Originally Posted by Asuriel
Thanks a lot, I'm verty astonished about these filters. Do you know if (in your experience) eletrolyte concentration may modify protein retention capability? If it is I could increase salt concentration to achieve good results. It's very important for me to solve this question.
You don't want to increase salt concentration for two reasons:
1) maldi-tof is sensitive to salts, typically desalt(or dilute) sample before spotting.
2) Dialysis can be used to remove small proteins if the MWCO is 10K. Very efficient with the Slide-A-Lyzer because you use either 100ul (mini) or up to 500ul (cassette) and dialyze against a very large volume like 1L (with an exchange to further pull out the small proteins). That dialysis of small proteins will work despite the ionic difference between buffers.
3) High ion concentration in the spin filters probably doesn't make a difference, since it is all size filtration.
BTW those spin filters are probably getting clogged with proteins (perhaps, glycoproteins, lipids may be in supernatants, depending on sample), thus the retention of the small proteins.