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

  • James G. Bollinger
  • Andrew B. Stergachis
  • Richard S. Johnson
  • Jarrett D. Egertson
  • Michael J. MacCossEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1410)

Abstract

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.

Key words

Targeted proteomics Selected reaction monitoring In vitro translation Human plasma proteome Proteotypic peptides 

Notes

Acknowledgments

This work was supported in part by National Institutes of Health grants P41 GM103533, R01 GM107142, and R01 GM107806.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • James G. Bollinger
    • 1
  • Andrew B. Stergachis
    • 1
  • Richard S. Johnson
    • 1
  • Jarrett D. Egertson
    • 1
  • Michael J. MacCoss
    • 1
    Email author
  1. 1.Department of Genome SciencesUniversity of WashingtonSeattleUSA

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