Hello everyone,
Is it possible to add a custom PTM modification? I would like to know if there is a way to define and include a user-specified PTM apart from the default modification list.
Welcome @Rajesh_saravanan
Hopefully we can explain how this works!
The fixed and variable modification choices exposed on the Galaxy MaxQuant form are derived from MaxQuant’s own modification definitions, not maintained separately by the Galaxy wrapper. The modifications available on the form are the only ones currently supported.
More details → FAQ: Including custom modifications into MaxQuant in Galaxy? / MaxQuant and MSstats for the analysis of label-free data / Proteomics
Unfortunately the inclusion of custom modifications is not possible by the user because it requires profound changes in the underlying code. Please let us know the modification you need by creating a new issue: GitHub · Where software is built entitled MaxQuant new modification request.
Making a request is how to proceed! The change would be made at the source then it will flow out to the public Galaxy servers and anyone running a local server (after each updates).
Please let us know if you would need any help with this. 