Comparison of peptide and protein fractionation methods in proteomics

Ekaterina Mostovenko, Chopie Hassan, Janine Rattke, André M. Deelder, Peter A. van Veelen, Magnus Palmblad

Research output: Contribution to journalArticle

26 Scopus citations


Multiple fractionation or separation methods are often combined in proteomics to improve signal-to-noise and proteome coverage and to reduce interference between peptides in quantitative proteomics. Furthermore, a given fractionation method provides additional information on the analytes, such as molecular weight, hydrophobicity or isoelectric point that can be used to improve identification, and to discover protein splice variants or large post-translational modifications. Here we describe a Taverna scientific workflow for analysis and comparison between strong cation exchange (SCX) chromatography, peptide isoelectric focusing (pIEF) and SDS-PAGE performed using robust capillary LC and ion trap tandem mass spectrometry.

Original languageEnglish (US)
Pages (from-to)30-37
Number of pages8
JournalEuPA Open Proteomics
StatePublished - Sep 13 2013
Externally publishedYes



  • Comparison
  • Isoelectric focusing
  • Scientific workflows
  • Strong cation exchange chromatography
  • Taverna

ASJC Scopus subject areas

  • Biochemistry

Cite this

Mostovenko, E., Hassan, C., Rattke, J., Deelder, A. M., van Veelen, P. A., & Palmblad, M. (2013). Comparison of peptide and protein fractionation methods in proteomics. EuPA Open Proteomics, 1, 30-37.