RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery

STAR Protoc. 2021 Oct 21;2(4):100875. doi: 10.1016/j.xpro.2021.100875. eCollection 2021 Dec 17.

Abstract

Identification of proteasomal spliced peptides (PSPs) by mass spectrometry (MS) is not possible with traditional search engines. Here, we provide a protocol for running RHybridFinder (RHF), an R package for the computational inference of putative PSPs detected by MS. RHF extracts high confidence scored de novo sequenced peptides identified by PEAKS software. Those peptides are then matched to protein databases to infer cis- or trans-spliced major histocompatibility complex (MHC)-associated peptides. RHF is relatively fast and straightforward. PSPs have to be validated experimentally. For complete details on the use and execution of the original protocol, please refer to Faridi et al. (2018).

Keywords: Bioinformatics; Cancer; Computer sciences; Immunology; Mass Spectrometry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Epitopes / genetics
  • Humans
  • Mass Spectrometry
  • Peptides* / chemistry
  • Peptides* / genetics
  • Proteasome Endopeptidase Complex* / chemistry
  • Proteasome Endopeptidase Complex* / genetics
  • Proteomics / methods*
  • Software*

Substances

  • Epitopes
  • Peptides
  • Proteasome Endopeptidase Complex

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