I modified the code to have more precise acid weights and I added frag17 (which subtracts a nitrogen and three hydrogen) and frag18 (which subtracts an oxygen and two hydrogen). For this scale frag17 and frag18 values are so very close that they overlap. Still, you can see that for the correct acid sequence there is a predicted line (orange or green) that closely lines with one of the MSMS values (when there isn’t an obvious gap in the MSMS data).
JainabJul 7th, 2009 :
Brian,
I think for these spectra you will see better alignment if you use precise acid mass and at least b-ion and y-ion masses. I am not sure how you are using those acid masses, because those acid masses somehow look different to me. As I remember valine mass is 99 Da. or Glycine mass as 57 Da, etc, but I see different here. frag17 and frag18 only calculates internal fragments masses when internal fragments loose amonia or water and those are not that important, but if you compare only b-ion and y-ion (as is compared in get ionTypes, before calling compareInternalFrags), you will see much better alignment. If you want may be I can help you understand how the calculations of those ion types are done. Since Morgan thinks that we can use that for quick visualization and it could be a useful tool, I think it is important that our alignment is correct. May be we can sit together sometimes this week.
adminJul 7th, 2009 :
Yes, you are right about the incorrectness of the acid weights I was
using last week (listed in the table you are probably referencing). I
have corrected for that and am using the exact weights used in GFS.
Jul 7th, 2009 :
Agreed, big improvement..
It would be good to label these for what they are called in the standard nomenclature, b-ions and y-ions.
Are you actually including both left-hand AND right hand fragments?
adminJul 7th, 2009 :
If by left hand / right hand you mean am I accounting for if a mass in our MSMS data is taken from the left or right side of the sequence, no I have not, but that would not be difficult. This plots the raw MSMS data, but I could also have it plot the reversed MSMS data (giving a symmetric image).
