Retrieve PTM (protein post translational modifications) for a list of protein coordinates (specific exons)

Question

[Lalla]

Dear all

I am analyzing a set of alternative spliced, protein-coding, exons. I have been able to map the exons coordinates to the corresponding protein coordinates and find domains annotated for those positions. Another question I would like to address is whether those spliced exons encode for protein sequences subjected to post-translational modifications (ptm) and if yes, which kind of modifications. I found some websites that report ptm, but I could not find a way to use those databases by querying just by coordinates (proteomic or genomic) and to do that in batch (I have 1000s of exons to analyze). Do you have any suggestion on how to proceed? I am working on mouse (using Ensembl mm9 as reference annotation).

Thanks in advance!

[Jean-Karim Heriche]

How to proceed would depend on the resources you're using. As a general way forward, since most databases have an option to bulk download their data, I would download the data, extract the PTM positions on their proteins and map this to your exons of interest.