Characterization of the human blood plasma proteome.
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.
Shen
Yufeng
Y
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA. rds@pnl.gov
Kim
Jeongkwon
J
Strittmatter
Eric F
EF
Jacobs
Jon M
JM
Camp
David G
DG
Fang
Ruihua
R
Tolié
Nikola
N
Moore
Ronald J
RJ
Smith
Richard D
RD
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
D007074:Immunoglobulin G; D010455:Peptides; D020543:Proteome; D012709:Serum Albumin