How to run denovo DIA data and obtain test data for PepNet?

[yangshu729]

Hello,

Thank you for sharing this great tool! I am currently working with denovo DIA data and encountered some confusion. From my understanding, the input for the DeepNovo-DIA model consists of feature.csv and mgf files, whereas PepNet only requires mgf file.

I have the following questions:

1. How can I run denovo DIA data with PepNet?
2. Could you please provide a sample test dataset (for example, plasma data) to run with PepNet?

I would greatly appreciate your help in clarifying these points. Thank you!

Best regards, Shu Yang