Methodology

Proteome Science

, 10:7

Open Access This content is freely available online to anyone, anywhere at any time.

MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration

  • Juraj LencoAffiliated withGeorgetown University, Department of Oncology, Lombardi Comprehensive Cancer CenterCenter for Biomedical Research, University Hospital Hradec Kralove
  • , Renny LanAffiliated withGeorgetown University, Department of Oncology, Lombardi Comprehensive Cancer Center
  • , Nathan EdwardsAffiliated withDepartment of Biochemistry and Molecular and Cellular Biology, Georgetown University
  • , Radoslav GoldmanAffiliated withGeorgetown University, Department of Oncology, Lombardi Comprehensive Cancer Center Email author 

Abstract

Naturally occurring native peptides provide important information about physiological states of an organism and its changes in disease conditions but protocols and methods for assessing their abundance are not well-developed. In this paper, we describe a simple procedure for the quantification of non-tryptic peptides in body fluids. The workflow includes an enrichment step followed by two-dimensional fractionation of native peptides and MS/MS data management facilitating the design and validation of LC- MRM MS assays. The added value of the workflow is demonstrated in the development of a triplex LC-MRM MS assay used for quantification of peptides potentially associated with the progression of liver disease to hepatocellular carcinoma.

Keywords

Native Peptides denaturing ultrafiltration MS/MS library MRM quantitation