains new peptide entities

Cellular and molecular uniqueness have recently gained eminent importance due to the large amount of data produced by the use of "omics" technologies. Although the uniqueness of peptides is a well-studied feature, an innovative and pioneering concept regarding the correlation of uniqueness, with the peptide amino acid sequence and the peptide length, is introduced and extensively analyzed for the first time in this work. We construct the human "Uniquome" by introducing the following novel peptide entities: "Core Unique Peptide" (CrUP) defined as the peptide whose sequence is accommodated, specifically and exclusively, only in one protein in a given proteome, and also bears the minimum length of an amino acid sequence; and, further, the "Composite Unique Peptide" (CmUP), the "Family Unique Peptides" (FUPs) and the "Universal Unique Peptides" (UUPs). We thoroughly analyze the human and 20 critical model organisms' proteomes. Our findings indicate that these novel peptides entities possess unique properties and crucial functions that have not been previously characterized, far beyond the identification of proteins from a single peptide, representing the "causative agents" for many other groups of peptides with important biological activities. Considering the complexity of proteomes, a systemic analysis of these new entities will enhance the potential for novel protein identification, functional prediction, and exploration of cellular and molecular uniqueness, setting new standards in medicine for advanced studies in deep proteomics/proteomes, and translational biology. Finally, our results suggest that, across species, the highly conserved sequences are not DNA nucleotides but CrUP entities.