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From: Jones, A. <And...@li...> - 2008-10-16 12:37:13
|
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 16 October 2008 12:29
> To: psi...@li...
> Subject: [Psidev-pi-dev] AnalysisXML PMF Example
>
> Hi All,
>
> There's an example PMF file here:
>
> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml
>
> The only small problem that I can see is that for
> <SpectrumIdentificationItem>
>
> the schema has:
> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
> maxOccurs="unbounded"/>
> <xsd:element ref="pf:Param" maxOccurs="unbounded"/>
>
> and I can't think of any required CV here
>
> To find it, search for
> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
> to say here here"
>
> I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees?
>
> David
>
> --
> 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
>
>
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|
|
From: David C. <dc...@ma...> - 2008-10-16 11:29:33
|
Hi All, There's an example PMF file here: http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? David -- 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: Jones, A. <And...@li...> - 2008-10-15 15:41:24
|
Last week on the call we decided on manually writing the OBO file... not ideal
but it is fairly easy.
The only plus side of OBO is that the ProDac people seem to be willing to make
sure that the validator works with schema + mapping file + OBO CV, I suspect
this would require quite a lot more work if we switched to OWL. Also, PSI wants
to have a coordinated CV strategy for all WGs – this means OBO for all us, or
opening up an old argument again J
Cheers
Andy
From: Angel Pizarro [mailto:an...@ma...]
Sent: 15 October 2008 15:33
To: psi...@li...
Subject: [Psidev-pi-dev] Have I ever mentioned that I don't like OBO edit?
So in creating CV terms for the various enzymes it is legal in the OBO format to
add any "name: value" pair to a term, but OBO-edit does not support this
feature. It will not even show the annotation if it is put manually in place. I
wanted to add a specific place for a "cleavage_rule_regx" but this won't fly in
OBO-edit
As for using another ontology editor, such as Protoge, it seems that the java
library used to transalate OBO into OWL will apply th ecomment rule to any
shriek ("!") even if it is escaped. Trying the perl tools now to see if they are
any better, but I would like to put on the table (again) that we use some other
format and tool for our CV other than OBO and OBO edit. The situation is uch
that I am even considering writing some ontology editing tool myself.
Any thought on this by anyoen?
-angel
|
|
From: Angel P. <an...@ma...> - 2008-10-15 15:26:09
|
So in creating CV terms for the various enzymes it is legal in the OBO
format to add any "name: value" pair to a term, but OBO-edit does not
support this feature. It will not even show the annotation if it is put
manually in place. I wanted to add a specific place for a
"cleavage_rule_regx" but this won't fly in OBO-edit
As for using another ontology editor, such as Protoge, it seems that the
java library used to transalate OBO into OWL will apply th ecomment rule to
any shriek ("!") even if it is escaped. Trying the perl tools now to see if
they are any better, but I would like to put on the table (again) that we
use some other format and tool for our CV other than OBO and OBO edit. The
situation is uch that I am even considering writing some ontology editing
tool myself.
Any thought on this by anyoen?
-angel
|
|
From: David C. <dc...@ma...> - 2008-10-15 15:10:37
|
Hi everyone, There will be an AnalysisXML working group conference call on Thursday at: http://www.timeanddate.com/worldclock/fixedtime.html?day=16&month=10&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/376 Agenda: 1. Review of minutes from last week. Looks as though many things have been done! 2. Review of the list of example files - what others are required? See: http://psidev.info/index.php?q=node/319#deliverablequicklinks for the current list. 3. Progress with mapping file. Current file at: http://code.google.com/p/psi-pi/source/browse/trunk/cv/axml-mapping.xml 4. The CV. What still needs doing and who is going to do it. Current obo file at: http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo 5. AOB Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 -- 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: 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 >> >> >> |
|
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 |
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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 > > |
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From: Matthew C. <mat...@va...> - 2008-10-13 17:30:01
