Closed GoogleCodeExporter closed 9 years ago
Original comment by eisena...@googlemail.com
on 10 Apr 2011 at 3:59
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
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
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
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
Original issue reported on code.google.com by
eisena...@googlemail.com
on 10 Apr 2011 at 3:58