Hydrophobic Peptide: Fragment Detection

[JSIGAFOOS]

I've had success using ion exchange to detect deletion peptides that 
reverse phase didn't resolve from the desired peptide.  If your peptide
has any basic residues, The NEST Group makes an SCX column that can be run
in the presence of CH3CN which has worked well for me. Another method
which has sometimes worked, is to run a reverse phase column buffered
(with a volatile buffer) to the pI of the peptide of interest.  This 
should increase the retention time of the peptide and  may resolve it from
the deletion peptide.  Good luck!
Disclaimer: I have no association with The Nest Group, but I do like their
columns!