Constrained De Novo Sequencing of neo-Epitope Peptides using Tandem Mass Spectrometry.

ABSTRACT: Neoepitope peptides are newly formed antigens presented by major histocompatibility complex class I (MHC-I) on cell surfaces. The cells presenting neoepitope peptides are recognized and subsequently killed by cytotoxic T-cells. Immunopeptidomic approaches aim to characterize the peptide repertoire (including neoepitope) associated with the MHC-I molecules on the surface of tumor cells using proteomic technologies, providing critical information for designing effective immunotherapy strategies. We developed a novel constrained de novo sequencing algorithm to identify neo-epitope peptides from tandem mass spectra acquired in immunopeptidomic analyses. Our method incorporates prior probabilities to putative peptides according to position specific scoring matrices (PSSMs) representing the sequ

SUBMITTER: Li S 

PROVIDER: S-EPMC6901291 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature