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ProteomicsIdentifying interaction partners of noncanonical peptides.
Studies have revealed dozens of functional peptides in putative ‘noncoding’ regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs). We comprehensively annotated genome-wide translated ORFs across five eukaryotic by analyzing ribosome profiling rea...
ORGANISM(S): Homo sapiens (Human) 
2024-05-23 | PXD037658 | Pride
Human Interaction protein Mass spectrometry Noncanonical open reading frames (ncorfs) Peptide 
ProteomicspXg: Comprehensive identification of noncanonical MHC-I-associated peptides from de novo peptide sequencing using RNA-Seq reads
Discovering 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 pep...
ORGANISM(S): Homo sapiens (Human) 
2024-02-28 | PXD048006 | Pride
Immunopeptidomics 
GenomicsDifferential gene expression analyses after noncanonical peptide overexpression
Differential gene expression analyses after noncanonical peptide overexpression
PRJNA892076 | ENA
TranscriptomicsDifferential gene expression analyses after noncanonical peptide overexpression
Ribosome profiling analyses showed thousands of translated open reading frames in a cell encoding noncanonical peptides. To examine their functional roles, we stably overexpressed two noncanonical peptides (uSLC35A4 and iPGRMC1) in MCF-7 cells. And then we performed RNA-seq to examine differential g...
ORGANISM(S): Homo sapiens 
2024-02-01 | GSE216093 | GEO
UnknownWidespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features.
Not available
S-EPMC10908861 | biostudies-literature
ProteomicsImmunogenic noncoding cryptic peptides dominate the antigenic landscape of ovarian cancer
Increased infiltration of CD3+ and CD8+ T cells into ovarian cancer (OC) tumors is linked to better prognosis, but the specific antigens involved are unclear. Recent data suggests that HLA-I can present peptides from noncoding genomic regions, known as noncanonical or cryptic peptides, but their imm...
ORGANISM(S): Homo sapiens (Human) 
2025-01-14 | PXD055609 | Pride
Immunopeptidomics Proteogenomics Noncanonical peptides Neoantigens 
ProteomicsGlobal proteogenomic analysis of human MHC I peptides derived from noncanonical reading frames
Using highthroughput mass spectrometry, we probed the sixreadingframe translation of human B cells’ transcriptome. We report that about 10% of MHC Iassociated peptides (MAPs) derive from noncanonical reading frames. These socalled cryptic MAPs originate from allegedly non- coding genomic sequences ...
ORGANISM(S): Homo sapiens (Human) 
2016-01-28 | PXD001898 | Pride
Proteogenomic cryptic mhc lc-msms maps 
UnknownpXg: Comprehensive Identification of Noncanonical MHC-I-Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads.
Not available
S-EPMC10979277 | biostudies-literature
UnknownThe Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides.
Not available
S-EPMC10236148 | biostudies-literature
UnknownAcid Cleavable Biotin-Alkyne Improves Sensitivity for Direct Detection of Biotin Labeled Peptides in Biorthogonal Noncanonical Amino Acid Tagging Analysis.
Not available
S-EPMC12067412 | biostudies-literature
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