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Hi David, The masses on this page http://www.matrixscience.com/help/aa_help.html do not appear to use the IUPAC atomic weights (which are the same as the NIST atomic weights). It's hard to tell because of the rounding, but several amino acids seem to be rounding off according to the Waters avg or at least something not quite the NIST avg: Waters NIST Mascot F 147.176600 147.173860 147.18 Y 163.176000 163.173260 163.18 Then there's this residue, which strangely rounds with NIST, so perhaps it is using the 12.01085 number Brendan mentioned. T 101.105100 101.103880 101.10 -Matt David Creasy wrote: > Hi Matt, > > Unimod (and hence Mascot) calculates residue masses from IUPAC atomic > weights: > > http://www.unimod.org/masses.html > http://www.webelements.com/periodicity/atomic_weight/ > > We are 'skirting' the problem in analysisXML by allowing the mass > values used by the search engine to be recorded in the analysisXML > instance documents. Any software that reads analysisXML documents > should probably use those values. > > David > > Matthew Chambers wrote: >> Hi all, >> >> Some discussion has come up within the ProteoWizard group and some >> collaborators (Jimmy Eng and Brendan MacLean) about how to calculate >> amino acid average masses. Currently, we are using the atomic weights >> from NIST: >> http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=html&isotype=some >> >> We calculate average mass (molecular weight) of a chemical formula in >> ProteoWizard by <count of element> * <atomic weight of element>. But >> when we calculate the average masses of the amino acids and then >> compare these to the online references for amino acid masses, the >> discrepancies are (IMO) unacceptable. >> >> A table showing some different values and references: >> expasy = >> http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html >> waters = a laminated reference sheet I have from Waters; it uses >> these atomic weights: C=12.011 H=1.00794 O=15.9994 N=14.00674 S=32.066 >> pwiz avg = element count * NIST atomic weight >> >> >> >> Waters mono Waters avg expasy avg pwiz mono pwiz avg Waters - >> pwiz for mono Waters - pwiz for avg >> Alanine A 71.037110 71.078800 71.078800 71.037114 71.077900 >> -0.000004 0.00090 >> Arginine R 156.101110 156.187600 156.187500 156.101111 >> 156.185680 -0.000001 0.00192 >> Asparagine N 114.042930 114.103900 114.103800 114.042927 >> 114.102640 0.000003 0.00126 >> Asparticacid D 115.026940 115.088600 115.088600 115.026943 >> 115.087400 -0.000003 0.00120 >> Cysteine C 103.009190 103.144800 103.138800 103.009184 >> 103.142900 0.000006 0.00190 >> Glutamicacid E 129.042590 129.115500 129.115500 129.042593 >> 129.113980 -0.000003 0.00152 >> Glutamine Q 128.058580 128.130800 128.130700 128.058578 >> 128.129220 0.000002 0.00158 >> Glycine G 57.021460 57.052000 57.051900 57.021464 57.051320 >> -0.000004 0.00068 >> Histidine H 137.058910 137.141200 137.141100 137.058912 >> 137.139280 -0.000002 0.00192 >> Isoleucine I 113.084060 113.159500 113.159400 113.084064 >> 113.157640 -0.000004 0.00186 >> Leucine L 113.084060 113.159500 113.159400 113.084064 >> 113.157640 -0.000004 0.00186 >> Lysine K 128.094960 128.174200 128.174100 128.094963 >> 128.172280 -0.000003 0.00192 >> Methionine M 131.040490 131.198600 131.192600 131.040485 >> 131.196060 0.000005 0.00254 >> Phenylalanine F 147.068410 147.176600 147.176600 147.068414 >> 147.173860 -0.000004 0.00274 >> Proline P 97.052760 97.116700 97.116700 97.052764 97.115180 >> -0.000004 0.00152 >> Serine S 87.032030 87.078200 87.078200 87.032028 87.077300 >> 0.000002 0.00090 >> Threonine T 101.047680 101.105100 101.105100 101.047678 >> 101.103880 0.000002 0.00122 >> Tryptophan W 186.079310 186.213300 186.213200 186.079313 >> 186.209900 -0.000003 0.00340 >> Tyrosine Y 163.063330 163.176000 163.176000 163.063329 >> 163.173260 0.000001 0.00274 >> Valine V 99.068410 99.132600 99.132600 99.068414 99.131060 >> -0.000004 0.00154 >> >> >> avg mono delta: -0.00000110 >> avg avg delta: 0.001756 >> >> For a peptide of 20 residues, the average delta for average mass >> calculations between the NIST atomic weights and the Waters atomic >> weights would be: 0.03512 >> Not a huge number in the average mass domain, but enough to make me >> worry. >> >> I think it's pretty clear that the 12.011 value for carbon is closer >> to the atomic weight used in the amino acid references that are >> widely used in the field. Several other references which I couldn't >> easily copy and paste also used similar average masses, e.g.: >> http://www.matrixscience.com/help/aa_help.html >> http://www.i-mass.com/guide/aamass.html (this looks like a scan of >> the Waters reference, same format and values) >> http://musclesurf.com/beverly-mass-amino.html (this is not an amino >> acid mass reference, but included for completeness) ;) >> >> More importantly, I couldn't find any amino acid average mass >> references that looked like they were calculated from the NIST atomic >> weights. >> >> So the question is: what atomic weights should researchers use to >> calculate amino acid masses? I suspect most software just stores the >> amino acid masses directly and avoids the problem, but it's an >> interesting issue to address for the PSI and more specifically the >> PSI-PI. :) >> >> Thanks, >> Matt >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 |
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From: Brendan M. <brendanx@u.washington.edu> - 2008-10-13 16:40:23
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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 > |
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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> |
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From: Matthew C. <mat...@va...> - 2008-10-13 15:12:52
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<!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: Jones, A. <And...@li...> - 2008-10-13 14:07:35
