Larry,
Two factors will influence transfer yield the most: acrylamide percentage
in the gel and SDS concentration in the gel and electrophoresis (not
transfer) buffer. Try casting 6% gel using 0.2% SDS concentration in the
gel and then run electrophoresis using electrophoresis buffer containing
0.2% SDS. Do not presoak the gel prior to transfer and try 0.5x Towbin
buffer (Tris/glycine) containing maximum 10% methanol. Do not add SDS to
transfer buffer.
Some proteins will not transfer with 100% yield regardless the conditions,
but the above steps should improve the yield.
Jacek Mozdzanowski
Bioanalytical Sciences
SmithKline Beecham