Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry

Anal Chem. 2004 Mar 15;76(6):1560-70. doi: 10.1021/ac0352171.


Human serum contains a complex array of proteolytically derived peptides (serum peptidome) that may provide a correlate of biological events occurring in the entire organism; for instance, as a diagnostic for solid tumors (Petricoin, E. F.; Ardekani, A. M.; Hitt, B. A.; Levine, P. J.; Fusaro, V. A.; Steinberg, S. M.; Mills, G. B.; Simone, C.; Fishman, D. A.; Kohn, E. C.; Liotta, L. Lancet 2002, 359, 572-577). Here, we describe a novel, automated technology platform for the simultaneous measurement of serum peptides that is simple, scalable, and generates highly reproducible patterns. Peptides are captured and concentrated using reversed-phase (RP) batch processing in a magnetic particle-based format, automated on a liquid handling robot, and followed by a MALDI TOF mass spectrometric readout. The protocol is based on a detailed investigation of serum handling, RP ligand and eluant selection, small-volume robotics design, an optimized spectral acquisition program, and consistent peak extraction plus binning across a study set. The improved sensitivity and resolution allowed detection of 400 polypeptides (0.8-15-kDa range) in a single droplet (approximately 50 microL) of serum, and almost 2000 unique peptides in larger sample sets, which can then be analyzed using common microarray data analysis software. A pilot study indicated that sera from brain tumor patients can be distinguished from controls based on a pattern of 274 peptide masses. This, in turn, served to create a learning algorithm that correctly predicted 96.4% of the samples as either normal or diseased.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Automation
  • Biomarkers, Tumor / blood
  • Blood Proteins / analysis*
  • Brain Neoplasms / blood*
  • Brain Neoplasms / diagnosis
  • Coated Materials, Biocompatible / chemistry*
  • Glioblastoma / blood*
  • Glioblastoma / diagnosis
  • Humans
  • Image Processing, Computer-Assisted / methods
  • Magnetics*
  • Peptides / blood*
  • Pilot Projects
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods*


  • Biomarkers, Tumor
  • Blood Proteins
  • Coated Materials, Biocompatible
  • Peptides