|
Hi all, A new version of the spec document has been uploaded by SVN (in the specification_document directory), and previous versions have been put in a subfolder. I think the document is getting there... Main tasks still to do: - Finish section on use cases when we have finally agreed the list online and made all the example files. - Import some parts of the example files to demonstrate a few specific points - Import the autogenerated documentation Before we can submit, the main outstanding issues are: - CV - looking through the CV there is still a fair bit of work to do, there's quite a few terms with missing or incorrect documentation - Mapping file - Finish example files. Prior to the call on Thurs, can we have a think about how we plan to get the CV into shape and discuss it as a main agenda item... Also new schema uploaded with a few bits of improved documentation. Cheers Andy |
|
From: Jones, A. <And...@li...> - 2008-10-13 08:55:50
|
Agreed - the two separate use cases are much clearer and can be supported. Cheers, Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 10 October 2008 17:06 > To: Jones, Andy > Cc: psi...@li... > Subject: Re: [Psidev-pi-dev] enzyme definition > > Hi all, > > Yes, the use case really isn't very clear (my fault) - and looking back > through some notes I think we are reading much more into this than is > required. It also looks as though I've 'mangled together' two separate > use cases that should be 1. I propose 2 different uses cases: > > 1. A PMF search and an MS-MS search of the same sample can be saved in > the same instance document as long as the result is one combined protein > list. > > 2. It should be possible to combine the results from multiple search > engines into one AnalysisXML document. For example, the peptide > identification results from two different search engines could be > combined using a third tool to give one set of protein results. > > > We don't have an example for #1 (but it's easy to produce one) > The MPC_example.axml is an example of the second case, and I can think > of at least one other tool that will want to produce something similar... > > I don't think that this would be moving the goal posts... any comments? > > http://psidev.info/index.php?q=node/371 > > David > > > Jones, Andy wrote: > > Hi all, > > > > I'm not sure we have completely solved this one: > > > > use case 3: > > > > "It should be possible to add the results of new searches to an existing instance > document. For example, a PMF search and an MS-MS search of the same sample > could be saved in the same instance document" > > > > In reality this use case is only be supported if there is one ProteinDetection > event producing one ProteinDetectionList i.e. protein detection was done taking > evidence from both PMF and MS/MS. > > > > I don't think we can really support it if we are implying that new proteins were > detected in a separate process then added to the same ProteinDetectionList for > two reasons: > > 1) It would be pretty difficult to sort out which proteins came from which process > when looking at the results > > 2) The entire list can have CVParams e.g. giving stats about the process such as > numSequences or such like, these wouldn't make sense if the list contained > results from more than one process. > > > > We should clarify the use case that we only supporting the more specific use > case above, or we need to change the schema to allow more than one > ProteinDetectionList (which we previously voted against to avoid the problem of > "what are the intermediate/final results"). > > > > Cheers > > Andy > > > > > > > > > > > > > >> -----Original Message----- > >> From: Martin Eisenacher [mailto:mar...@ru...] > >> Sent: 09 October 2008 17:31 > >> To: 'David Creasy'; psi...@li... > >> Subject: Re: [Psidev-pi-dev] enzyme definition > >> > >> Dear PSI-PI workers, > >> > >> I committed minor schema changes (as agreed in TeleCon 9th of October): > >> > >> 1) changed cardinality of <cvParam> child of <Enzyme> to: one to many (to > allow > >> synonyms) > >> > >> 2) restricted CTermGain and NTermGain to "[A-Za-z0-9 ] (basic letters of a > >> chemical formula) (can be refined later) > >> > >> Bye > >> Martin > >> > >>> -----Ursprüngliche Nachricht----- > >>> Von: David Creasy [mailto:dc...@ma...] > >>> Gesendet: Wednesday, October 08, 2008 7:02 PM > >>> An: psi...@li... > >>> Betreff: Re: [Psidev-pi-dev] enzyme definition > >>> > >>> Hi Martin, > >>> > >>> No, they've not been added to the CV yet. There are still a couple of > >>> unresolved issues at: > >>> > >>> http://code.google.com/p/psi-pi/issues/detail?id=30#c30 > >>> > >>> Any comments welcome, and then we can add to the CV and sign off this > issue. > >>> > >>> David > >>> > >>> Martin Eisenacher wrote: > >>>> Hi Angel, hi David, > >>>> > >>>> I've seen some progress on the CV terms for common enzymes > >>>> including some OBO lines from Angel in the issue list. > >>>> > >>>> But the svn obo file seems to be unchanged. > >>>> Or have you changed the location? > >>>> > >>>> Would be great to use it in some examples... > >>>> > >>>> Bye > >>>> Martin > >>>> > >>>> > >>> -- > >>> 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 > >>> > >>> ------------------------------------------------------------------------- > >>> 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 > >> > >> ------------------------------------------------------------------------- > >> 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 > > > > ------------------------------------------------------------------------- > > 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...> - 2008-10-10 16:05:54
