[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

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Comment #21 on issue 44 by dcreasy: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Regarding comment 19: Could we have an example with a modification with a  
neutral
loss defined?

The Mascot 15N example specifies Oxidation, and this can have a neutral  
loss of:
<umod:NeutralLoss avge_mass="64.1069" composition="H(4) C O S" flag="false"
mono_mass="63.998285">

Unfortunately, this seems to get lost in the conversion of the unimod.xml to
unimod.obo file, so this needs to be fixed. (Please, Martin!)

We should probably also specify, for each peptide match, which neutral  
loss, if any,
was 'dominant' and/or used for scoring.
Two pieces of information are required: The position and the loss, and  
there can of
course be multiple neutral losses.
For an example sequence of ALNVMESK, we'd want to specify that it is  
residue 5, and
the loss is 63.998285

There are 3 possible places for CV terms for this:
1.
     <Peptide id="peptide_21_1">
       <peptideSequence>ALNVMESK</peptideSequence>
       <Modification location="5" residues="M"  
monoisotopicMassDelta="15.994919">
         <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" />
--->    <cpParam accession="MS:1001xxx" name="neutral loss" cvRef="PSI-MS"
value="63.998285" />
       </Modification>
     </Peptide>


2. Or, it could be with other cv terms directly under:
     <SpectrumIdentificationItem id="SII_21_1"
But to cope with multiple pairs of values, this would require a structure  
similar to
the one under <Peptide> and therefore a change to the schema

3. In the fragment arrays (remember it's the 5th residue that is  
methionine):

     <SpectrumIdentificationItem id="SII_21_1"
       <Fragmentation>
         <IonType index="1 2 3 4 5" charge="1">
           <cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b  
ion"/>
           <FragmentArray values="72.09201 185.11602 299.24156 398.31937  
481.32147 "
Measure_ref="m_mz"/>
           <FragmentArray values="1.217 0.5765 0.9995 0.3048 0.6491"
Measure_ref="m_intensity"/>
           <FragmentArray values="0.0476 -0.0124 0.0702 0.0796 0.0446"
Measure_ref="m_error"/>
--->      <FragmentArray values="0, 0, 0, 0, 63.998285"  
Measure_ref="m_neutral_loss"/>
         </IonType>


And we'd also need to define m_neutral_loss:

     <AnalysisData>
       <SpectrumIdentificationList id="SIL_1" numSequencesSearched="4944">
         <FragmentationTable>
           <Measure id="m_m_neutral_loss">
--->        <cvParam cvRef="PSI-MS" accession="MS:100xxxx" name="product  
ion neutral
loss"/>
           </Measure>


I propose #3 - anyone disagree? Perhaps we can discuss at the telecon.


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