Deb,
My understanding is that the sequence is known. In such a case the best
approach is to "custom craft" sequencing cycles. Longer cleavage time is
necessary for proline and shorter time for all the other residues.
Switching to the gas phase could be helpful, too. With this approach you
should be able to improve the lag (carryover) and reduce the washout quite
a bit. Check: W.H.Vensel, D.D.Kasarda, Techniques in Protein Chemistry II,
pp 181-190.
Jacek Mozdzanowski
Analytical Sciences
SmithKline Beecham