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Re: [Psidev-pi-dev] Calculating amino acid average masses
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From: David C. <dc...@ma...> - 2008-10-13 16:29:41
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> <title></title> </head> <body bgcolor="#ffffff" text="#000000"> Hi Matt,<br> <br> Unimod (and hence Mascot) calculates residue masses from IUPAC atomic weights:<br> <br> <a class="moz-txt-link-freetext" href="http://www.unimod.org/masses.html">http://www.unimod.org/masses.html</a><br> <a class="moz-txt-link-freetext" href="http://www.webelements.com/periodicity/atomic_weight/">http://www.webelements.com/periodicity/atomic_weight/</a><br> <br> 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.<br> <br> David<br> <br> Matthew Chambers wrote: <blockquote cite="mid:48F...@va..." type="cite"><font color="#000000">Hi all,<br> <br> 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: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://physics.nist.gov/PhysRefData/Compositions/index.html">http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=html&isotype=some</a><br> <br> 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.<br> <br> A table showing some different values and references:<br> expasy = <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html">http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html</a><br> 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<br> pwiz avg = element count * NIST atomic weight<br> <br> </font> <table style="border-collapse: collapse; width: 640pt;" border="0" cellpadding="0" cellspacing="0" width="851"> <col style="width: 73pt;" width="97"> <col style="width: 15pt;" width="20"> <col style="width: 68pt;" width="90"> <col style="width: 66pt;" span="4" width="88"> <col style="width: 116pt;" width="154"> <col style="width: 104pt;" width="138"> <tbody> <tr style="height: 15pt;" height="20"> <td style="height: 15pt; width: 73pt;" height="20" width="97"><font color="#000000"><br> </font></td> <td style="width: 15pt;" width="20"><font color="#000000"><br> </font></td> <td class="xl63" style="width: 68pt;" width="90"><font color="#000000">Waters mono</font></td> <td class="xl63" style="width: 66pt;" width="88"><font color="#000000">Waters avg </font></td> <td class="xl63" style="width: 66pt;" width="88"><font color="#000000">expasy avg</font></td> <td class="xl63" style="width: 66pt;" width="88"><font color="#000000">pwiz mono</font></td> <td class="xl63" style="width: 66pt;" width="88"><font color="#000000">pwiz avg</font></td> <td class="xl63" style="width: 116pt;" width="154"><font color="#000000">Waters - pwiz for mono</font></td> <td class="xl63" style="width: 104pt;" width="138"><font color="#000000">Waters - pwiz for avg</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Alanine</font></td> <td><font color="#000000">A</font></td> <td class="xl64" align="right"><font color="#000000">71.037110</font></td> <td class="xl64" align="right"><font color="#000000">71.078800</font></td> <td class="xl64" align="right"><font color="#000000">71.078800</font></td> <td class="xl64" align="right"><font color="#000000">71.037114</font></td> <td class="xl64" align="right"><font color="#000000">71.077900</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00090</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Arginine</font></td> <td><font color="#000000">R</font></td> <td class="xl64" align="right"><font color="#000000">156.101110</font></td> <td class="xl64" align="right"><font color="#000000">156.187600</font></td> <td class="xl64" align="right"><font color="#000000">156.187500</font></td> <td class="xl64" align="right"><font color="#000000">156.101111</font></td> <td class="xl64" align="right"><font color="#000000">156.185680</font></td> <td class="xl64" align="right"><font color="#000000">-0.000001</font></td> <td class="xl65" align="right"><font color="#000000">0.00192</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Asparagine</font></td> <td><font color="#000000">N</font></td> <td class="xl64" align="right"><font color="#000000">114.042930</font></td> <td class="xl64" align="right"><font color="#000000">114.103900</font></td> <td class="xl64" align="right"><font color="#000000">114.103800</font></td> <td class="xl64" align="right"><font color="#000000">114.042927</font></td> <td class="xl64" align="right"><font color="#000000">114.102640</font></td> <td class="xl64" align="right"><font color="#000000">0.000003</font></td> <td class="xl65" align="right"><font color="#000000">0.00126</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Asparticacid</font></td> <td><font color="#000000">D</font></td> <td class="xl64" align="right"><font color="#000000">115.026940</font></td> <td class="xl64" align="right"><font color="#000000">115.088600</font></td> <td class="xl64" align="right"><font color="#000000">115.088600</font></td> <td class="xl64" align="right"><font color="#000000">115.026943</font></td> <td class="xl64" align="right"><font color="#000000">115.087400</font></td> <td class="xl64" align="right"><font color="#000000">-0.000003</font></td> <td class="xl65" align="right"><font color="#000000">0.00120</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Cysteine</font></td> <td><font color="#000000">C</font></td> <td class="xl64" align="right"><font color="#000000">103.009190</font></td> <td class="xl64" align="right"><font color="#000000">103.144800</font></td> <td class="xl64" align="right"><font color="#000000">103.138800</font></td> <td class="xl64" align="right"><font