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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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More than 1000 different isolation windows #976

Open joachims1956 opened 6 months ago

joachims1956 commented 6 months ago

Hello,

Thanks for developing this amazing software. Currently we are analyzing mouse tumor samples in DIANN. In these analysis we get the warning that DIA-NN is using "more than 1000 different isolation windows". What does it mean? And is there anything to avoid this warning? Please find below a screenshot of the used DIA-NN parameters and an additional screenshot showing the warning.

Thank you very much. Ofir_diann_mouse_tumour_sample_warning_isolation_windows Ofir_diann_parameters_mouse_tumours

vdemichev commented 6 months ago

Usually happens when analysing DDA data with DIA-NN. You can see how exactly the windows are encoded by supplying --export-windows to DIA-NN, it will then create a text file next to the raw file with the window scheme.

joachims1956 commented 6 months ago

Ok, great, thanks a lot for your support.