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Issues from Korean community #62

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Kyung-Hoon Kwon asked the Korean Proteomics Informatics community abd forwarded 
some issues from Prof. Eun Ok Paek:

"1. Description of novel modification
She predicts the modification from the gap of mass peaks and biologist confirms 
it from wet lab experiment. When identifying quite novel modification, we need 
data format to describe it.

2. Details of disulfide bonding
When we find out the disulfide bonding, we want to keep the information on the 
Cysteines. Please provide the way to insert the information of Cysteine 
positions which make disulfide bonding.

3. Sumoylation information
About the sumoylation modification, it involves additional information, what 
kind of sumoylation occured."

Original issue reported on code.google.com by eisena...@googlemail.com on 10 Apr 2011 at 3:58

GoogleCodeExporter commented 8 years ago

Original comment by eisena...@googlemail.com on 10 Apr 2011 at 3:59

GoogleCodeExporter commented 8 years ago 
There were some comments from David Creasy to these issues:
reg. 1.: "This is already being discussed here:
http://code.google.com/p/psi-pi/issues/detail?id=57
... I think that there is some disagreement about what is best, so your input 
and the use case above is very valuable."

reg. 3.: "There are 7 different SUMO mods in Unimod - something that isn't 
there?
What information would you like to include? ..." This is also related to issue 
57

Original comment by eisena...@googlemail.com on 11 Apr 2011 at 9:07

GoogleCodeExporter commented 8 years ago 
Heidelberg:
reg. 2: no problem in specifying it as a PARAMETER (it is implicite for the 
special software or a CV Param of this SpectrumIdentificationProtocol).
For reporting the disulfide bond as a RESULT could probably be solved by new CV 
terms for use within <Peptide><Modification> like:
<cvParam accession="" name="Disulfide Bond" cvRef=""/>
<cvParam accession="" name="Disulfide Bond Partner Peptide" 
value="peptideB_id"/>
<cvParam accession="" name="Disulfide Bond Partner Peptide residue location" 
value="14"/>

Original comment by eisena...@googlemail.com on 12 Apr 2011 at 12:41

GoogleCodeExporter commented 8 years ago 
Heidelberg:
reg.3: Korean community will deliver an example, e.g. to clarify whether the 
cross-linked peptide is varying or known. In the former case searching seems to 
be impossible due to exponential search space. In the latter case a work-around 
could be to add all prefix or suffix masses as modifications.

Original comment by eisena...@googlemail.com on 12 Apr 2011 at 12:51

GoogleCodeExporter commented 8 years ago 
1. For the Sumoylation related information issue, it is a CV related problem. 
The are already terms in UniMod.
2. Details of disulfide bonding. At the moment this information cannot be 
extracted from any search engine, only from very specialized software. We 
decided that it is better to leave it out (at least for now) of our supported 
used cases. It could be supported probably as it was outlined in Heidelberg.

Original comment by javizca74@gmail.com on 21 Apr 2011 at 6:11