Your browser doesn't support javascript.
loading
Empirical Evaluation of the Use of Computational HLA Binding as an Early Filter to the Mass Spectrometry-Based Epitope Discovery Workflow.
Bouzid, Rachid; de Beijer, Monique T A; Luijten, Robbie J; Bezstarosti, Karel; Kessler, Amy L; Bruno, Marco J; Peppelenbosch, Maikel P; Demmers, Jeroen A A; Buschow, Sonja I.
Afiliación
  • Bouzid R; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • de Beijer MTA; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Luijten RJ; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Bezstarosti K; Proteomics Center, Erasmus MC, Department of Biochemistry, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Kessler AL; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Bruno MJ; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Peppelenbosch MP; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Demmers JAA; Proteomics Center, Erasmus MC, Department of Biochemistry, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
  • Buschow SI; Erasmus MC, Department of Gastroenterology and Hepatology, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
Cancers (Basel) ; 13(10)2021 May 12.
Article en En | MEDLINE | ID: mdl-34065814
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.
Palabras clave

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Cancers (Basel) Año: 2021 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Suiza

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Cancers (Basel) Año: 2021 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Suiza