Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards

Methods Mol Biol. 2016;1410:207-21. doi: 10.1007/978-1-4939-3524-6_12.


In targeted proteomics, the development of robust methodologies is dependent upon the selection of a set of optimal peptides for each protein-of-interest. Unfortunately, predicting which peptides and respective product ion transitions provide the greatest signal-to-noise ratio in a particular assay matrix is complicated. Using in vitro synthesized proteins as analytical standards, we report here an empirically driven method for the selection of said peptides in a human plasma assay matrix.

Keywords: Human plasma proteome; In vitro translation; Proteotypic peptides; Selected reaction monitoring; Targeted proteomics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Blood Proteins / analysis
  • Humans
  • Peptides / analysis
  • Proteomics / methods*


  • Blood Proteins
  • Peptides