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HUPO-PSI / mzIdentML

Repository for mzIdentML and the corresponding examples
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Examples using non-exported Unimod crosslink mods #143

Open chambm opened 5 months ago

chambm commented 5 months ago

I'm not really sure whether this is a Unimod problem or an example file problem, but the multiple_spectra and scores_and_thresholds examples for 1.3 use UNIMOD accessions that are not present in either unimod.xml or unimod.obo. The accessions are accessible on Unimod's web form and it's not clear from looking at the missing entries why they are missing from the exported files. But there are many Xlink mods that do make it into the exported files, so the example files should probably use those.

<cvParam accession="UNIMOD:1842" cvRef="UNIMOD" name="Xlink:DSSO"/> <cvParam accession="UNIMOD:2000" name="Xlink:SDA" cvRef="UNIMOD"/>

lutzfischer commented 2 months ago

the reason here is that there are actually two unimod.xml versions. The "traditional" one and a new one that has been expanded to hold crosslinker relevant information.

Description is here: http://www.unimod.org/xlink.html XML file: http://www.unimod.org/xml/unimod_xl.xml Schema: http://www.unimod.org/xmlns/schema/unimod_2/unimod_2.xsd

Not sure what is the plan for merging.

edeutsch commented 2 months ago

This came up recently for ProteomeXchange and PanoramaPublic. Since very few systems seem to use this parallel system, the solution was to select a different Unimod entry that had the same delta mass and seemed effectively the same and was present in the main export file.

It does seem it would be useful to understand what the intent of Unimod is: is the intent for the foreseeable future to have two export files and all of our software systems ought to start using both files instead of the main one? Or can than be merged at the source?

chambm commented 2 months ago

It seems the unimod_xl.xml file does not currently have a corresponding OBO file, which is what I use. I don't have much trouble adding another OBO file, so I've contacted the Unimod folks and they're going to add that unimod_xl.obo. I understand why they did it (the xlink page explains the compatibility concerns), but it would be nice if they added a 3rd artifact (e.g. "unimod_xl_all.xml") that combined the two files.