title: Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry.
abstract: Strategies for removal of high abundance proteins have been increasingly utilized in proteomic studies of serum/plasma and other body fluids to enhance the detection of low abundance proteins and achieve broader proteome coverage; however, both the reproducibility and specificity of the high abundance protein depletion process still represent common concerns. Here we report a detailed evaluation of immunoaffinity subtraction performed applying the ProteomeLab IgY-12 system that is commonly used in human serum/plasma proteome characterization in combination with high resolution LC-MS/MS. Plasma samples were repeatedly processed using this approach, and the resulting flow-through fractions and bound fractions were individually analyzed for comparison. The removal of target proteins by the immunoaffinity subtraction system and the overall process was highly reproducible. Non-target proteins, including one spiked protein standard (rabbit glyceraldehyde-3-phosphate dehydrogenase), were also observed to bind to the column at different levels but also in a reproducible manner. The results suggest that multiprotein immunoaffinity subtraction systems can be readily integrated into quantitative strategies to enhance detection of low abundance proteins in biomarker discovery studies.
authors.affiliation: Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Wei-Jun
authors.initials: WJ
authors.lastname: Qian
authors.forename: Heather M
authors.initials: HM
authors.lastname: Mottaz
authors.forename: Marina A
authors.initials: MA
authors.lastname: Gritsenko
authors.forename: Angela D
authors.initials: AD
authors.lastname: Norbeck
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D015415:Biomarkers / Q000032:analysis; D001798:Blood Proteins / Q000032:analysis* / Q000276:immunology; D002846:Chromatography, Affinity / Q000295:instrumentation*; D006801:Humans; D007136:Immunoglobulins / Q000276:immunology; D020543:Proteome / Q000032:analysis* / Q000276:immunology; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D015415:Biomarkers; D001798:Blood Proteins; C016512:IgY; D007136:Immunoglobulins; D020543:Proteome