title: Characterization of the human blood plasma proteome.
abstract: We describe methods for broad characterization of the human plasma proteome. The combination of stepwise immunoglobulin G (IgG) and albumin protein depletion by affinity chromatography and ultrahigh-efficiency capillary liquid chromatography separations coupled to ion trap-tandem mass spectrometry enabled identification of 2392 proteins from a single plasma sample with an estimated confidence level of > 94%, and an additional 2198 proteins with an estimated confidence level of 80%. The relative abundances of the identified proteins span a range of over eight orders of magnitude in concentration (< 30 pg/mL to approximately 30 mg/mL), facilitated by the attomole-level sensitivity of the analysis methods. More than 80% of the observed proteins demonstrate interactions with IgG and/or albumin, and the human plasma protein loss in the affinity chromatography/strong cation exchange/reversed-phase liquid chromatography-tandem mass spectrometry methodology was investigated in detail. The results of this study provide a basis for a wide range of plasma proteomics studies, including broad quantitation of relative abundances in comparative studies of the identification of novel protein disease markers, as well as further studies of protein-protein interactions.
authors.affiliation: Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA. rds@pnl.gov
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: Jeongkwon
authors.initials: J
authors.lastname: Kim
authors.forename: Eric F
authors.initials: EF
authors.lastname: Strittmatter
authors.forename: Jon M
authors.initials: JM
authors.lastname: Jacobs
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Ruihua
authors.initials: R
authors.lastname: Fang
authors.forename: Nikola
authors.initials: N
authors.lastname: Tolié
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D000818:Animals; D002846:Chromatography, Affinity; D002853:Chromatography, Liquid / Q000379:methods; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D007074:Immunoglobulin G / Q000302:isolation & purification; D013058:Mass Spectrometry / Q000379:methods; D010449:Peptide Mapping; D010455:Peptides / Q000302:isolation & purification; D010949:Plasma / Q000737:chemistry*; D020543:Proteome; D040901:Proteomics / Q000379:methods; D012709:Serum Albumin / Q000302:isolation & purification
chemical_list: D007074:Immunoglobulin G; D010455:Peptides; D020543:Proteome; D012709:Serum Albumin