pXg: Comprehensive identification of noncanonical MHC-I-associated peptides from de novo peptide sequencing using RNA-Seq reads

Mol Cell Proteomics. 2024 Feb 23:100743. doi: 10.1016/j.mcpro.2024.100743. Online ahead of print.ABSTRACTDiscovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as ncMAPs (noncanonical MHC-I-associated peptides), that bind to major histocompatibility complex I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy hasn't been widely applied for ncMAP identification because there is not a good way to estimate its false-positive rates. In order to completely and accurately identify immunopeptides using de novo peptide sequencing, we describe a unique pipeline called pXg. In contrast to current pipelines, it makes use of genomic data, RNA-Seq abundance and sequencing quality, in addition to proteomic features to increase the sensitivity and specificity of peptide identification. We show that the peptide-spectrum match quality and genetic traits have a clear relationship, showing that they can be utilized to evaluate peptide-spectrum matches. From ten samples, we found 24,449 cMAPs (canonical MHC-I-associated peptides) and 956 ncMAPs by using a target-decoy competition. 387 ncMAPs and 1,611 cMAPs were new identifications that had not yet been published. We discovered 11 ncMAPs produced from a squirrel monkey retrovirus ...
Source: Molecular and Cellular Proteomics : MCP - Category: Molecular Biology Authors: Source Type: research