|
Hi all, Yes, the use case really isn't very clear (my fault) - and looking back through some notes I think we are reading much more into this than is required. It also looks as though I've 'mangled together' two separate use cases that should be 1. I propose 2 different uses cases: 1. A PMF search and an MS-MS search of the same sample can be saved in the same instance document as long as the result is one combined protein list. 2. It should be possible to combine the results from multiple search engines into one AnalysisXML document. For example, the peptide identification results from two different search engines could be combined using a third tool to give one set of protein results. We don't have an example for #1 (but it's easy to produce one) The MPC_example.axml is an example of the second case, and I can think of at least one other tool that will want to produce something similar... I don't think that this would be moving the goal posts... any comments? http://psidev.info/index.php?q=node/371 David Jones, Andy wrote: > Hi all, > > I'm not sure we have completely solved this one: > > use case 3: > > "It should be possible to add the results of new searches to an existing instance document. For example, a PMF search and an MS-MS search of the same sample could be saved in the same instance document" > > In reality this use case is only be supported if there is one ProteinDetection event producing one ProteinDetectionList i.e. protein detection was done taking evidence from both PMF and MS/MS. > > I don't think we can really support it if we are implying that new proteins were detected in a separate process then added to the same ProteinDetectionList for two reasons: > 1) It would be pretty difficult to sort out which proteins came from which process when looking at the results > 2) The entire list can have CVParams e.g. giving stats about the process such as numSequences or such like, these wouldn't make sense if the list contained results from more than one process. > > We should clarify the use case that we only supporting the more specific use case above, or we need to change the schema to allow more than one ProteinDetectionList (which we previously voted against to avoid the problem of "what are the intermediate/final results"). > > Cheers > Andy > > > > > > >> -----Original Message----- >> From: Martin Eisenacher [mailto:mar...@ru...] >> Sent: 09 October 2008 17:31 >> To: 'David Creasy'; psi...@li... >> Subject: Re: [Psidev-pi-dev] enzyme definition >> >> Dear PSI-PI workers, >> >> I committed minor schema changes (as agreed in TeleCon 9th of October): >> >> 1) changed cardinality of <cvParam> child of <Enzyme> to: one to many (to allow >> synonyms) >> >> 2) restricted CTermGain and NTermGain to "[A-Za-z0-9 ] (basic letters of a >> chemical formula) (can be refined later) >> >> Bye >> Martin >> >>> -----Ursprüngliche Nachricht----- >>> Von: David Creasy [mailto:dc...@ma...] >>> Gesendet: Wednesday, October 08, 2008 7:02 PM >>> An: psi...@li... >>> Betreff: Re: [Psidev-pi-dev] enzyme definition >>> >>> Hi Martin, >>> >>> No, they've not been added to the CV yet. There are still a couple of >>> unresolved issues at: >>> >>> http://code.google.com/p/psi-pi/issues/detail?id=30#c30 >>> >>> Any comments welcome, and then we can add to the CV and sign off this issue. >>> >>> David >>> >>> Martin Eisenacher wrote: >>>> Hi Angel, hi David, >>>> >>>> I've seen some progress on the CV terms for common enzymes >>>> including some OBO lines from Angel in the issue list. >>>> >>>> But the svn obo file seems to be unchanged. >>>> Or have you changed the location? >>>> >>>> Would be great to use it in some examples... >>>> >>>> Bye >>>> Martin >>>> >>>> >>> -- >>> 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 >>> >>> ------------------------------------------------------------------------- >>> 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 >> >> ------------------------------------------------------------------------- >> 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 > > ------------------------------------------------------------------------- > 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 |
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From: Jones, A. <And...@li...> - 2008-10-10 11:07:03
|
