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

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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
>
>