You can build AlphaPeptDeep AI-generated libraries in Skyline using the following steps:
Select "Peptide Settings..." in the "Settings" menu to bring up the "Peptide Settings" dialog.
In the "Peptide Settings" dialog, select "Library" tab and click "Build..." to open the "Build Library" dialog.
Provide a name for the library in the "Name:" text box, provide a valid output location for saving the library in the "Output path:" text box.
Select "AlphaPeptDeep" radio button as the "Data source" then click "Finish"
To allow Skyline to install the necessary python environment for running AlphaPeptDeep, click "OK" to proceed.
To enable python to install and operate properly, the Windows registry key "LongPathsEnabled" must be set on the computer. You must provide
Administrator credentials to allow Skyline to change the registry, or you can change the registry through Windows as an Administrator, see
This python installation and configuration process can sometimes take 10 to 15 minutes, depending on the speed of the internet connection,
please be patient.
If the computer is equipped with an Nvidia Graphical Processing Unit, a dialog will appear asking if you want to install Cuda Library for faster
performance of AlphaPeptDeep modelling. This step requires Administrator credentials to install Nvidia software on the computer. If you
have Administrator credentials, and want GPU-enabled support click "Yes", otherwise if you don't have Administrator credentials but want to
use GPU-enabled processing consult with your system administrator for help. Alternatively, you can click "No" and use AlphaPeptDeep with
CPU-processing for building libraries.
This message indicates that the Python virtual environment setup by Skyline for AlphaPeptDeep went to completion.
Library building will commence once "OK" is clicked.
