Discovery of naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass spectrometry for vaccine development

An important approach for developing a safer smallpox vaccine is to identify naturally processed immunogenic vaccinia-derived peptides rather than live whole vaccinia virus We used two-dimensional liquid chromatography Coupled to mass spectrometry to identify 116 vaccinia peptides, encoded by 61 open reading frames, from a B-cell line (homozygous for HLA class IA*0201, B*1501, and C*03) after infection with vaccinia virus (Dryvax) Importantly, 68 of these peptides are conserved in variola, providing insight into the peptides that induce protection against smallpox. Twenty-one of these 68 conserved peptides were I I amino acids long or longer, outside of the range of most predictive algorithms Thus, direct identification of naturally processed and presented FILA peptides gives important information not provided by current Computational methods for identifying potential vaccinia epitopes (C) 2009 Elsevier Ltd All rights reserved.