Hi all, I'm not sure we have completely solved this one: use case 3: "It should be possible to add the results of new searches to an existing instance document. For example, a PMF search and an MS-MS search of the same sample could be saved in the same instance document" In reality this use case is only be supported if there is one ProteinDetection event producing one ProteinDetectionList i.e. protein detection was done taking evidence from both PMF and MS/MS. I don't think we can really support it if we are implying that new proteins were detected in a separate process then added to the same ProteinDetectionList for two reasons: 1) It would be pretty difficult to sort out which proteins came from which process when looking at the results 2) The entire list can have CVParams e.g. giving stats about the process such as numSequences or such like, these wouldn't make sense if the list contained results from more than one process. We should clarify the use case that we only supporting the more specific use case above, or we need to change the schema to allow more than one ProteinDetectionList (which we previously voted against to avoid the problem of "what are the intermediate/final results"). Cheers Andy > -----Original Message----- > From: Martin Eisenacher [mailto:mar...@ru...] > Sent: 09 October 2008 17:31 > To: 'David Creasy'; psi...@li... > Subject: Re: [Psidev-pi-dev] enzyme definition > > Dear PSI-PI workers, > > I committed minor schema changes (as agreed in TeleCon 9th of October): > > 1) changed cardinality of <cvParam> child of <Enzyme> to: one to many (to allow > synonyms) > > 2) restricted CTermGain and NTermGain to "[A-Za-z0-9 ] (basic letters of a > chemical formula) (can be refined later) > > Bye > Martin > > > -----Ursprüngliche Nachricht----- > > Von: David Creasy [mailto:dc...@ma...] > > Gesendet: Wednesday, October 08, 2008 7:02 PM > > An: psi...@li... > > Betreff: Re: [Psidev-pi-dev] enzyme definition > > > > Hi Martin, > > > > No, they've not been added to the CV yet. There are still a couple of > > unresolved issues at: > > > > http://code.google.com/p/psi-pi/issues/detail?id=30#c30 > > > > Any comments welcome, and then we can add to the CV and sign off this issue. > > > > David > > > > Martin Eisenacher wrote: > > > Hi Angel, hi David, > > > > > > I've seen some progress on the CV terms for common enzymes > > > including some OBO lines from Angel in the issue list. > > > > > > But the svn obo file seems to be unchanged. > > > Or have you changed the location? > > > > > > Would be great to use it in some examples... > > > > > > Bye > > > Martin > > > > > > > > > > -- > > 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 > > > > ------------------------------------------------------------------------- > > 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 > > > ------------------------------------------------------------------------- > 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 |
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From: Jones, A. <And...@li...> - 2008-10-10 09:20:01
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Hi all, New schema updated: - Moved numSequencesSearched to SpectrumIdentificationList - Changed element SpectraData_ref and attribute ref to element: InputSpectra and attribute: SpectraData_ref - Changed element SpectrumIdentificationList_ref to InputSpectrumIdentifications and attribute ref to SpectrumIdentificationList_ref - Some documentation added One minor problem was that the schema Martin uploaded yesterday evening was in conflict with my changes. I have re-added the changes below to my version and overwritten this. Going forward we should probably agree after each call who is going to make changes to the schema so we don't have different versions checked out at the same time. Cheers Andy > -----Original Message----- > From: Martin Eisenacher [mailto:mar...@ru...] > Sent: 09 October 2008 17:31 > To: 'David Creasy'; psi...@li... > Subject: Re: [Psidev-pi-dev] enzyme definition > > Dear PSI-PI workers, > > I committed minor schema changes (as agreed in TeleCon 9th of October): > > 1) changed cardinality of <cvParam> child of <Enzyme> to: one to many (to allow > synonyms) > > 2) restricted CTermGain and NTermGain to "[A-Za-z0-9 ] (basic letters of a > chemical formula) (can be refined later) > > Bye > Martin > > > -----Ursprüngliche Nachricht----- > > Von: David Creasy [mailto:dc...@ma...] > > Gesendet: Wednesday, October 08, 2008 7:02 PM > > An: psi...@li... > > Betreff: Re: [Psidev-pi-dev] enzyme definition > > > > Hi Martin, > > > > No, they've not been added to the CV yet. There are still a couple of > > unresolved issues at: > > > > http://code.google.com/p/psi-pi/issues/detail?id=30#c30 > > > > Any comments welcome, and then we can add to the CV and sign off this issue. > > > > David > > > > Martin Eisenacher wrote: > > > Hi Angel, hi David, > > > > > > I've seen some progress on the CV terms for common enzymes > > > including some OBO lines from Angel in the issue list. > > > > > > But the svn obo file seems to be unchanged. > > > Or have you changed the location? > > > > > > Would be great to use it in some examples... > > > > > > Bye > > > Martin > > > > > > > > > > -- > > 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 > > > > ------------------------------------------------------------------------- > > 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 > > > ------------------------------------------------------------------------- > 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 |
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From: Martin E. <mar...@ru...> - 2008-10-09 16:32:54
