Re: [Psidev-pi-dev] Calculating amino acid average masses

[Brendan M. <brendanx@u.washington.edu>]

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...> 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
>