Write valid ProteomeXchange XML for datasets that do not have any Unimod modifications #500
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…odifications with Unimod Ids. Instead write: <cvParam cvRef="MS" accession="MS:1002864" name="No PTMs are included in the dataset"/> so that we do not get XML validations errors from ProteomeXchange. Modifications without Unimod Ids are not supported by ProteomeXchange so we skip writing them to the XML file that is submitted to ProteomeXchange.
labkey-jeckels
approved these changes
Feb 4, 2025
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Rationale
<ModificationList>element in the XML submitted to ProteomeXchange requires at least one cvParam subelement. https://proteomecentral.proteomexchange.org/schemas/proteomeXchange-1.4.0.html#ModificationList. We can add cvParam subelements only for modifications that have a Unimod Id. XML generated for datasets that do not have any modifications with Unimod Ids fail validation on the ProteomeXchange server.Changes
<cvParam cvRef="MS" accession="MS:1002864" name="No PTMs are included in the dataset"/>