Custom modifications in Nucleic Acid Search Engine

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1

Hi,

I’ve been trying to get NASE to map RNA using RNAse T1 but I can’t get it to identify cyclic phosphorylation on the oligos derived from the digestion. Can anyone help with this or with the addition of custom modifications to the list of modifications in the search engine?

Thanks a lot
Lucio

2

Hi Lucio!

I think for such algorithm-specific questions, it would be better to post on an OpenMS channel.

https://openms.readthedocs.io/en/latest/quick-reference/contact-us.html

There you will most likely find an RNA MS expert.

You probably need to add something in the KNIME/Eclipse/plugins/de.openms.*/payload/share/OpenMS/CHEMISTRY/Custom_RNA_modifications.tsv

Best wishes
Julianus

3

But then the KNIME nodes probably have to be rebuilt, since they only suggest the modifications that have been present at time of building.
Not the best solution. You probably need to ask the developer of the tool to add another option for custom modifications.

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