Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers

Anal Biochem. 2007 Mar 1;362(1):44-54. doi: 10.1016/j.ab.2006.12.023. Epub 2006 Dec 20.


A major bottleneck for validation of new clinical diagnostics is the development of highly sensitive and specific assays for quantifying proteins. We previously described a method, stable isotope standards with capture by antipeptide antibodies, wherein a specific tryptic peptide is selected as a stoichiometric representative of the protein from which it is cleaved, is enriched from biological samples using immobilized antibodies, and is quantitated using mass spectrometry against a spiked internal standard to yield a measure of protein concentration. In this study, we optimized a magnetic-bead-based platform amenable to high-throughput peptide capture and demonstrated that antibody capture followed by mass spectrometry can achieve ion signal enhancements on the order of 10(3), with precision (CVs <10%) and accuracy (relative error approximately 20%) sufficient for quantifying biomarkers in the physiologically relevant ng/mL range. These methods are generally applicable to any protein or biological fluid of interest and hold great potential for providing a desperately needed bridging technology between biomarker discovery and clinical application.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies / chemistry*
  • Biomarkers / analysis*
  • Biomarkers / blood
  • Chromatography, Liquid / methods
  • Humans
  • Mass Spectrometry / methods*
  • Microspheres*
  • Peptides / chemistry
  • Peptides / isolation & purification*
  • Proteomics / methods
  • Reproducibility of Results
  • Spectrometry, Mass, Electrospray Ionization / methods


  • Antibodies
  • Biomarkers
  • Peptides