Help with Lutefisk - de novo sequencing

Dear fellow ABRF'ers,

 

We've been trying to do some De-novo sequencing with data obtained by LC/MS/MS on a Bruker Esquire ion trap.  In order to test the capabilities of the "Lutefisk" program at coming up with valid proposed sequences, we're using a 12mer synthetic peptide.  I'm getting results but nothing close to the correct sequence.  Does anyone have any clues as to how to obtain better results? 

 

  The spectra of the synthetic peptide in question contains most predicted Y ions and many of the B's with a few "a-B-Y's" present.  It comes from the +2 precursor and looks very clean. I'm using a list of deconvolved masses and intensities (a few B ions are +2) .  I have no edman data and I'm not giving any proposed sequences.  I've tried loosening up the tollerances but this didn't help and the ions match the predicted masses within +/- 0.4 amu any how.  The peptide is not a tryptic peptide - sequence is PPA YRP PNA PIL.  It seems that I must be doing something wroing with lutefisk if it doesn't give good results with a spectrum of this quality.

 

Any suggestions would be appreciated!

 

Alan Higbee

Biopolymer Facility

Roswell Park Cancer Institute