About predicting the library

[Clovernana]

Hi,
Thanks for your good job .And I intend to predict a library by deepDIA method.And I have run the test code and get a predicted library with a size of 350449kb.And I try to import it to the DIANN,and I have noticed that it has been imported into the spectronaut in the instruction.Uh, I have get the information that the library in spectronaut is also applicable to DIANN.But the real test is totally different for this predicted library.Could you please give some tips about this library for DIANN ?Thank you so much!

Clover

[yyi17]

Maybe there are a few differences of compatible column names between Spectronaut and DIA-NN. Spectronaut will automatically generate these columns, while I have not tested library generation for DIA-NN. It seems you can manually change ModifiedSequence to ModifiedPeptide. Since the current version of DeepDIA does not support any variable modifications, you can add a new column FullUniModPeptideName to the library table, by replace modification names in ModifiedSequence with UniMod IDs. The LabeledSequence column can be generated similarly.