title: Plasma biomarker discovery using 3D protein profiling coupled with label-free quantitation.
abstract: In-depth quantitative profiling of human plasma samples for biomarker discovery remains quite challenging. One promising alternative to chemical derivatization with stable isotope labels for quantitative comparisons is direct, label-free, quantitative comparison of raw LC-MS data. But, in order to achieve high-sensitivity detection of low-abundance proteins, plasma proteins must be extensively pre-fractionated, and results from LC-MS runs of all fractions must be integrated efficiently in order to avoid misidentification of variations in fractionation from sample to sample as "apparent" biomarkers. This protocol describes a powerful 3D protein profiling method for comprehensive analysis of human serum or plasma proteomes, which combines abundant protein depletion and high-sensitivity GeLC-MS/MS with label-free quantitation of candidate biomarkers.
authors.affiliation: Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA.
authors.forename: Lynn A
authors.initials: LA
authors.lastname: Beer
authors.forename: Hsin-Yao
authors.initials: HY
authors.lastname: Tang
authors.forename: Kurt T
authors.initials: KT
authors.lastname: Barnhart
authors.forename: David W
authors.initials: DW
authors.lastname: Speicher
mesh_terms: D000478:Alkylation; D015415:Biomarkers / Q000097:blood*; D011232:Chemical Precipitation; D002853:Chromatography, Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D000431:Ethanol; D006801:Humans; D013058:Mass Spectrometry; D010084:Oxidation-Reduction; D040901:Proteomics / Q000379:methods*; D044967:Serum; D013194:Staining and Labeling; D014357:Trypsin / Q000378:metabolism
chemical_list: D015415:Biomarkers; D000431:Ethanol; D014357:Trypsin