title: Accurate mass precursor ion data and tandem mass spectrometry identify a class I human leukocyte antigen A*0201-presented peptide originating from vaccinia virus.
abstract: We have used accurate mass precursor ion data generated on a hybrid linear-ion trap-Fourier transform ion cyclotron resonance mass spectrometer to augment tandem mass spectrometry (MS/MS) data generated on two different instrument types. Results from these experiments have allowed us for the first time to identify a naturally processed peptide presented by a class I human leukocyte antigen allele (HLA-A*0201) that was isolated from B cells infected by live vaccinia, the viral agent of the smallpox vaccine. The accurate mass data, in conjunction with MS/MS data, was able to identify the sequence IVIEAIHTV (aa 187-195) from the protein thymidylate kinase of vaccinia, distinguishing it from a similar sequence IVLEAIAEH: a "self-peptide" from the human protein phospholipase Cbeta3. Accurate mass data for the doubly charged species from the naturally processed and presented peptide was 497.8006, which was within 0.8 ppm of the calculated m/z of 497.8002, while being -37.3 ppm from the calculated m/z (497.7820) of the second-ranked peptide sequence IVLEAIAEH. Accurate mass data ranged from less than 0.1 to 1.2 ppm for other peptides identified in this sample. A BLAST search shows this sequence, IVIEAIHTV, is conserved in the same protein of a number of other orthopoxviruses, including the variola (smallpox) virus. Additionally, accurate mass data were able to uncover a false positive search result that was not distinguished by scoring of the match to the MS/MS data.
authors.affiliation: The W. M. Keck FT-ICR Mass Spectrometry Laboratory, and Mayo Proteomics Research Center, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Johnson
authors.forename: Inna G
authors.initials: IG
authors.lastname: Ovsyannikova
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Madden
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Poland
authors.forename: David C
authors.initials: DC
authors.lastname: Muddiman
mesh_terms: D000595:Amino Acid Sequence; D006680:HLA Antigens / Q000737:chemistry* / Q000276:immunology; D006367:HeLa Cells; D006801:Humans; D007118:Immunoassay / Q000379:methods*; D008832:Microchemistry / Q000379:methods; D008969:Molecular Sequence Data; D009703:Nucleoside-Phosphate Kinase / Q000737:chemistry / Q000276:immunology; D010455:Peptides / Q000032:analysis / Q000737:chemistry*; D011498:Protein Precursors / Q000032:analysis / Q000737:chemistry; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*; D014616:Vaccinia virus / Q000737:chemistry* / Q000276:immunology; D014764:Viral Proteins / Q000032:analysis / Q000737:chemistry*
chemical_list: D006680:HLA Antigens; D010455:Peptides; D011498:Protein Precursors; D014764:Viral Proteins; D009703:Nucleoside-Phosphate Kinase; C020093:dTMP kinase