[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Cross-Linking fragment annotations (#32)

[Eugen N. <not...@gi...>]

We are trying to implement fragment annotations for cross-linked peptides in OpenMS and uploaded an example file under examples/1_2examples/crosslinking/OpenxQuest_example.mzid.

In the case of cross-linking we have fragments resulting from cleavages of both peptides in one spectrum. Therefore distributing the annotations between several SIIs would make further usage e.g. visualization of these annotations more complicated and the separation would not be possible in more complex fragmentation patterns, e.g. cross-linked fragments where both peptides were cleaved. So we would prefer to store the annotations for one PSM under one SII, e.g. the light alpha case.

The example suggests adapting FragmentArray to also carry strings (words) or have an additional array carrying these (not in the example). 
The specific CVs we would need are:
One Array for "cross-link chain" containing CV strings for "donor" or "acceptor" for each fragment.
One Array for "cross-link ion category" containing CV strings for "common ion" or "cross-linked ion" for each fragment.
The example file shows roughly how that could look like.

Another way to do it would be to introduce additional IonTypes and therefore separate these types into different arrays. In that case we would need all four combinations of donor/receiver with common/cross-linked


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