Proteomics

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Analysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS

ABSTRACT: An increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is in general challenging due to the poly-specificity nature of the data. We here outline a general pipeline for dealing with this challenge, and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in-silico models. We illustrate the approach here in the context of MHCI molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in-vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T cell epitopes.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Bos Taurus (bovine)

TISSUE(S): Leukocyte, Cell Culture

DISEASE(S): Theileriasis

SUBMITTER: Nicola Ternette  

LAB HEAD: Nicola Ternette

PROVIDER: PXD008151 | Pride | 2017-11-20

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
1011_A10_Tpm_PEAKS_129_peptides_1_1_0.mzid Mzid
104003_A14_PEAKS_126_peptides_1_1_0.mzid Mzid
2229_A14_Tpm_PEAKS_124_peptides_1_1_0.mzid Mzid
500004_A10_PEAKS_127_peptides_1_1_0.mzid Mzid
641_A18_Tpm_PEAKS_125_peptides_1_1_0.mzid Mzid
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Publications

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data.

Nielsen Morten M   Connelley Tim T   Ternette Nicola N  

Journal of proteome research 20171114 1

Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling a  ...[more]

PMID: 29115832

Publication: 1/2

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