RHybridFinder

RHybridFinder infers putative proteasomal spliced peptides (PSPs) from mass spectrometry (MS) de novo sequencing data to enable detection of cis- and trans-spliced major histocompatibility complex (MHC)-associated peptides in immunopeptidomics.

Key Features:

• R package implementation: Provided as an R package for computational inference of proteasomal spliced peptides.
• Integration with PEAKS: Integrates with PEAKS software to extract high-confidence de novo sequenced peptides from MS data.
• Database matching: Matches extracted peptide sequences against protein databases to infer cis- or trans-spliced MHC-associated peptides.
• Addresses MS search engine limitations: Implements a specialized protocol for detecting PSPs that are challenging to identify with traditional MS-based search engines.
• Computational efficiency: Performs computationally efficient processing of immunopeptidomic MS data.
• Experimental validation requirement: Computationally inferred candidate spliced peptides require experimental validation.

Scientific Applications:

• Immunopeptidomics: Enables identification of PSPs to study MHC-associated peptide diversity and specificity.
• Antigen presentation research: Supports investigation of proteasomal splicing effects on antigen presentation and immune recognition.
• Vaccine development: Contributes to discovery of antigenic peptides relevant for vaccine design.
• Cancer immunotherapy: Assists identification of spliced epitopes and neoantigens relevant to cancer immunotherapy.

Methodology:

Leverages PEAKS de novo sequencing output to obtain high-confidence peptide sequences and matches those sequences against protein databases to infer cis- or trans-spliced MHC-associated peptides.