{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Korchak JA"],"funding":["NHLBI NIH HHS","NIGMS NIH HHS"],"pubmed_abstract":["Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2024.04.01.587549"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11014528"],"repository":["biostudies-literature"],"pubmed_title":["IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection."],"pmcid":["PMC11014528"],"funding_grant_id":["R35 GM142647","T32 HL007284"],"pubmed_authors":["Jordan BT","Fenix A","Lehe M","Watts EF","Korchak JA","Bandyopadhyay S","Jeffery ED","Sheynkman GM","Wilhelm M"],"additional_accession":[]},"is_claimable":false,"name":"IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.","description":"Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Apr","modification":"2026-04-08T15:29:07.699Z","creation":"2026-04-08T04:47:16.834Z"},"accession":"S-EPMC11014528","cross_references":{"pubmed":["38617311"],"doi":["10.1101/2024.04.01.587549"]}}