A different way to protein inference?

[ht-lau]

Hi,
I am wondering how do you think about protein inference and quantification in this way,
https://www.nature.com/articles/s41467-023-41558-2

and do you think this can be implemented as an option?

HT

[anesvi]

Bing Zhang's GitHub page has the SEPepQuant code (it is in R) and instructions on how to run it. It takes FragPipe output as input. I don't see a need to reimplement it. However, we are discussing putting up a server running various downstream tools that are compatible with FragPipe, and can possibly put SEPepQuant there.