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Re: [Psidev-pi-dev] Calculating amino acid average masses
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From: Matthew C. <mat...@va...> - 2008-10-13 17:30:01
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Hi David, The masses on this page http://www.matrixscience.com/help/aa_help.html do not appear to use the IUPAC atomic weights (which are the same as the NIST atomic weights). It's hard to tell because of the rounding, but several amino acids seem to be rounding off according to the Waters avg or at least something not quite the NIST avg: Waters NIST Mascot F 147.176600 147.173860 147.18 Y 163.176000 163.173260 163.18 Then there's this residue, which strangely rounds with NIST, so perhaps it is using the 12.01085 number Brendan mentioned. T 101.105100 101.103880 101.10 -Matt David Creasy wrote: > Hi Matt, > > Unimod (and hence Mascot) calculates residue masses from IUPAC atomic > weights: > > http://www.unimod.org/masses.html > http://www.webelements.com/periodicity/atomic_weight/ > > We are 'skirting' the problem in analysisXML by allowing the mass > values used by the search engine to be recorded in the analysisXML > instance documents. Any software that reads analysisXML documents > should probably use those values. > > David > > Matthew Chambers 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 >> >> 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 >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> 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=/ >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 |