color="#000000">103.009184</font></td> <td class="xl64" align="right"><font color="#000000">103.142900</font></td> <td class="xl64" align="right"><font color="#000000">0.000006</font></td> <td class="xl65" align="right"><font color="#000000">0.00190</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Glutamicacid</font></td> <td><font color="#000000">E</font></td> <td class="xl64" align="right"><font color="#000000">129.042590</font></td> <td class="xl64" align="right"><font color="#000000">129.115500</font></td> <td class="xl64" align="right"><font color="#000000">129.115500</font></td> <td class="xl64" align="right"><font color="#000000">129.042593</font></td> <td class="xl64" align="right"><font color="#000000">129.113980</font></td> <td class="xl64" align="right"><font color="#000000">-0.000003</font></td> <td class="xl65" align="right"><font color="#000000">0.00152</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Glutamine</font></td> <td><font color="#000000">Q</font></td> <td class="xl64" align="right"><font color="#000000">128.058580</font></td> <td class="xl64" align="right"><font color="#000000">128.130800</font></td> <td class="xl64" align="right"><font color="#000000">128.130700</font></td> <td class="xl64" align="right"><font color="#000000">128.058578</font></td> <td class="xl64" align="right"><font color="#000000">128.129220</font></td> <td class="xl64" align="right"><font color="#000000">0.000002</font></td> <td class="xl65" align="right"><font color="#000000">0.00158</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Glycine</font></td> <td><font color="#000000">G</font></td> <td class="xl64" align="right"><font color="#000000">57.021460</font></td> <td class="xl64" align="right"><font color="#000000">57.052000</font></td> <td class="xl64" align="right"><font color="#000000">57.051900</font></td> <td class="xl64" align="right"><font color="#000000">57.021464</font></td> <td class="xl64" align="right"><font color="#000000">57.051320</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00068</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Histidine</font></td> <td><font color="#000000">H</font></td> <td class="xl64" align="right"><font color="#000000">137.058910</font></td> <td class="xl64" align="right"><font color="#000000">137.141200</font></td> <td class="xl64" align="right"><font color="#000000">137.141100</font></td> <td class="xl64" align="right"><font color="#000000">137.058912</font></td> <td class="xl64" align="right"><font color="#000000">137.139280</font></td> <td class="xl64" align="right"><font color="#000000">-0.000002</font></td> <td class="xl65" align="right"><font color="#000000">0.00192</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Isoleucine</font></td> <td><font color="#000000">I</font></td> <td class="xl64" align="right"><font color="#000000">113.084060</font></td> <td class="xl64" align="right"><font color="#000000">113.159500</font></td> <td class="xl64" align="right"><font color="#000000">113.159400</font></td> <td class="xl64" align="right"><font color="#000000">113.084064</font></td> <td class="xl64" align="right"><font color="#000000">113.157640</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00186</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Leucine</font></td> <td><font color="#000000">L</font></td> <td class="xl64" align="right"><font color="#000000">113.084060</font></td> <td class="xl64" align="right"><font color="#000000">113.159500</font></td> <td class="xl64" align="right"><font color="#000000">113.159400</font></td> <td class="xl64" align="right"><font color="#000000">113.084064</font></td> <td class="xl64" align="right"><font color="#000000">113.157640</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00186</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Lysine</font></td> <td><font color="#000000">K</font></td> <td class="xl64" align="right"><font color="#000000">128.094960</font></td> <td class="xl64" align="right"><font color="#000000">128.174200</font></td> <td class="xl64" align="right"><font color="#000000">128.174100</font></td> <td class="xl64" align="right"><font color="#000000">128.094963</font></td> <td class="xl64" align="right"><font color="#000000">128.172280</font></td> <td class="xl64" align="right"><font color="#000000">-0.000003</font></td> <td class="xl65" align="right"><font color="#000000">0.00192</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Methionine</font></td> <td><font color="#000000">M</font></td> <td class="xl64" align="right"><font color="#000000">131.040490</font></td> <td class="xl64" align="right"><font color="#000000">131.198600</font></td> <td class="xl64" align="right"><font color="#000000">131.192600</font></td> <td class="xl64" align="right"><font color="#000000">131.040485</font></td> <td class="xl64" align="right"><font color="#000000">131.196060</font></td> <td class="xl64" align="right"><font color="#000000">0.000005</font></td> <td class="xl65" align="right"><font color="#000000">0.00254</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Phenylalanine</font></td> <td><font color="#000000">F</font></td> <td class="xl64" align="right"><font color="#000000">147.068410</font></td> <td class="xl64" align="right"><font color="#000000">147.176600</font></td> <td class="xl64" align="right"><font color="#000000">147.176600</font></td> <td class="xl64" align="right"><font color="#000000">147.068414</font></td> <td class="xl64" align="right"><font color="#000000">147.173860</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00274</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Proline</font></td> <td><font