MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review


  • Author: Andreatta, Massimo

    Universidad Nacional de San Martin, Argentina

  • Author: Nicastri, Annalisa

    University of Oxford, United Kingdom

  • Author: Peng, Xu

    University of Oxford, United Kingdom

  • Author: Hancock, Gemma

    University of Oxford, United Kingdom

  • Author: Dorrell, Lucy

    University of Oxford, United Kingdom

  • Author: Ternette, Nicola

    University of Oxford, United Kingdom

  • Author: Nielsen, Morten

    Department of Health Technology, Technical University of Denmark

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LC–MS/MS has become the standard platform for the characterization of immunopeptidomes, the collection of peptides naturally presented by major histocompatibility complex molecules to the cell surface. The protocols and algorithms used for immunopeptidomics data analysis are based on tools developed for traditional bottom-up proteomics that address the identification of peptides generated by tryptic digestion. Such algorithms are generally not tailored to the specific requirements of MHC ligand identification and, as a consequence, immunopeptidomics datasets suffer from dismissal of informative spectral information and high false discovery rates. Here, a new pipeline for the refinement of peptide-spectrum matches (PSM) is proposed, based on the assumption that immunopeptidomes contain a limited number of recurring peptide motifs, corresponding to MHC specificities. Sequence motifs are learned directly from the individual peptidome by training a prediction model on high-confidence PSMs. The model is then applied to PSM candidates with lower confidence, and sequences that score significantly higher than random peptides are rescued as likely true ligands. The pipeline is applied to MHC class I immunopeptidomes from three different species, and it is shown that it can increase the number of identified ligands by up to 20–30%, while effectively removing false positives and products of co-precipitation. Spectral validation using synthetic peptides confirms the identity of a large proportion of rescued ligands in the experimental peptidome.

Original languageEnglish
Article number1800357
Issue number4
Number of pages7
Publication statusPublished - 2019
CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • Machine learning, Mass spectrometry, MHC, Peptidome, Sequence motifs

ID: 170250727