Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis

Research output: Contribution to journalArticle


Blood plasma is the most complex human-derived proteome, containing other tissue proteomes as subsets. This proteome has only been partially characterized due to the extremely wide dynamic range of the plasma proteins of more than ten orders of magnitude. Thus, the reduction in sample complexity prior to mass spectrometric analysis is particularly important and alternative separation methodologies are required to more effectively mine the lower abundant plasma proteins. Here, we demonstrated a novel separation approach using 2-D free-flow electrophoresis (FFE) separating proteins and peptides in solution according to their pI prior to LC-MS/MS. We used the combination of sequential protein and peptide separation by first separating the plasma proteins into specific FFE fractions. Tryptic digests of the separated proteins were generated and subsequently separated using FFE. The protein separation medium was optimized to segregate albumin into specific fractions containing only few other proteins. An optimization of throughput for the protein separation reduced the separation time of 1 mL of plasma to approximately 3 h providing sufficient material for digestion and the subsequent peptide separation. Our approach revealed low-abundant proteins (e.g., L-selectin at 17 ng/mL and vascular endothelial-cadherin precursor at 30 ng/mL) and several tissue leakage products, thus providing a powerful orthogonal separation step in the proteomics workflow.


  • Mikkel Nissum
  • Sabine Kuhfuss
  • Monika Hauptmann
  • Christian Obermaier
  • Ute Sukop
  • Robert Wildgruber
  • Gerhard Weber
  • Christoph Eckerskorn
  • Johan Malmström
External organisations
  • ETH Zürich
Research areas and keywords


  • Blood Protein Electrophoresis, Blood Proteins, Electrophoresis, Gel, Two-Dimensional, Electrophoresis, Polyacrylamide Gel, Humans, Hydrogen-Ion Concentration, Isoelectric Focusing, Isoelectric Point, Peptide Fragments, Proteome, Proteomics, Serum Albumin, Tandem Mass Spectrometry, Trypsin, Journal Article
Original languageEnglish
Pages (from-to)4218-27
Number of pages10
Issue number23
Publication statusPublished - 2007 Dec
Publication categoryResearch
Externally publishedYes