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Dear PSI-PI workers, I committed minor schema changes (as agreed in TeleCon 9th of October): 1) changed cardinality of <cvParam> child of <Enzyme> to: one to many (to allow synonyms) 2) restricted CTermGain and NTermGain to "[A-Za-z0-9 ] (basic letters of a chemical formula) (can be refined later) Bye Martin > -----Ursprüngliche Nachricht----- > Von: David Creasy [mailto:dc...@ma...] > Gesendet: Wednesday, October 08, 2008 7:02 PM > An: psi...@li... > Betreff: Re: [Psidev-pi-dev] enzyme definition > > Hi Martin, > > No, they've not been added to the CV yet. There are still a couple of > unresolved issues at: > > http://code.google.com/p/psi-pi/issues/detail?id=30#c30 > > Any comments welcome, and then we can add to the CV and sign off this issue. > > David > > Martin Eisenacher wrote: > > Hi Angel, hi David, > > > > I've seen some progress on the CV terms for common enzymes > > including some OBO lines from Angel in the issue list. > > > > But the svn obo file seems to be unchanged. > > Or have you changed the location? > > > > Would be great to use it in some examples... > > > > Bye > > Martin > > > > > > -- > 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 > > ------------------------------------------------------------------------- > 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 |
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From: Martin E. <mar...@ru...> - 2008-10-09 14:56:29
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> Each instance of cvParam should have a KeyRef for cvList (cvRef) but it would require putting in the > XPath of each one individually (I don't think XSD:KeyRef supports an XPath to select of node of a > particular name anywhere in the document). I can't be bothered adding all these KeyRefs at this stage > but we should probably try to do this before submission... More important seems, that the cv elements of the cvList have no "id" attribute, so all cvRef attributes point to nothing. Regarding KeyRefs I tried some syntax with * in the XPaths, but that didn't work indeed... Bye Martin > > -----Original Message----- > > From: Jones, Andy [mailto:And...@li...] > > Sent: 26 September 2008 10:44 > > To: psi...@li... > > Subject: [Psidev-pi-dev] New schema committed > > > > Some changes to the schema uploaded by SVN. As discussed on the call, it seems > > to make sense to have the summary collections at the top of the file e.g. cvList, > > AnalysisSoftware etc. > > > > > > > > ------------------------------------------------------------------------- > > 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 > > ------------------------------------------------------------------------- > 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 |
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From: Martin E. <mar...@ru...> - 2008-10-09 14:45:03
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I agree to drop the CustomModification element,
but think we need a "count" attribute for PMF or multiple modifications
on one amino acid in MS/MS (rare case).
We should suggest in the documentation not to use
<Modification>
<cvParam name = "phosphorylation to tyrosine"/>
</Modification>
<Modification>
<cvParam name = "phosphorylation to tyrosine"/>
</Modification>
but the variant with count="2".
I have no opinion whether to suggest
1) use CV term "phosph to tyrosine" and no residue attribute or
2) CV term "phosph" and attribute "residue=tyrosine"
(both may be possible and is correct).
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Tuesday, September 30, 2008 1:36 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] Modifications
I think the count attribute is just confusing, if two modifications have been identified, just have two entries of the
Modification element?
I don't personally find the count attribute confusing, but don't have a strong preference. Also, see next item.
There would still be an issue of how to specify which residue has been modified but basically this is the same issue for
standard and custom mods i.e. the CV tells you the mod and the residue?
Not necessarily. Suppose that you have 2 phosphorylated residues, PMF and the peptide is STYSTYSTYK
I still don't see how to encode this?
These two things are sort of related in that I'd like to only have one mechanism for describing mods if possible. My
suggestion is that it is done as follows:
<Modification>
<cvParam name = "phosphorylation"/>
</Modification>
<Modification>
<cvParam name = "phosphorylation"/>
</Modification>
Since from PMF this is all the information we have i.e. we don't know the location or the residue (we may have a mass
delta value though?).
If we know the residues modified, then it is encoded as follows:
<Modification location = "3">
<cvParam name = "phosphorylation to tyrosine"/>
</Modification>
<Modification location = "6">
<cvParam name = "phosphorylation to tyrosine"/>
</Modification>
I agree this use of CV terms doesn't appear ideal but the current schema allows you to encode the same information in
lots of different ways, say two tyrosines are phosphorylated:
<CustomMod count = "2" residue = "Y">
<cvParam name = "phosphorylation"/>
</CustomMod>
OR
<Modification>
<cvParam name = "phosphorylation to tyrosine"/>
</Modification>
<Modification>
<cvParam name = "phosphorylation to tyrosine"/>
</Modification>
OR
<CustomMod count = "2" >
<cvParam name = "phosphorylation to tyrosine"/>
</CustomMod>
I think we ought to discuss the pros and cons of encoding the mod and the residue modified in one single CV term - it
should work in theory but it seems like more work for parsers than just having an attribute for residue = "Y"...
