Is there any initial file of the manual selected spectrum index?

[TerminatorJ]

I need to align my own protein photo, but I cannot get the manual picked index the same as in the original paper.
How can I do my own prediction according to the model you supply in the example path?

[li-li-github]

I'm sorry for the late reply.

What do you mean by "manual picked index"?
What do you want to align your protein photo with?