Error exporting custom PTMs

compomics / peptide-shaker

Interpretation of proteomics identification results

http://compomics.github.io/projects/peptide-shaker.html

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Error exporting custom PTMs #500

Closed juank1892 closed 1 year ago

juank1892 commented 1 year ago

Hi Peptide-Shaker team,

I am getting the following error:

Cannot invoke "com.compomics.util.pride.CvTerm.getOntology()" because "cvTerm" is null.`

I recently got back to this tool and I am really happy to see its exports working on Skyline. However, I performed a search with some custom PTMs that are not in Unimod and I am wondering if there is a way to export a mzIdentML for follow-up work on Skyline?

Sincerely, Juan C.

hbarsnes commented 1 year ago

Hi Juan,

Thanks for letting us know about this one! Here is a beta version that should solve the problem: https://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/2.2.18-beta/PeptideShaker-2.2.18-beta.zip

Hopefully this version will allow you to generate a valid mzIdentML file even when having custom PTMs without Unimod mapping.

Best regards, Harald

hbarsnes commented 1 year ago

The issue has been resolved in PeptideShaker 2.2.18 which has now been officially released.