High-resolution separation of peptides by sodium dodecyl sulfate-polyacrylamide gel "focusing"

As a follow-up of our previous report (Anal. Chem. 2007, 79, 821-827) on analytical SDS-PAGE focusing, a refinement of the method for separation of peptides in the small to medium M(r) range (0.5-10 kDa) is here reported, based on a shallow gradient of immobilized positive charges (0-10 mM) onto a minimally sieving polyacrylamide gel matrix (4%T, 2.5%C). Unlike conventional SDS-PAGE, which rarely can achieve the separations of polypeptide chains below a critical value of 10 kDa, the present method can be fine-tuned to perform such separations even down to a size of only 500 Da. In the case of larger fragments, the major peptide zones are shown, under microscope observation, to be composed by envelopes of bands as narrow as 20-100 microm, spaced at regular intervals of 100-150 microm. It is hypothesized that such larger peptides could form complexes with rather small SDS micelles and that such peptide-SDS complexes could differ in charge by just a single negative charge.