Menu
▾
▴
psidev-pi-dev
|
From: Matthew C. <mat...@va...> - 2008-10-13 15:12:52
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> </head> <body alink="#ee0000" bgcolor="#ffffff" link="#0000ee" text="#c0c0c0" vlink="#551a8b"> <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 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 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 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 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 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> </body> </html> |
|
From: David C. <dc...@ma...> - 2008-10-13 16:29:41
|
<!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> |
|
From: Brendan M. <brendanx@u.washington.edu> - 2008-10-13 16:40:23
|
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 > |
|
From: Matthew C. <mat...@va...> - 2008-10-13 17:30:01
|
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 |
|
From: David C. <dc...@ma...> - 2008-10-13 17:50:46
|
Hi Matt, Ah yes... looks as though we've not updated the help page since we made the change to use unimod. You can see the residue masses calculated in Unimod by searching for <umod:amino_acids> in the xml here: http://www.unimod.org/xml/unimod.xml F: 147.1739 Y: 163.1733 T: 101.1039 Which are the same as the NIST values (but rounded). Sorry about that, we'll update the help page.... David Matthew Chambers wrote: > 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 -- 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 |
|
From: Matthew C. <mat...@va...> - 2008-10-13 17:34:22
|
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 > > |
|
From: Brendan M. <brendanx@u.washington.edu> - 2008-10-13 18:18:35
|
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 >> >> >> |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X