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Re: [Psidev-pi-dev] Calculating amino acid average masses
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From: Brendan M. <brendanx@u.washington.edu> - 2008-10-13 18:18:35
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Ah, yes. I neglected to add the proposed value from the Beavis article itself: Wikipedia = 12.01109 Waters = 12.011 Beavis = 12.0109 Matthews & Hayes = 12.01085 NIST = 12.0107 Certainly the Beavis and Matthews & Hayes values are close to agreement, and with only 4-digit precision are actually equal. Given the lack of publication for Matthews & Hayes, the Beavis value is likely the most defensible standard. --Brendan On Mon, Oct 13, 2008 at 10:33 AM, Matthew Chambers < mat...@va...> wrote: > Thanks for the very informative C12 enrichment link Brendan. > > Are the NIST numbers not intended to reflect the standard > mineral/atmospheric abundances? I was actually mixed up thinking biology > was enriching for C13 instead. Is theaverage 13C/12C ratio calculable from > the Beavis article the optimal value? > > -Matt > > > Brendan MacLean wrote: > >> Hi all, >> >> I am working with Mike MacCoss, and he pointed me to this article by Ron >> Beavis: >> >> >> http://pubs.acs.org/cgi-bin/archive.cgi/ancham/1993/65/i04/pdf/ac00052a030.pdf >> >> The 12.011 value for carbon is, I am told, THE standard 1.11% C13 value >> derived from carbonate rocks and atmospheric C02. My own web search yielded >> the following summary explanation of C12 enrichment in living organisms >> (with its own references): >> >> http://www.madsci.org/posts/archives/2003-06/1055532737.Bc.r.html >> >> Mike favors the value 1.0958793% C13, which was derived by Dwight Matthews >> and John Hayes in the 70s, but may never have been reported. >> >> To summarize the proposed values: >> Wikipedia = 12.01109 >> Waters = 12.011 >> Matthews & Hayes = 12.01085 >> NIST = 12.0107 >> >> If we agree that the standard mineral/atmospheric value is the 12.011(09) >> number, then the Matthews & Hayes value comes in roughly at the center of >> the range reported in the Beavis article: "The data in Figure 1 indicate >> that the 13C/12C ratio found in proteins varies between 12.0107 C m(c) C >> 12.0111 u (or -10 > 6 > -40)." While the NIST number is in fact the >> reported lower bound. >> >> For a lot of applications, these numbers will have little impact on >> results. We would propose, however, that where accuracy in this value is >> important, neither the mineral/atmospheric standard, nor the NIST lower >> extreme for biological samples can be considered the optimal value. >> >> --Brendan >> >> On Mon, Oct 13, 2008 at 8:12 AM, Matthew Chambers < >> mat...@va... <mailto:mat...@va...>> >> wrote: >> >> Hi all, >> >> Some discussion has come up within the ProteoWizard group and some >> collaborators (Jimmy Eng and Brendan MacLean) about how to >> calculate amino acid average masses. Currently, we are using the >> atomic weights from NIST: >> >> http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=html&isotype=some >> <http://physics.nist.gov/PhysRefData/Compositions/index.html> >> >> >> We calculate average mass (molecular weight) of a chemical formula >> in ProteoWizard by <count of element> * <atomic weight of >> element>. But when we calculate the average masses of the amino >> acids and then compare these to the online references for amino >> acid masses, the discrepancies are (IMO) unacceptable. >> >> A table showing some different values and references: >> expasy = >> >> http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html >> waters = a laminated reference sheet I have from Waters; it uses >> these atomic weights: C=12.011 H=1.00794 O=15.9994 N=14.00674 S=32.066 >> pwiz avg = element count * NIST atomic weight >> >> >> Waters mono Waters avg expasy avg pwiz mono >> pwiz avg Waters >> - pwiz for mono Waters - pwiz for avg >> Alanine A 71.037110 71.078800 71.078800 >> 71.037114 >> 71.077900 -0.000004 0.00090 >> Arginine R 156.101110 156.187600 156.187500 >> 156.101111 >> 156.185680 -0.000001 0.00192 >> Asparagine N 114.042930 114.103900 114.103800 >> 114.042927 >> 114.102640 0.000003 0.00126 >> Asparticacid D 115.026940 115.088600 115.088600 >> 115.026943 >> 115.087400 -0.000003 0.00120 >> Cysteine C 103.009190 103.144800 103.138800 >> 103.009184 >> 103.142900 0.000006 0.00190 >> Glutamicacid E 129.042590 129.115500 129.115500 >> 129.042593 >> 129.113980 -0.000003 0.00152 >> Glutamine Q 128.058580 128.130800 128.130700 >> 128.058578 >> 128.129220 0.000002 0.00158 >> Glycine G 57.021460 57.052000 57.051900 >> 57.021464 >> 57.051320 -0.000004 0.00068 >> Histidine H 137.058910 137.141200 137.141100 >> 137.058912 >> 137.139280 -0.000002 0.00192 >> Isoleucine I 113.084060 113.159500 113.159400 >> 113.084064 >> 113.157640 -0.000004 0.00186 >> Leucine L 113.084060 113.159500 113.159400 >> 113.084064 >> 113.157640 -0.000004 0.00186 >> Lysine K 128.094960 128.174200 128.174100 >> 128.094963 >> 128.172280 -0.000003 0.00192 >> Methionine M 131.040490 131.198600 131.192600 >> 131.040485 >> 131.196060 0.000005 0.00254 >> Phenylalanine F 147.068410 147.176600 147.176600 >> 147.068414 >> 147.173860 -0.000004 0.00274 >> Proline P 97.052760 97.116700 97.116700 >> 97.052764 >> 97.115180 -0.000004 0.00152 >> Serine S 87.032030 87.078200 87.078200 >> 87.032028 87.077300 >> 0.000002 0.00090 >> Threonine T 101.047680 101.105100 101.105100 >> 101.047678 >> 101.103880 0.000002 0.00122 >> Tryptophan W 186.079310 186.213300 186.213200 >> 186.079313 >> 186.209900 -0.000003 0.00340 >> Tyrosine Y 163.063330 163.176000 163.176000 >> 163.063329 >> 163.173260 0.000001 0.00274 >> Valine V 99.068410 99.132600 99.132600 >> 99.068414 99.131060 >> -0.000004 0.00154 >> >> >> avg mono delta: -0.00000110 >> avg avg delta: 0.001756 >> >> For a peptide of 20 residues, the average delta for average mass >> calculations between the NIST atomic weights and the Waters atomic >> weights would be: 0.03512 >> Not a huge number in the average mass domain, but enough to make >> me worry. >> >> I think it's pretty clear that the 12.011 value for carbon is >> closer to the atomic weight used in the amino acid references that >> are widely used in the field. Several other references which I >> couldn't easily copy and paste also used similar average masses, e.g.: >> http://www.matrixscience.com/help/aa_help.html >> http://www.i-mass.com/guide/aamass.html (this looks like a scan of >> the Waters reference, same format and values) >> http://musclesurf.com/beverly-mass-amino.html (this is not an >> amino acid mass reference, but included for completeness) ;) >> >> More importantly, I couldn't find any amino acid average mass >> references that looked like they were calculated from the NIST >> atomic weights. >> >> So the question is: what atomic weights should researchers use to >> calculate amino acid masses? I suspect most software just stores >> the amino acid masses directly and avoids the problem, but it's an >> interesting issue to address for the PSI and more specifically the >> PSI-PI. :) >> >> Thanks, >> Matt >> >> >> |
