{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Korchak JA"],"funding":["NHLBI NIH HHS","National Heart, Lung, and Blood Institute","National Institute of General Medical Sciences","NIGMS NIH HHS"],"pagination":["2614-2630"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11544703"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["35(11)"],"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 predefined 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 (lrRNA-seq) data to predict potential protein isoforms with "],"journal":["Journal of the American Society for Mass Spectrometry"],"pubmed_title":["IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection."],"pmcid":["PMC11544703"],"funding_grant_id":["T32HL007284","R35 GM142647","R35GM142647","T32 HL007284"],"pubmed_authors":["Jordan BT","Fenix A","Watts EF","Korchak JA","Bandyopadhyay S","Lehe MD","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 predefined 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 (lrRNA-seq) data to predict potential protein isoforms with ","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Nov","modification":"2026-06-03T00:35:09.584Z","creation":"2025-04-19T14:38:55.662Z"},"accession":"S-EPMC11544703","cross_references":{"pubmed":["39012054"],"doi":["10.1021/jasms.4c00119"]}}