Rapid empirical discovery of optimal peptides for targeted proteomics

Nat Methods. 2011 Nov 6;8(12):1041-3. doi: 10.1038/nmeth.1770.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Screening Assays*
  • Humans
  • Peptide Biosynthesis
  • Peptides / analysis*
  • Proteomics / methods*
  • Transcription Factors / analysis


  • Peptides
  • Transcription Factors