Have you sequenced the 8000 mass peptides? If its maldi, you might try
finding an electrospray instrument and getting some sequence on those
peptides. You may be looking at contaminants (I once analyzed an actin
prep that had very faint contaminants in the high mass range, but gave a
lot of contaminating peptides, I assume that the contaminants didn't stain
very well). In general, we use a mixture of trypsin and endolys to carry
out difficult digests, and you might try adding the proteinases in two
aliquots, half at the beginning, and the other half several hours later.
Katheryn Resing
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