RT Journal Article
SR Electronic
T1 Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.11.23.469647
DO 10.1101/2021.11.23.469647
A1 Kaabinejadian, Saghar
A1 Barra, Carolina
A1 Alvarez, Bruno
A1 Yari, Hooman
A1 Hildebrand, William H
A1 Nielsen, Morten
YR 2021
UL http://biorxiv.org/content/early/2021/11/23/2021.11.23.469647.abstract
AB Mass spectrometry (MS) based immunopeptidomics is used in several biomedical applications including neo-epitope discovery in oncology and next-generation vaccine development. Immunopeptidome data are highly complex given the expression of multiple HLA alleles on the cell membrane and presence of co-immunoprecipitated contaminants. The absence of tools that accurately deal with these challenges is currently a major bottleneck for the large-scale application of this technique. Here, we present the MHCMotifDecon that benefits from state-of-the-art HLA class-I and class-II predictions to accurately deconvolute immunopeptidome datasets and assign individual ligands to the most likely HLA allele while discarding co-purified contaminants. We have benchmarked the tool against other state-of-the-art methods and illustrated its application on experimental datasets for HLA-DR demonstrating a previously underappreciated role for HLA-DRB3/4/5 molecules in defining HLA class II immune repertoires. With its ease of use MHCMotifDecon can efficiently guide interpretation of immunopeptidome datasets, serving the discovery of novel T cell targets.Competing Interest StatementThe authors have declared no competing interest.