PNNL

Abstract

Recent multidimensional liquid chromatography MS/MS studies have contributed to the identification of large numbers of expressed proteins for numerous species. The present study couples size exclusion chromatography of intact proteins with strong cation exchange chromatography to detect tryptically digested peptides in the global protein mixture of human mammary epithelial cells (HMECs) based upon the use of very high resolution, reversed phase capillary LC–MS/MS. A total of >6,200 unique peptides were identified with high confidence covering 1,700 different proteins, out of which 93% were mapped to chromosomal locations providing an estimated 4.4% coverage of the annotated human genome based upon the National Center for Biotechnology Information (NCBI). This database provides a baseline for comparison against variations in other genetically and environmentally perturbed systems. Proteins identified were categorized based upon intracellular location and biological process with the identification of numerous receptors, regulatory proteins, and extracellular proteins, demonstrating the usefulness of this application in the global analysis of human cells for future comparative studies.