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-De Novo Peptide Sequencing Tutorial


2nd De Novo Exercise

the q-TOF answer page




The correct sequence for this peptide is, LFTGHPETLEK

The first thing that we did was to look at the low end of the spectrum for low mass clues.  We saw the immonium ions for H, F, and K, which let us know that we may encounter these amino acids in the sequence.

We did the math to determine the next to last y ion.  

1271.66 - AA residue mass = penultimate y ion

We then proceeded to look for the next amino acid residue and labeled the peaks.  We then did the calculation to determine the corresponding b ion and looked for a ions to confirm.  With this data set, as long as you start with the y ion series the going is pretty straightforward.  The mass accuracy of the q-TOF helps because you know that any amino acid call should be within 30 mmu.  

If you tried to follow the b ion series your going would be tougher, because there are gaps that would force you to make several double amino acid jumps, and that's pretty hard, but still easier than with ion trap or triple quad data..  We don't have a lot of experience with q-TOF data, but it appears that the y ion series is dominant.  Luckily we were able to determine the b1 ion which was a good surprise.


Here is the correct sequence


Here is the sequence that we determined from the y ion series



We determined the entire sequence, yippee!   Hopefully you got it right too!.  If you would like to look at our scribblings, here they are in .pdf format.






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