Small molecules in Skyline daily and Panorama upload

Small molecules in Skyline daily and Panorama upload Chris  2017-10-27 02:29:10
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) (

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 ( 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.

Nick Shulman responded:  2017-10-27 14:56:59
Can you send us your file?
You can upload it here:

I will also contact you by email in case you do not want to upload that file to that public location.
vsharma responded:  2017-10-27 15:04:36
Hi Chris,

In the last couple of months there have been some changes in the Skyline document for small molecules that are not yet supported in Panorama. That is why you are seeing this error. I will look into fixing it next week and get back to you.

Chris responded:  2017-10-27 16:02:32
Dear Nick and Vagisha,

I have uploaded the file to the public location. The file is named, "standards with ladder" with the comment: "Skyline Daily Small Molecule". Hopefully uploading the skyline assay will help you.

Chris responded:  2018-01-01 20:27:15
Hi Nick and Vagisha,

Works great now, thanks!