RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery.
STAR Protoc
; 2(4): 100875, 2021 12 17.
Article
em En
| MEDLINE
| ID: mdl-34746858
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).
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Peptídeos
/
Software
/
Proteômica
/
Complexo de Endopeptidases do Proteassoma
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
STAR Protoc
Ano de publicação:
2021
Tipo de documento:
Article