Plasma biomarker discovery using 3D protein profiling coupled with label-free quantitation

Methods Mol Biol. 2011:728:3-27. doi: 10.1007/978-1-61779-068-3_1.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alkylation
  • Biomarkers / blood*
  • Chemical Precipitation
  • Chromatography, Liquid
  • Electrophoresis, Polyacrylamide Gel
  • Ethanol
  • Humans
  • Mass Spectrometry
  • Oxidation-Reduction
  • Proteomics / methods*
  • Serum
  • Staining and Labeling
  • Trypsin / metabolism

Substances

  • Biomarkers
  • Ethanol
  • Trypsin