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Modification localization #71

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
As some post-identification "modification scoring" algorithms can limit the 
location to SOME positions, we could think about allowing a comma-separated 
list of integers as location attribute. Specifying the algorithm names should 
be possible through CV terms. Specifying their resulting score values should be 
possible by annotating CV terms to <SpectrumIdentificationItem>.

Original issue reported on code.google.com by eisena...@googlemail.com on 9 Sep 2012 at 2:38

GoogleCodeExporter commented 8 years ago 
During the San Diego meeting Andy suggested a work-around for that issue using 
CV terms; and that suggestion was discussed (and agreed?). 
Please could anyone add a link to meeting minutes or other documentation, what 
that suggestion / decision was?

Original comment by eisena...@googlemail.com on 9 Sep 2012 at 7:27

GoogleCodeExporter commented 8 years ago 
I would also like to emphasize the importance of adding localization scoring 
(journals have done the same).  I understand there are complexities but as long 
as the algorithm is documented, the files should be easy enough to read (e.g., 
during protein grouping and/or quantitation).  My current work around 
(NCI/CPTAC common pipeline) is to convert the file to TSV and add score columns 
for phospho data -- not ideal.

Cheers -

Paul

Original comment by rudni...@gmail.com on 9 Jan 2013 at 2:00

GoogleCodeExporter commented 8 years ago 
Mod localisation has been further discussed at PSI2013.

Some sketches of how this can be done (examples to follow here), but still a 
number of open issues.

ACTION: Andy to coordinate building some example encodings and circulate. Will 
need some calls and a recommendation document writing.

Original comment by andrewro...@googlemail.com on 17 Apr 2013 at 1:57