biostudies-literatureUnknownKorchak JANHLBI NIH HHSNIGMS NIH HHSAlternative 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 withbioRxiv : the preprint server for biology2024.04.01.587549https://www.ebi.ac.uk/biostudies/studies/S-EPMC11014528biostudies-literatureIS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.PMC11014528R35 GM142647T32 HL007284Jordan BTFenix ALehe MWatts EFKorchak JABandyopadhyay SJeffery EDSheynkman GMWilhelm MfalseIS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.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 with2024-01-01T00:00:00Z2024 Apr2026-04-08T15:29:07.699Z2026-04-08T04:47:16.834ZS-EPMC110145283861731110.1101/2024.04.01.587549