Cheers, Andy
From: David Creasy [mailto:dc...@ma...]
Sent: 30 September 2008 10:55
To: psi...@li...
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] Modifications
Hi,
Comments in line below:
Jones, Andy wrote:
Hi all,
I'd like to get the mods part of the schema sorted in time for the call this week if possible. There are quite a few
different aspects in issues 3 and 35 so I'll try to summarise it here:
In the SpectrumIdentificationProtocol we have:
<SearchModification fixedMod="false" >
<ModName accession="MOD:TODO" name="SMA (N-term)" cvRef="PSI-MOD" />
<MassValue value="127.063324" unitAccession="PSI:xxxx" unitName="Da" />
<SpecificityRule accession="" cvRef="" name="" unitAccession="" unitName="" />
</SearchModification>
On Peptide we have:
<Modification location="13">
<pf:cvParam accession="TODO: (requires quite a bit of code)" name="SMA (K)" cvRef="PSI-MOD" />
</Modification>
OR
<SubstitutionModification originalResidue="K" replacementResidue="M" location="2">
<pf:cvParam cvRef="" accession="" name=""/>
</SubstitutionModification>
(Note the datatypes were set to int for original and replaceResidue so I have fixed this to be the same alphabet as for
pre and post).
OR
<CustomModification location="2" monoisotopicMassDelta="21.21" count="1" residue = "M">
<pf:cvParam cvRef="" accession="" name=""/>
</CustomModification>
PSI-MOD can specify a modification and the residue that has been modified, although the terms are not always intuitive
for our purposes. For example, as far as I can tell "oxidation to L-methionine sulfoxide" would be the standard term
for a methionine oxidation, correct?
Um, I don't think so. It looks to me as though Oxidation of Methionine is possibly missing PSI-MOD at the moment...
I would expect there to be a DiffFormula: "O 1" and from unimod the PSI-MS name is "Oxidation".
So, it looks as though something may be wrong here... I've cc'd psi...@li... so hopefully
someone will correct/enlighten us.
(The .obo file hasn't been updated since 20th April, and I know that there have been changes since then.)
Comments on current schema:
I'm not sure we need CustomModification, I would prefer just to have the Modification element, making location optional
and adding the mass delta attributes to Modification.
Sounds fine. And the CV would be optional too?
I think the count attribute is just confusing, if two modifications have been identified, just have two entries of the
Modification element?
I don't personally find the count attribute confusing, but don't have a strong preference. Also, see next item.
There would still be an issue of how to specify which residue has been modified but basically this is the same issue for
standard and custom mods i.e. the CV tells you the mod and the residue?
Not necessarily. Suppose that you have 2 phosphorylated residues, PMF and the peptide is STYSTYSTYK
I still don't see how to encode this?
I disagree that we should use the same element for the searched and the found modification. We do not need to report the
specificity on the found modifications and in most cases you would not report the mass delta for a found modification
(presumably this would only make any sense for MS1 data?)
OK
On SearchModification, are we agreed that we want to report the MassValue (i.e. mass of residue +/- mod) rather than say
a MassDelta (mass of mod only)?
No! I think a delta is better. Suppose that you are performing an 14N/15N experiment and want to use Oxidation. That
would mean having two separate SearchModifications.
(Also, I don't think that PSI-MOD should have this, but that's a separate issue...)
I think we should add documentation that MassValue is optional since the mod mass is part of the CV, but if reported the
MassValue "overrides" the mass value from the CV.
SubstitutionMod inherits a mandatory association to Param, this needs to be changed since in most cases a CV term would
not be required.
Thoughts?
