Multidimensional proteome analysis of human mammary epithelial cells.
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 the separation of tryptically digested peptides using a combination of strong cation exchange and high resolution, reversed phase capillary chromatography to identify proteins extracted from human mammary epithelial cells (HMECs). In addition to conventional conservative criteria for protein identifications, the confidence levels were additionally increased through the use of peptide normalized elution times (NET) for the liquid chromatographic separation step. The combined approach resulted in a total of 5838 unique peptides identified covering 1574 different proteins with an estimated 4% gene coverage of the human genome, as annotated by 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.
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
Jon M
JM
Jacobs
Heather M
HM
Mottaz
Li-Rong
LR
Yu
David J
DJ
Anderson
Ronald J
RJ
Moore
Wan-Nan U
WN
Chen
Kenneth J
KJ
Auberry
Eric F
EF
Strittmatter
Matthew E
ME
Monroe
Brian D
BD
Thrall
David G
DG
Camp
Richard D
RD
Smith
D002460:Cell Line; D002850:Chromatography, Gel; D002851:Chromatography, High Pressure Liquid; D004847:Epithelial Cells / Q000737:chemistry*; D005260:Female; D006801:Humans; D042361:Mammary Glands, Human / Q000166:cytology*; D010446:Peptide Fragments / Q000302:isolation & purification; D010449:Peptide Mapping; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
D010446:Peptide Fragments; D011506:Proteins