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Article

Empirical Evaluation of the Use of Computational HLA Binding as an Early Filter to the Mass Spectrometry-Based Epitope Discovery Workflow

1
Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
2
Proteomics Center, Erasmus MC, Department of Biochemistry, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
*
Author to whom correspondence should be addressed.
Academic Editor: Mark Molloy
Cancers 2021, 13(10), 2307; https://doi.org/10.3390/cancers13102307
Received: 22 March 2021 / Revised: 6 May 2021 / Accepted: 6 May 2021 / Published: 12 May 2021
(This article belongs to the Special Issue Proteomics in Cancer)
Many different human leukocyte antigen (HLA)-types exist across the population that each binds a specific motif of amino acids. HLA-peptide complexes are the driving force behind recognition of cancers and infected cells by cytotoxic T cells. HLA-immunopeptidomics aims to identify peptides derived from (cancer) antigens in the HLA-binding cleft with mass spectrometry (MS). Peptides eluted from HLA are analyzed by MS and translated to a protein derived amino acid sequence by specialized software. These software packages use statistical thresholds to limit false discoveries and return only the most confidently identified peptides. However, we believe, as do others, that many useful peptides can still be found in the excluded pool of peptides. This idea drove the development of specialized algorithms that utilize HLA specific motifs to retrieve additional relevant peptides. It is unknown, however, how many peptides could potentially be found in this pool. By adjusting the statistical threshold, we empirically demonstrate the vastness of valuable data beyond the traditional thresholds that await to be discovered.
Immunopeptidomics is used to identify novel epitopes for (therapeutic) vaccination strategies in cancer and infectious disease. Various false discovery rates (FDRs) are applied in the field when converting liquid chromatography-tandem mass spectrometry (LC-MS/MS) spectra to peptides. Subsequently, large efforts have recently been made to rescue peptides of lower confidence. However, it remains unclear what the overall relation is between the FDR threshold and the percentage of obtained HLA-binders. We here directly evaluated the effect of varying FDR thresholds on the resulting immunopeptidomes of HLA-eluates from human cancer cell lines and primary hepatocyte isolates using HLA-binding algorithms. Additional peptides obtained using less stringent FDR-thresholds, although generally derived from poorer spectra, still contained a high amount of HLA-binders and confirmed recently developed tools that tap into this pool of otherwise ignored peptides. Most of these peptides were identified with improved confidence when cell input was increased, supporting the validity and potential of these identifications. Altogether, our data suggest that increasing the FDR threshold for peptide identification in conjunction with data filtering by HLA-binding prediction, is a valid and highly potent method to more efficient exhaustion of immunopeptidome datasets for epitope discovery and reveals the extent of peptides to be rescued by recently developed algorithms. View Full-Text
Keywords: cancer; immunopeptidomics; antigen presentation; HLA-peptide cancer; immunopeptidomics; antigen presentation; HLA-peptide
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MDPI and ACS Style

Bouzid, R.; de Beijer, M.T.A.; Luijten, R.J.; Bezstarosti, K.; Kessler, A.L.; Bruno, M.J.; Peppelenbosch, M.P.; Demmers, J.A.A.; Buschow, S.I. Empirical Evaluation of the Use of Computational HLA Binding as an Early Filter to the Mass Spectrometry-Based Epitope Discovery Workflow. Cancers 2021, 13, 2307. https://doi.org/10.3390/cancers13102307

AMA Style

Bouzid R, de Beijer MTA, Luijten RJ, Bezstarosti K, Kessler AL, Bruno MJ, Peppelenbosch MP, Demmers JAA, Buschow SI. Empirical Evaluation of the Use of Computational HLA Binding as an Early Filter to the Mass Spectrometry-Based Epitope Discovery Workflow. Cancers. 2021; 13(10):2307. https://doi.org/10.3390/cancers13102307

Chicago/Turabian Style

Bouzid, Rachid, Monique T. A. de Beijer, Robbie J. Luijten, Karel Bezstarosti, Amy L. Kessler, Marco J. Bruno, Maikel P. Peppelenbosch, Jeroen A. A. Demmers, and Sonja I. Buschow. 2021. "Empirical Evaluation of the Use of Computational HLA Binding as an Early Filter to the Mass Spectrometry-Based Epitope Discovery Workflow" Cancers 13, no. 10: 2307. https://doi.org/10.3390/cancers13102307

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