Recently posted to the support board by a Skyline user:

I'm thinking about the automatic pipeline that would build spectral library from replicate experiments and use it for MS1 quantitation of these experiments.

I can already automate the building of Spectral Libraries using BlibBuilder.exe. And also, once Skyline project is defined (i.e. Spectral Libraries and protein sequence database imported) I can import replicate MS experiments using SkylineRunner. The missing things are:
  1) the ability to specify spectral library for a Skyline project via SkylineRunner (when I look at .sky XML it looks like there is no way to specify the library by file location, it has to be registered from Skyline GUI; please correct me if I'm wrong)
  2) the ability to import FASTA sequence database via SkylineRunner

Decided Kaipo would be better for this, since he is already working in this code.

Kaipo has implemented these additions and they have been released in 1.4.1.5600

From Alexey:
One minor thing is that in the FASTA files import GUI the user is being asked if proteins that have no peptides in the spectral library should be discarded.
As far as I understand, there is no similar option in SkylineRunner, so all the proteins are kept, and that increases the size of .sky file by approximately 20Mb.
It would be nice to have an option/command to discard unreferenced proteins from the Skyline project to save the space and processing times.

Brendan: I think this should be the default, and we can add a flag that allows someone to keep everything, but I expect this to be an infrequently used option.

Didn't make v2.1. Next release.

Kaipo implemented this for Skyline 3.5.