title: Rapid empirical discovery of optimal peptides for targeted proteomics.
abstract: We report a method for high-throughput, cost-efficient empirical discovery of optimal proteotypic peptides and fragment ions for targeted proteomics applications using in vitro-synthesized proteins. We demonstrate the approach using human transcription factors, which are typically difficult, low-abundance targets and empirically derived proteotypic peptides for 98% of the target proteins. We show that targeted proteomic assays developed using our approach facilitate robust in vivo quantification of human transcription factors.
authors: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
authors: Andrew B
authors: AB
authors: Stergachis
authors: Brendan
authors: B
authors: MacLean
authors: Kristen
authors: K
authors: Lee
authors: John A
authors: JA
authors: Stamatoyannopoulos
authors: Michael J
authors: MJ
authors: MacCoss
mesh_terms: D057166:High-Throughput Screening Assays; D006801:Humans; D010452:Peptide Biosynthesis; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D014157:Transcription Factors / Q000032:analysis
chemical_list: D010455:Peptides; D014157:Transcription Factors