Re: [Psidev-pi-dev] FW: Spec doc

[Andreas B. <be...@in...>]

Hi Pierre-Alain,

> Just a question about these tolerances:
> if one need to specify a union of 2 sets of tolerances, such as 200ppm
> and 0.1Da (which means 200ppm with a minimum of 0.1Da), can one just
> have twice the pair of tolerances? for instance:
>       <FragmentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus
> value" value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221"
> unitName="dalton" unitCvRef="UO" />
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm"
> unitCvRef="UO" />
>       </FragmentTolerance>
At the moment this cannot be done. And just repeating the terms would be 
confusing in my opinion. The meaning that one is a minimum mass tolerance and 
the other one is the one used if it is greater than the threshold would not be 
directly obvious while reading the file. If we want to support such constructs 
we need schema changes here, I think. Are there any search engines which allow 
for such a specification of the tolerance?

Cheers,
A.



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