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Re: [Psidev-ms-dev] [Psidev-pi-dev] splitting series and loss concepts in CV
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From: David C. <dc...@ma...> - 2009-11-18 12:30:04
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Hi Eric,<br>
<br>
We had assumed that the losses/gains that accompany a modification are
currently defined as as part of the modification definition. In theory,
this cuts down the combinations a little. (However, even this doesn't
help define which loss/gain is actually being recorded). <br>
<br>
A split as you suggest sounds like a very good idea to me. We obviously
can't get rid of the existing CV terms, but we can mark them as
obsolete (or deprecated?). I don't think that any change is required to
the mzIdentML schema or to the validator, but we would need to update
examples and documentation at the next mzIdentML rev. <br>
<br>
So, we could keep the existing 'backbone' series, and just add new
losses terms?<br>
<br>
btw, have you relocated down south or maybe you are suggesting we need
terms:<br>
<br>
[Term]<br>
id: MS:123456<br>
name: frag: y'<br>
<br>
[Term]<br>
id: MS:987654<br>
name: all<br>
def: All imaginable losses. Only to be used with MS:123456... ;)<br>
<br>
David<br>
<br>
Eric Deutsch wrote:
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<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Hi mzIdentMLers, I have a
question for y’all:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">We have tried to reuse
some mzIdentML bits in TraML and have
hit a potential snag. This is in a section where we provide information
about
the interpretation of a peak. We have something like this:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><interpretation><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"> <cvParam cvRef="MS"
accession="MS:1001222" name="frag: b ion - H2O"/><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"> <cvParam cvRef="MS"
accession="MS:1000903" name="product ion series ordinal"
value="9"/><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"> <cvParam cvRef="MS"
accession="MS:1000904" name="product ion m/z delta"
value="-0.43"/><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"></interpretation><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">This is meant to indicate
the peak that is being referenced
may be interpreted (among more than one possible interpretation
sometimes) as being
0.43 Da away from the predicted m/z of the b9 ion with a single water
loss. This
often comes from a spectrum library which tends to identify peaks in
this way.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">From the CV, I find
something like this:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><img id="_x0000_i1025"
src="cid:par...@ma..." height="402"
width="251"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Now it seems like there
are at least a dozen losses that are
not super uncommon, including multiple losses. Going down the road
we’re
going, there will be a combinatorial explosion of terms if we aim to be
complete. For example, some things that the SpectraST code can deal
with when
identifying peaks in addition to single water and ammonia loss:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">+18 is water gain. -34 is
-NH3/-NH3, -35 is -NH3/-H2O and
-36 is -H2O/-H2O. -44 is -CO2, -45 is -HCONH2 and -46 is -HCOOH. There
is also
-64, -82 for -HOSCH3 and -HOSCH3/-H2O -- these are common when there is
an
oxidized methionine. Then there is -91 for CAM-cysteine and -80, -98
and -116
for phosphates<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">So where I’m going with
this is: can we split these
two concept categories and split the series (b,y,z, etc.) from the
losses that
could be incurred? Obviously this will impact mzIdentML.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Thanks,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Eric<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span
style="font-size: 12pt;"><o:p> </o:p></span></font></p>
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<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
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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
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