Larger Proteins Vanish During Gel Run

Hi,

This problem was recently related to me by several protein-running
members of my lab. I don't know where to begin looking for answers for
such an intermittent problem in both pre-cast and self-made SDS-PAGE
gels, so I thought I'd ask here.

As the gel runs, the visible Bio-Rad dual color protein standard bands
are seen to start to separate, later the larger ones (100-250 kD) start
to fade, then vanish. The smaller ones seem fine, dye front fine too.
Post-transfer Ponceau S stain shows there was a loss of protein in the
sample lanes in that same upper size range as well - just like the
marker. Smaller proteins and smaller markers are all there.

Since this happens to the commercial marker (in it's own loading
buffer) and the protein/lysate samples (in our own), in both precast
and self-cast gels, the only thing in common would seem to be the
electrophoresis buffer - but that's made in large volumes and used for
multiple gels - and the problem doesn't show all the time...

Thanks for any comments.

Steve