Human Short Peptide Variation Database
Search  MultiSearch  Examples Links
Help  Download About References
The Human Short Peptide Variation Database (HSPVdb) is constructed primarily for the purpose of finding human T cell epitopes and identifying minor histocompatibility antigens (mHags) in combination with mass spectrometry, but can be used to identify any short (hypothetical) peptide of human origin. Since commonly used protein databases like UniProt, IPI and RefSeqP contain a minimal level of redundancy, they are not suitable data sources for matching peptides of naturally variant gene products. The HSPVdb addresses this problem by incorporating peptides from ARFs and peptide variation arising from single nucleotide polymorphisms (SNPs). The database can be downloaded for mass spectrometry-based proteomics applications, using search engines like MASCOT, SEQUEST, X!Tandem and Phenyx.
From: "Making sense of mass destruction: quantitating MHC class I antigen presentation", Jonathan W. Yewdell, Eric Reits & Jacques Neefjes,
Nature Reviews Immunology 3, 952-961 (December 2003) doi:10.1038/nri1250
Courtesy Eric Reits
HLA ligandome, antigen processing
The proteasome and several other proteases (some probably as yet unknown) play an important role in a continuous protein turn-over in the cell. As a result of this protein break down peptides may arise which might be translocated by the transporter associated with antigen presentation (TAP) into the endoplasmic reticulum (ER). In the ER peptides may be further trimmed and be loaded into HLA class I molecules. From there the peptide-loaded HLA-molecules are transported to the surface where they are on display to CD8+ T-lymphocytes. For further information see: references.

HLA-peptidome/ligandome & variation
HLA-presented peptides are generated from the proteome, derived from the consensus coding sequences and all possible variations. Variation in the presented peptide repertoire may arise from translation in alternative reading frames, the occurence of non-synonymous SNPs, frameshifts, deletions and alternative splicing.

T cell epitopes
Altered presented peptides may elicit an immune response. Tumor antigens from ARFs and mHags are examples.