I can think of a couple of things to try. Negative mode is an easy one. If
that fails, the problem is possibly due to suppression of the 4kD signal by the
smaller peptide. Sometimes simple dilution reduces this effect. Or, depending
on how much effort you want to expend, you could both confirm this hypothesis
and find the missing peptide by trying a reverse-phase separation. With some
luck, this could be done on a Ziptip, if not, then a normal C-18 column. Once
the 4kD peptide is on its own, it will likely give a signal. Good luck.
Arnie Falick
PE Biosystems
Foster City, CA
FalickAM@pebio.com