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

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Hi Phil,

Just to be sure I've not misunderstood... from below, each fragment ion 
takes approx 500 bytes. Lets assume a conservative average of 20 
fragment matches per spectrum and a modest search with 100k spectra. 
Assuming that we just report fragment matches for the top match for each 
spectrum, this would result in a file that is 500 x 20 x 100,000 = 1Gb. 
If we reported fragment matches for the the top 10 matches for each 
spectrum, this would be 10Gb. Is this reasonable and acceptable?

David

Phil Jones @ EBI wrote:
> 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
> 
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