PT  - JOURNAL ARTICLE
AU  - Kaabinejadian, Saghar
AU  - Barra, Carolina
AU  - Alvarez, Bruno
AU  - Yari, Hooman
AU  - Hildebrand, William H
AU  - Nielsen, Morten
TI  - Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome
AID  - 10.1101/2021.11.23.469647
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.11.23.469647
4099  - http://biorxiv.org/content/early/2021/11/23/2021.11.23.469647.short
4100  - http://biorxiv.org/content/early/2021/11/23/2021.11.23.469647.full
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.