HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands.

ABSTRACT: T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem mass spectra are matched against hypothetical spectra generated from known protein sequence databases. Commonly used protein databases contain a minimal level of redundancy, and thus, are not suitable data sources for searching polymorphic T cell epitopes, either in normal or ARFs. At the same time, however, these databases contain much non-polymorphic sequence information, thereby complicating the matching of recorded and theoretical spectra, and increasing the potential for finding false posit

SUBMITTER: Nijveen H 

PROVIDER: S-EPMC3035791 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature