Use of High Ionic Strength Buffers for the Separation of Proteins and Peptides with Capillary Electrophoresis

Abstract The use of high ionic strength buffers with capillary electrophoresis in untreated fused silica capillaries is demonstrated for the separation of proteins and peptides. Short, small i.d. (20–25 urn) capillaries are useful as a quick screening tool for protein analysis. Electrcpherograms of standard proteins run from pH 5.0 to 10.0 in 0.5 M sodium phosphate buffers suggest that at these high ionic strengths, the proteins (relative to the electroosmotic flow markers) are not always predictable functions of their pI's. Consecutive runs of standard proteins yield excellent migration time and peak area reproducibility. Milk proteins, particularly the caseins, could be separated with the addition of 4 M urea to the buffer. Alternatively, the addition of a zwitterion to a phosphate-based buffer provide different selectivities for the protein standards. The accompanying reduction in ionic strength allows for the use of wider diameter (50 μm) and longer (57 cm) capillaries. Finally, an improved micropreparative separation of peptides from a tryptic digest is demonstrated with a high ionic strength borate buffer. Using a 200 μm i.d. capillary and an automated fraction-collection protocol, individual peaks are isolated and sequenced from a single run.