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

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 sco...

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Bibliographic Details
Published in:STAR protocols 2021-12, Vol.2 (4), p.100875-100875, Article 100875
Main Authors: Saab, Frederic, Hamelin, David J., Ma, Qing, Kovalchik, Kevin A., Sirois, Isabelle, Faridi, Pouya, Li, Chen, Purcell, Anthony W., Kubiniok, Peter, Caron, Etienne
Format: Article
Language:English
Subjects:
Bioinformatics
Cancer
Computer sciences
Databases, Protein
Epitopes - genetics
Humans
Immunology
Mass Spectrometry
Peptides - chemistry
Peptides - genetics
Proteasome Endopeptidase Complex - chemistry
Proteasome Endopeptidase Complex - genetics
Proteomics - methods
Protocol
Software
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Summary: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). [Display omitted] •RHybridFinder (RHF) is an improved R package for the discovery of spliced peptides•RHF builds upon the algorithm published in Faridi et al. (2018)•RHF uses MS data analyzed in PEAKS•The spliced peptide candidates generated by RHF need to be validated experimentally 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 MHC-associated peptides. RHF is relatively fast and straightforward. PSPs have to be validated experimentally.
ISSN:2666-1667
2666-1667
DOI:10.1016/j.xpro.2021.100875