Combinatorial ligand libraries as a two-dimensional method for proteome analysis

• Combinatorial peptide ligand libraries can be used via a two-dimensional capture.
• Ionic capture is implemented at low ionic strength (25 mM salt).
• “Hydrophobic” capture is driven by 1 M ammonium sulphate (lyotropic salt of the Hofmeister series).
• This 2D methodology drastically diminishes protein losses during capture.

The present report tries to assess the possibility of performing capture of proteomes via combinatorial peptide ligand libraries (CPLL) in a two-dimensional (2D) mode, i.e. via orthogonal complementarity in the capture phase. To that aim, serum proteins are captured at physiological pH either at low ionic strength (25 mM NaCl) or at high concentrations of lyotropic salts of the Hofmeister series (1 M ammonium sulphate) favouring hydrophobic interaction. Indeed such 2D mechanisms seems to be operative, since 52% of the captured proteins are common to the two capture modes, 20% are specific only of the “ionic” interaction mode and 28% are found only in the “hydrophobically” driven interaction. As an additional bonus, losses of protein species from the initial sample, one of the major drawbacks of CPLLs, are diminished to about 5% and are found only in the ionic capture, whereas the hydrophobically engendered capture is loss-free.