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Rappsilber-Laboratory / build-xiview

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Error: mzidentML file does not specify fragment ions #92

Closed Suparat-Scheu closed 8 months ago

Suparat-Scheu commented 2 years ago

Hi, I got another message when I try to upload .mzid file

log id: gnvv5kgj7hrkipqfn1ih0nmsj3_1662128916.log (include this in the github issue) warning type: IonParsing message: mzidentML file does not specify fragment ions. id: SIR_12; SIR_12; SIR_103; SIR_103; SIR_263; SIR_263; SIR_303; SIR_303; SIR_331; SIR_331; SIR_381; SIR_381; SIR_389; SIR_389; SIR_486; SIR_486; SIR_534; SIR_534; SIR_626; SIR_626; SIR_642; SIR_642; SIR_817; SIR_817; SIR_830; SIR_830; SIR_833; SIR_833; SIR_935; SIR_935; SIR_939; SIR_939; SIR_943; SIR_943; SIR_994; SIR_994; SIR_1018; SIR_1026; SIR_1026; SIR_1069; SIR_1069; SIR_1120; SIR_1120; SIR_1248; SIR_1248; SIR_1255; SIR_1255; SIR_1281; SIR_1281; SIR_1330 ...

could you suggest how to fix this?

Thank you Suparat

colin-combe commented 2 years ago

hi, its a bug/flaw in our mzIdentML parser. It's OK to ignore the "error", but do pick the correct ions searched for (you should see a dialog asking for this). The ion series searched for should be specified in the AdditionalSearchParams in the mzIdentML, but even if they are there they are getting ignored. The bug will go away when the parser is updated but that is likely to be a couple of months away. cheers, colin

Suparat-Scheu commented 2 years ago

I see. thank you Colin