Alan,
Rich is better qualified to offer advice, but as he is currently out of
town at a conference, I'll
take a shot. The first thing is that Lutefisk is primary designed for, and
certainly most extensivly
tested with, tryptic peptides as that is almost exclusively what we deal
with. That said, have you
set Proteolysis to 'N' (none of the above) in the Extras section of the
Lutefisk.params file? The
default of 'T' (Tryptic) would cause Lutefisk to assume that the C-terminal
residue should be
either Lys or Arg and likely lead to nonsensnse possibilites for a
non-tryptic peptide. Also be
sure that Fragmentation Pattern in the Subsequenceing section is set to 'L'
(ion trap).
Regards,
Alex
>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
_______________________________________________________________________
J. Alex Taylor, Ph.D. jataylor@nwlink.com
_______________________________________________________________________
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