From: Brendan M. <brendanx@u.washington.edu> - 2008-08-28 15:52:51
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Interesting. In X! Tandem I also went with mass calculated from the chemical formula, as I found in most cases this matched exactly with what X! Tandem and Comet had hard-coded, and fixed a few bugs where they didn't match. Looking at my formulas, they are the residue formulas (-2 H, -1 O from those in AminoAcid.cpp). I did throw in the towel on amino acid average masses, which I tried calculating from atomic average masses, but found these in no way resembled what Jimmy had in Comet (although neither X! Tandem nor Comet documented the sources of any of their magic numbers). Does anyone on this list have insight into the average masses? Darren, I see that MassDistribution information is stored in Cemistry.Info.Record, but I also only see monoisotopicMass() and molecularWeight() on the Formula class. Is the latter equivalent to average mass, or are average masses NYI? Anyway, I am totally for building the information reliably from formulas, as Miramatch is not the first tool to have a typo in the amino acid masses. It would also be a great service to the community to create a test data set with a table of expected precursor and fragment ion masses for several peptides. Perhaps I could generate one with X! Tandem, and we could test against PWiz until we all agree on the correct expected outputs? --Brendan On Thu, Aug 28, 2008 at 7:55 AM, Matthew Chambers < mat...@va...> wrote: > Darren Kessner wrote: > > 1) The amino acid formulas are what you typically see in reference > > material, and they include the full amine and carboxyl groups. When > > the peptide bond is formed, a single water molecule is lost. I don't > > like the idea of storing redundant information, and it seemed more > > natural to store the full formula rather than the residue formula. > > You could add a function to return the residue formula -- if you do > > this, just make sure to add back one water molecule when you are > > summing to get peptide molecular weights. > This is not a big deal, but I think it will be confusing to users. I > have never seen reference material include the water on individual amino > acids. I checked the first several links that came up on Google for > "amino acid masses" and "amino acid mass table" and the reference links > all use only the residue formula: > > http://www.proteinsandproteomics.org/content/free/tables_1/table08.pdf > > http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html > http://www.matrixscience.com/help/aa_help.html > http://ionsource.com/Card/aatable/aatable.htm > > Is there any objection to me changing it according to these references? > Since I intend for my additions to the Peptide class to support > modifications (including terminal modifications), it would be less > confusing to work from the residue formula. :) > > > 3) I'd like to know more about why there are differences in the > > calculators before we decide on this... > After further examination, it's not so bad as I thought. I think we'll > be ok. I did find a residue in MyriMatch's built-in mass map that had > the wrong monoisotopic mass probably by typo - only by about 0.01 though. > :) > > -Matt > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > proteowizard-developer mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-developer > |