Can I create a hybrid library from fasta digest library and dda library?

[050114dragon]

Can I create a hybrid library from fasta digest and dda library? the dda library was created by fragpipe using fractionation dda data。

[vdemichev]

Hi,

This is in general not recommended.

Better:

• Generate an in silico predicted lib.
• Search the raw data with the DDA lib (with MBR off) and generate a DIA-based spectral library based on that. Unless the library contains some exotic modifications, it's recommended to select the 'Deep learning' checkbox for this step.
• Search the raw data with the in silico predicted lib (with MBR off) and generate a DIA-based spectral library based on that.
• Research the data while loading both DIA-based libs (generated from the above steps) using two --lib commands in 'Additional options'.

Ideally also switch to DIA-NN 1.9.1.

Best, Vadim