[Psidev-pi-dev] Fragment Ions in analysisXML - how it is currently handled in PRIDE (Issue 28)

[Phil J. @ E. <pj...@eb...>]

Hi,

Regarding Issue 28
<http://code.google.com/p/psi-pi/issues/detail?id=28> "support
reporting of fragment ions"

As a suggestion of how this might be tackled:

The latest development version of the PRIDE database includes a very
simple mechanism
for recording fragment ion information, illustrated below.  (Please
note - made up data.)

In this example, CV terms are used to define the type of ion and
related information
/ annotation.  Note that this is even more simple that the suggestion
made by Andy
above - no attempt is made here to indicate which residue has been
called for each
fragment ion - it is just listing the ions.

Also note that while the PeptideItem is referencing the mass spectrum (which is
reported in detail in the associated mzData file), the individual
fragment ions are
just reporting the m/z value and not attempting to make any kind of
hard reference to
the spectrum.

As you can see, this has been developed in collaboration with Waters,
with output
from the ProteinLynx Global Server. (Actual values / sequence have
been changed).

One possible change would be to make the m/z value an attribute of the
FragmentIon element, as this value will be mandatory and required to
relate the fragment ion to the correct peak on the mass spectrum.  The
CV used for the annotation would also need to be part of the PI CV ??

Note that in the existing model, there are other terms available, to
allow any kind of fragment ion to be described (not just B and Y ions)

In the context of analysisXML, the <FragmentIon/> elements would be
children of a <SpectrumIdentificationResultItem/>

best regards,

Phil.

<PeptideItem>
<Sequence>LFQQSQWTREVFSNSCK</Sequence>
<Start>435</Start>
<End>460</End>
<SpectrumReference>123</SpectrumReference>
<FragmentIon>
<cvParam cvLabel="Waters" accession="PLGS:00032" name="b ion" value="3"/>
<cvParam cvLabel="Waters" accession="PLGS:00024" name="product ion
m/z" value="379.2215"/>
<cvParam cvLabel="Waters" accession="PLGS:00025" name="product ion
intensity" value="1382.0"/>
<cvParam cvLabel="Waters" accession="PLGS:00026" name="product ion m/z
error" value="-7.1543"/>
<cvParam cvLabel="Waters" accession="PLGS:00027" name="product ion
retention time error" value="0.0207"/>
</FragmentIon>
<FragmentIon>
<cvParam cvLabel="Waters" accession="PLGS:00032" name="b ion" value="4"/>
<cvParam cvLabel="Waters" accession="PLGS:00024" name="product ion
m/z" value="534.2811"/>
<cvParam cvLabel="Waters" accession="PLGS:00025" name="product ion
intensity" value="1242.0"/>
<cvParam cvLabel="Waters" accession="PLGS:00026" name="product ion m/z
error" value="-8.2315"/>
<cvParam cvLabel="Waters" accession="PLGS:00027" name="product ion
retention time error" value="0.0029"/>
</FragmentIon>
<FragmentIon>
<cvParam cvLabel="Waters" accession="PLGS:00031" name="y ion" value="3"/>
<cvParam cvLabel="Waters" accession="PLGS:00024" name="product ion
m/z" value="394.1813"/>
<cvParam cvLabel="Waters" accession="PLGS:00025" name="product ion
intensity" value="1917.0"/>
<cvParam cvLabel="Waters" accession="PLGS:00026" name="product ion m/z
error" value="-14.7098"/>
<cvParam cvLabel="Waters" accession="PLGS:00027" name="product ion
retention time error" value="-0.0013"/>
</FragmentIon>
<FragmentIon>
<cvParam cvLabel="Waters" accession="PLGS:00035" name="y ion -H2O" value="3"/>
<cvParam cvLabel="Waters" accession="PLGS:00024" name="product ion
m/z" value="367.1669"/>
<cvParam cvLabel="Waters" accession="PLGS:00025" name="product ion
intensity" value="345.0"/>
<cvParam cvLabel="Waters" accession="PLGS:00026" name="product ion m/z
error" value="-18.767"/>
<cvParam cvLabel="Waters" accession="PLGS:00027" name="product ion
retention time error" value="0.0025"/>
</FragmentIon>
<additional>
<cvParam cvLabel="Waters" accession="PLGS:00014" name="precursor mass"
value="1971.9194"/>
<cvParam cvLabel="Waters" accession="PLGS:00015" name="precursor
intensity" value="181349.0"/>
<cvParam cvLabel="Waters" accession="PLGS:00016" name="precursor error
in ppm" value="0.8043"/>
<cvParam cvLabel="Waters" accession="PLGS:00017" name="precursor
retention time in minutes" value="57.3537"/>
<cvParam cvLabel="Waters" accession="PLGS:00019" name="product ion
mass RMS error" value="14.5969"/>
<cvParam cvLabel="Waters" accession="PLGS:00020" name="product ion
retention time RMS error" value="0.0093"/>
<cvParam cvLabel="Waters" accession="PLGS:00021" name="weighted
average charge state" value="2.2"/>
<cvParam cvLabel="Waters" accession="PLGS:00039" name="pass one match"
value="" />
</additional>
</PeptideItem>


--
Phil Jones
Senior Software Engineer
PRIDE Project Team
PANDA Group, EMBL-EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
UK.

Work phone: +44 1223 492662 (NEW NUMBER)
Skype: philip-jones