|Small molecules in Skyline daily and Panorama upload||christopher ashwood||2017-10-27|
Dear Panorama support,
I've been trying to upload small molecule assays from Skyline Daily (molecules defined by chemical formula rather than defined monoisotopic mass). The assay works fine but publishing it to Panorama gives me the following error:
27 Oct 2017 02:24:23,783 ERROR: Uncaught exception in PipelineJob: (DONE) (File_name_redacted.sky.zip)
java.lang.IllegalStateException: Missing attribute mass_monoisotopic for element molecule.
I understand a workaround might be to specify the monoisotopic mass but I would prefer if the mass derived from chemical formula/adduct could be used from Skyline Daily (126.96.36.19992. Am I doing something wrong that would cause this error?
Edit: I've tried a workaround of saving the Skyline assay as non-daily v3.7 but this causes errors when trying to open it in Skyline v3.7 ("Custom ions must specify a formula or valid monoisotopic and average masses"). So this workaround is not possible.