title: Exploration of peptides bound to MHC class I molecules in melanoma.
abstract: Advancements in high-resolution HPLC and mass spectrometry have reinvigorated the application of this technology to identify peptides eluted from immunopurified MHC class I molecules. Three melanoma cell lines were assessed using w6/32 isolation, peptide elution and HPLC purification; peptides were identified by mass spectrometry. A total of 13,829 peptides were identified; 83-87% of these were 8-11 mers. Only approximately 15% have been described before. Subcellular locations of the source proteins showed even sampling; mRNA expression and total protein length were predictive of the number of peptides detected from a single protein. HLA-type binding prediction for 10,078 9/10 mer peptides assigned 88-95% to a patient-specific HLA subtype, revealing a disparity in strength of predicted binding. HLA-B*27-specific isolation successfully identified some peptides not found using w6/32. Sixty peptides were selected for immune screening, based on source protein and predicted HLA binding; no new peptides recognized by antimelanoma T cells were discovered. Additionally, mass spectrometry was unable to identify several epitopes targeted ex vivo by one patient's T cells.
authors: Oncogenomics Research Group, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Qld, Australia.
authors: Antonia L
authors: AL
authors: Pritchard
authors: Marcus L
authors: ML
authors: Hastie
authors: Michelle
authors: M
authors: Neller
authors: Jeffrey J
authors: JJ
authors: Gorman
authors: Chris W
authors: CW
authors: Schmidt
authors: Nicholas K
authors: NK
authors: Hayward
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000906:Antibodies / Q000378:metabolism; D000951:Antigens, Neoplasm / Q000378:metabolism; D045744:Cell Line, Tumor; D000939:Epitopes; D015972:Gene Expression Regulation, Neoplastic; D015395:Histocompatibility Antigens Class I / Q000378:metabolism*; D006801:Humans; D007109:Immunity; D013058:Mass Spectrometry; D008545:Melanoma / Q000235:genetics / Q000276:immunology*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D013347:Subcellular Fractions / Q000378:metabolism
chemical_list: D000906:Antibodies; D000951:Antigens, Neoplasm; D000939:Epitopes; D015395:Histocompatibility Antigens Class I; D010455:Peptides; D012333:RNA, Messenger
keywords: MHC class I; antigen; epitope; mass spectrometry; melanoma; peptide; proteome