report of neutral losses

[GoogleCodeExporter]

At the moment only some fixed neutral losses are possible for fragmentation 
information (e.g. "y-ion-H2O").

E.g. Eric and Pierre-Alain suggest to separate the ion type from the neutral 
loss, e.g. having CV terms "y ion" and "neutral loss H2O" and be able to 
combine them freely.

CAUTION: There are also parameter for neutral loss considerations, e.g. "param: 
y-ion-H2O" for Mascot. These are not affected!

Original issue reported on code.google.com by eisena...@googlemail.com on 11 Apr 2011 at 3:43

[GoogleCodeExporter]

PRIDE team asked to think about the consequence of having separate CV terms:
then the size of the mzIdentML files and the objects and database entries and 
complexity of the object model would grow .

Combined "ion type - neutral loss type" terms in the CV would help to reduce 
this complexity. Of course, the CV file would grow, but we already have tons of 
terms.

Original comment by eisena...@googlemail.com on 12 Apr 2011 at 10:02

[GoogleCodeExporter]

We agreed on the proposal from Eric and Pierre-Alain.

New cvParams will be created describing the ion types and the various neutral 
losses. Furthermore, the old cvParams that currently describe the fragment ion 
types will be set obsolete. David from the EBI will take care of the ontology 
changes.

Original comment by johannes...@gmail.com on 13 Apr 2011 at 8:54

• Changed state: Started

[GoogleCodeExporter]

We agreed on the suggested changes. The cv will be updated by David (EBI) 
accordingly.

Original comment by johannes...@gmail.com on 21 Apr 2011 at 4:04

• Changed state: Done