MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration
1 Georgetown University, Department of Oncology, Lombardi Comprehensive Cancer Center, 3970 Reservoir Rd NW, Washington, DC 20057, USA
2 Georgetown University, Department of Biochemistry and Molecular and Cellular Biology, Washington, DC, USA
3 Current address: University Hospital Hradec Kralove; Center for Biomedical Research; Sokolska 581; 500 05 Hradec Kralove; Czech Republic
Proteome Science 2012, 10:7 doi:10.1186/1477-5956-10-7Published: 4 February 2012
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.