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Re: [Psidev-mod-vocab] [Psidev-pi-dev] Modifications
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From: David C. <dc...@ma...> - 2008-09-30 09:54:58
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Hi,<br>
<br>
Comments in line below:<br>
<br>
Jones, Andy wrote:
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<!--[if gte mso 9]><xml>
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<div class="Section1">
<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In the SpectrumIdentificationProtocol we have:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <SearchModification fixedMod="false"
><o:p></o:p></p>
<p class="MsoNormal"> <ModName accession="MOD:TODO"
name="SMA (N-term)" cvRef="PSI-MOD" /><o:p></o:p></p>
<p class="MsoNormal"> <MassValue value="127.063324"
unitAccession="PSI:xxxx" unitName="Da" /><o:p></o:p></p>
<p class="MsoNormal"> <SpecificityRule accession=""
cvRef="" name="" unitAccession=""
unitName="" /><o:p></o:p></p>
<p class="MsoNormal"> </SearchModification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On Peptide we have:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <Modification location="13"><o:p></o:p></p>
<p class="MsoNormal"> <pf:cvParam accession="TODO:
(requires quite
a bit of code)" name="SMA (K)" cvRef="PSI-MOD" /><o:p></o:p></p>
<p class="MsoNormal"> </Modification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">OR<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <SubstitutionModification
originalResidue="K" replacementResidue="M"
location="2"><o:p></o:p></p>
<p class="MsoNormal"> <pf:cvParam cvRef=""
accession="" name=""/><o:p></o:p></p>
<p class="MsoNormal"> </SubstitutionModification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(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).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">OR<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <CustomModification location="2"
monoisotopicMassDelta="21.21" count="1" residue = “M”><o:p></o:p></p>
<p class="MsoNormal"> <pf:cvParam cvRef=""
accession="" name=""/><o:p></o:p></p>
<p class="MsoNormal"> </CustomModification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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?</p>
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</blockquote>
Um, I don't think so. It looks to me as though Oxidation of Methionine
is possibly missing PSI-MOD at the moment...<br>
I would expect there to be a DiffFormula: "O 1" and from unimod the
PSI-MS name is "Oxidation".<br>
So, it looks as though something may be wrong here... I've cc'd
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a> so hopefully someone will
correct/enlighten us.<br>
(The .obo file hasn't been updated since 20th April, and I know that
there have been changes since then.)<br>
<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Comments on current schema:<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->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.</p>
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</blockquote>
Sounds fine. And the CV would be optional too?<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"> I think the
count attribute
is just confusing, if two modifications have been identified, just have
two
entries of the Modification element? </p>
</div>
</blockquote>
I don't personally find the count attribute confusing, but don't have a
strong preference. Also, see next item.<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;">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?</p>
</div>
</blockquote>
Not necessarily. Suppose that you have 2 phosphorylated residues, PMF
and the peptide is STYSTYSTYK<br>
I still don't see how to encode this?<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"> <o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->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?)</p>
</div>
</blockquote>
OK<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->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)?</p>
</div>
</blockquote>
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.<br>
(Also, I don't think that PSI-MOD should have this, but that's a
separate issue...)<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->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.<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->SubstitutionMod inherits a mandatory
association to
Param, this needs to be changed since in most cases a CV term would not
be
required.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thoughts?<o:p></o:p></p>
<p class="MsoNormal">Cheers, Andy<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
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