color="#000000">P</font></td> <td class="xl64" align="right"><font color="#000000">97.052760</font></td> <td class="xl64" align="right"><font color="#000000">97.116700</font></td> <td class="xl64" align="right"><font color="#000000">97.116700</font></td> <td class="xl64" align="right"><font color="#000000">97.052764</font></td> <td class="xl64" align="right"><font color="#000000">97.115180</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00152</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Serine</font></td> <td><font color="#000000">S</font></td> <td class="xl64" align="right"><font color="#000000">87.032030</font></td> <td class="xl64" align="right"><font color="#000000">87.078200</font></td> <td class="xl64" align="right"><font color="#000000">87.078200</font></td> <td class="xl64" align="right"><font color="#000000">87.032028</font></td> <td class="xl64" align="right"><font color="#000000">87.077300</font></td> <td class="xl64" align="right"><font color="#000000">0.000002</font></td> <td class="xl65" align="right"><font color="#000000">0.00090</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Threonine</font></td> <td><font color="#000000">T</font></td> <td class="xl64" align="right"><font color="#000000">101.047680</font></td> <td class="xl64" align="right"><font color="#000000">101.105100</font></td> <td class="xl64" align="right"><font color="#000000">101.105100</font></td> <td class="xl64" align="right"><font color="#000000">101.047678</font></td> <td class="xl64" align="right"><font color="#000000">101.103880</font></td> <td class="xl64" align="right"><font color="#000000">0.000002</font></td> <td class="xl65" align="right"><font color="#000000">0.00122</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Tryptophan</font></td> <td><font color="#000000">W</font></td> <td class="xl64" align="right"><font color="#000000">186.079310</font></td> <td class="xl64" align="right"><font color="#000000">186.213300</font></td> <td class="xl64" align="right"><font color="#000000">186.213200</font></td> <td class="xl64" align="right"><font color="#000000">186.079313</font></td> <td class="xl64" align="right"><font color="#000000">186.209900</font></td> <td class="xl64" align="right"><font color="#000000">-0.000003</font></td> <td class="xl65" align="right"><font color="#000000">0.00340</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Tyrosine</font></td> <td><font color="#000000">Y</font></td> <td class="xl64" align="right"><font color="#000000">163.063330</font></td> <td class="xl64" align="right"><font color="#000000">163.176000</font></td> <td class="xl64" align="right"><font color="#000000">163.176000</font></td> <td class="xl64" align="right"><font color="#000000">163.063329</font></td> <td class="xl64" align="right"><font color="#000000">163.173260</font></td> <td class="xl64" align="right"><font color="#000000">0.000001</font></td> <td class="xl65" align="right"><font color="#000000">0.00274</font></td> </tr> <tr style="height: 15pt;" height="20"> <td style="height: 15pt;" height="20"><font color="#000000">Valine</font></td> <td><font color="#000000">V</font></td> <td class="xl64" align="right"><font color="#000000">99.068410</font></td> <td class="xl64" align="right"><font color="#000000">99.132600</font></td> <td class="xl64" align="right"><font color="#000000">99.132600</font></td> <td class="xl64" align="right"><font color="#000000">99.068414</font></td> <td class="xl64" align="right"><font color="#000000">99.131060</font></td> <td class="xl64" align="right"><font color="#000000">-0.000004</font></td> <td class="xl65" align="right"><font color="#000000">0.00154</font></td> </tr> </tbody> </table> <font color="#000000"><br> avg mono delta: -0.00000110<br> avg avg delta: 0.001756<br> <br> 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<br> Not a huge number in the average mass domain, but enough to make me worry.<br> <br> 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.:<br> <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.matrixscience.com/help/aa_help.html">http://www.matrixscience.com/help/aa_help.html</a><br> <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.i-mass.com/guide/aamass.html">http://www.i-mass.com/guide/aamass.html</a> (this looks like a scan of the Waters reference, same format and values)<br> <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://musclesurf.com/beverly-mass-amino.html">http://musclesurf.com/beverly-mass-amino.html</a> (this is not an amino acid mass reference, but included for completeness) ;)<br> <br> More importantly, I couldn't find any amino acid average mass references that looked like they were calculated from the NIST atomic weights.<br> <br> 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. :)<br> <br> Thanks,<br> Matt<br> </font> <pre wrap=""> <hr size="4" width="90%"> ------------------------------------------------------------------------- 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 <a class="moz-txt-link-freetext" href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a></pre> <pre wrap=""> <hr size="4" width="90%"> _______________________________________________ Psidev-pi-dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a> </pre> </blockquote> <br> <pre class="moz-signature" cols="72">-- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 <a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a> <a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a> Matrix Science Ltd. is registered in England and Wales Company number 3533898</pre> </body> </html> |
