Electrokinetic removal of dodecyl sulfate micelles from digested protein samples prior to electrospray-ionization mass spectrometry

In proteomics, dodecyl sulfate (DS^–) as sodium salt is commonly used in protein solubilization prior to tryptic digestion, but the presence of the DS^– hampers the electrospray ionization mass spectrometric (ESI-MS) analysis. The development of DS^– depletion techniques is therefore important especially when dealing with small samples where there could be poor sensitivity due to sample loss or dilution during sample preparation. Here, we present a simple and fast electrokinetic removal method of DS^– from small volumes of peptide and digested protein samples prior to ESI-MS. The selective removal was accomplished using an acidic extraction solution (ES) containing acetonitrile (ACN) inside a fused-silica capillary that was dipped into the sample. The use of acidic ES suppressed the electroosmotic flow; allowing the electrokinetic movement of DS^– monomers and micelles into the capillary. The high amount of ACN present at the tip of the capillary served to collapse the micelles migrating into the capillary, thereby releasing the peptides that were bound to these micelles, facilitating peptide retention in the sample and efficient DS^– removal. Increased % MS signal intensity (SI) restoration of the peptide was observed, while DS^– removal was unaffected when the amount of ACN in the ES was increased. This is because of the micelle to solvent stacking mechanism (effective electrophoretic mobility reversal) working at high concentration of ACN for the improved recovery of the peptides. % MS SI restoration for the Z-Gly-Gly-Val and bradykinin peptides were 75–83% while % MS SI reduction of DS^– was up to 99% under optimal conditions, that is, 40% ACN in the ES. Higher % peptide recoveries from digested protein samples were obtained using the proposed method compared to the conventional cold acetone precipitation method.