A total of 15,199 peptide antigens, called PETs, were designed from 3694 proteins representing 418 proteomes. Within each proteome, PETs were selected from unique regions of protein sequence using heuristic blastp algorithms optimal for short peptide sequence comparison (23, 29). Peptide antigens representative of predicted surface epitopes from a protein sequence were selected (40, 41). Peptides were mostly 10 to 12 amino acids in length to contain two to three potential antibody epitopes (42). Predicted peptide sequences with secondary structures including alpha helix and beta sheet were omitted (43). Special sequences including transmembrane motif, signal peptide, and posttranslational modification motif were also not selected. Only disordered or surface-looped regions were selected. Hydrophobic peptides were not selected, and peptide hydrophilicity was calculated by the Hopp and Woods method (44). Last, peptides with more than one cysteine in the sequence were omitted to avoid synthesis difficulties.

All the peptide antigens were chemically synthesized by GL Biochem (Shanghai) Ltd. The purity and molecular weight of each peptide were evaluated with high-performance LC and MS.

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