Ionnis,
Just in for a little while today and don't have much time, but for what
it's worth:
If you haven't already, you might have a look at Fernandez et al.(1994)
Anal. Biochem. 218, 112-117. For our digestions on PVDF, 1%
octylbeta-D-glucopyranoside seems to have less effect on MALDI relative to
triton-X and should work in solution as long as you don't have to
concentrate. If SDS is unavoidable, you might explore adding additional up
to 5-10% to improve signal strength (Amado et. al. (1997) Anal. Chem. 69,
1102-1106). We find that other in-situ MALDI cleanup methods, such as those
which fall under the heading of "wash" procedures (e.g. Xiang and Beavis
(1994) R. Commun. Mass Spectrom. 8, 199-204) don't work, at least in our
hands, as the detergent does an effective job of dissolving the matrix and
it's goodbye sample. Finally, you might explore the use of ion-exchange
resins to remove the SDS prior to reverse phase chromatography (LC
Packings, Michrom Bioresources and others).
best of luck