Exploring New Proteome Space: Combining Lys-N Proteolytic Digestion and Strong Cation Exchange (SCX) Separation in Peptide-Centric MS-Driven Proteomics

  • Nadia Taouatas
  • Shabaz Mohammed
  • Albert J.R. Heck
Part of the Methods in Molecular Biology book series (MIMB, volume 753)


The current advances in mass spectrometry technology have led to the possibility of analyzing more complex biological samples such as entire proteomes. Here, we describe a new and powerful methodology that combines the use of the metalloendopeptidase Lys-N and strong cation exchange with mass spectrometric analysis. The approach described here allows one to separate peptides with different functional groups. The peptides we are able to isolate are N-terminal peptides, phosphorylated peptides with a single lysine, peptides with a single basic residue (lysine), and peptides with multiply basic residues. When this separation strategy is combined with tandem mass spectrometry that involves both collision-induced dissociation and electron transfer dissociation, one can achieve an optimal targeted strategy for proteome analysis.

Key words

Strong cation exchange (SCX) Lys-N mass spectrometry tandem mass spectrometry electron transfer dissociation 



The work was supported by the Netherlands Proteomics Center.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Nadia Taouatas
    • 1
  • Shabaz Mohammed
    • 1
  • Albert J.R. Heck
    • 1
  1. 1.Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtThe Netherlands

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