Cheers, Andy
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--
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
|
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From: David C. <dc...@ma...> - 2008-10-08 18:28:48
|
Hi everyone, There will be an AnalysisXML working group conference call on Thursday at: http://www.timeanddate.com/worldclock/fixedtime.html?day=9&month=10&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/374 Agenda: 1. Use cases have been updated here: http://psidev.info/index.php?q=node/371 Any further comments? Comment for number 3 still to be resolved. 2. Progress with issues 3 and 35 from the issues list http://code.google.com/p/psi-pi/issues/list waiting on feedback from PSI-MOD group? 3. Enzyme issues: http://code.google.com/p/psi-pi/issues/detail?id=30 Final remaining issue (no enzyme!), plus who is going to add to CV. 4. Progress with CV (Jenny) 5. Progress with documentation (Andy, Martin, Eric) 6. Mono/average masses (Martin) http://code.google.com/p/psi-pi/issues/detail?id=37 7. Progress on outstanding issues from previous telecons: - MIAPE table (David) - still to do - Mascot N15 example (David) - Completed. - SVN tags for example instance docs (Phil) - n/a - Issue 28 - add fragmentation to CV (Phil) 8. AOB Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 -- 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 ------------------------------------------------------------------------- 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 ------------------------------------------------------------------------- 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 |
|
From: David C. <dc...@ma...> - 2008-10-08 17:02:35
|
Hi Martin, No, they've not been added to the CV yet. There are still a couple of unresolved issues at: http://code.google.com/p/psi-pi/issues/detail?id=30#c30 Any comments welcome, and then we can add to the CV and sign off this issue. David Martin Eisenacher wrote: > Hi Angel, hi David, > > I've seen some progress on the CV terms for common enzymes > including some OBO lines from Angel in the issue list. > > But the svn obo file seems to be unchanged. > Or have you changed the location? > > Would be great to use it in some examples... > > Bye > Martin > > -- 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...> - 2008-10-06 10:14:01
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Hi everyone, I've added a Mascot 14N/15N example again in the examples directory under SVN: http://code.google.com/p/psi-pi/source/browse/trunk/examples/Mascot_N15_example.axml After changes discussed a while back, there are still separate MassTables for 14N and 15N, but there's now only one SpectrumIdentificationList and there is a MassTable_ref for each peptide. Andy, looks as though there are no Keys / KeyRefs for the MassTable_ref? We'd use the same approach for a search engine that allows a mix of average and monoisotopic masses. Any feedback appreciated as always. David David Creasy wrote: > Minutes are here (thank you Phil): > > http://psidev.info/index.php?q=node/374 > > > > David Creasy wrote: >> Hi everyone, >> >> There will be an AnalysisXML working group conference call on Thursday >> at: >> http://www.timeanddate.com/worldclock/fixedtime.html?day=2&month=10&year=2008&hour=16&min=0&sec=0&p1=136 >> >> >> Minutes from last meeting at: >> http://psidev.info/index.php?q=node/372 >> >> Agenda: >> >> 1. Is a later time for calls possible to make it easier for Eric? >> >> 2. Review of comments on the use cases at: >> http://psidev.info/index.php?q=node/371 >> >> 3. Issues 3 and 35 from the issues list >> http://code.google.com/p/psi-pi/issues/list >> and subsequent email discussion on the list >> >> 4. Feedback from example instance docs >> >> 5. Progress with CV (Jenny) >> >> 6. Documentation (Andy, Martin, Eric) >> >> 7. Progress on outstanding issues from previous telecons: >> - MIAPE table (David) >> - Mascot N15 example (David) >> - SVN tags for example instance docs (Phil) >> - Mono/average masses (Martin) >> - Enzyme examples (David + others) >> - Issue 28 - fragmentation CV (Phil) >> >> 8. AOB >> >> Dial in details: >> >> + Germany: 08001012079 >> + Switzerland: 0800000860 >> + UK: 08081095644 >> + USA: 1-866-314-3683 >> + Generic international: +44 2083222500 (UK number) >> >> access code: 297427 >> > -- 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 |
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From: David C. <dc...@ma...> - 2008-10-06 09:13:52
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Minutes are here (thank you Phil): http://psidev.info/index.php?q=node/374 David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on Thursday at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=2&month=10&year=2008&hour=16&min=0&sec=0&p1=136 > > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/372 > > Agenda: > > 1. Is a later time for calls possible to make it easier for Eric? > > 2. Review of comments on the use cases at: > http://psidev.info/index.php?q=node/371 > > 3. Issues 3 and 35 from the issues list > http://code.google.com/p/psi-pi/issues/list > and subsequent email discussion on the list > > 4. Feedback from example instance docs > > 5. Progress with CV (Jenny) > > 6. Documentation (Andy, Martin, Eric) > > 7. Progress on outstanding issues from previous telecons: > - MIAPE table (David) > - Mascot N15 example (David) > - SVN tags for example instance docs (Phil) > - Mono/average masses (Martin) > - Enzyme examples (David + others) > - Issue 28 - fragmentation CV (Phil) > > 8. AOB > > Dial in details: > > + Germany: 08001012079 > + Switzerland: 0800000860 > + UK: 08081095644 > + USA: 1-866-314-3683 > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > -- 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 |
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From: Jones, A. <And...@li...> - 2008-10-03 12:20:30
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New schema committed following yesterday's discussion: -Updated modifications: removed CustomModification; Added residues attribute, average and mono mass delta to Modification; added some documentation - On SearchModification, changed MassValue to MassDelta - Several of the attributes still had an underscore, these have been removed - On ProteinDetectionProtocol, changed _runtimeParams to AnalysisParams; I've also uploaded an Excel spreadsheet in the CV directory that contains the XPaths for all the CVParams and some notes on the requirements for CV terms - we can use this build the mapping file. Cheers Andy |
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