Data management and functional annotation of the Korean reference plasma proteome

As human plasma is clinically valuable, reference data from healthy donors can be a useful source for serological biomarker studies. To make a reliable protein catalog of the Korean plasma proteome, various experimental methods, such as 1-D HPLC, 2-D LC, and narrow ranged 2-DE prior to MALDI-TOF and LC-MS/MS, were used to identify unique plasma proteins in this population. To compile candidates with high confidence, two different search engines were used to select proteins with a false discovery rate of less than or equal to 1%. From this rigorous selection process, we initially identified 494 distinct Korean plasma proteins. After multilevel stepwise filtrations with stringent, identification parameters were applied to acquire plasma protein list with the maximum confidence; a total 185 distinct plasma proteins were identified and integrated into our Korean human plasma proteome project database along with several bioinformatics analysis results, including gene ontology, biological pathways, tissue expression, and disease association. This is the first publicly available single ethnic group-specific plasma proteome database (http://proteomix.org/ khppp/).