Thanks for your questions. I will try and respond individually.
- Can skyline import scheduled MRM files from AbSciex for lipidomics?
Yes, there have been a fairly large number of application that have used Skyline for lipid analysis. If you look at the Small Molecule tutorials you will gain some examples of how it has been used. https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials
There is even a nice External Tool that has been developed for use with Skyline to build targeted lipidomics assays. https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=LipidCreator
- Can Skyline help with peak picking and flag transition that are falling outside of integration parameters in data sets with more than 2000 runs?
There are a number of tools in Skyline for peak picking etc... If you run your analyses in batches, Skyline definitely makes manual QC of the ok. We have worked on a project called LINCS that did >5000 perturbations and those were all manually checked by an expert operator.
- Can we intergrade our batch normalization algorithm within Skyline?
Skyline can generate reports and those reports can be batch corrected. Basically we prep and run samples in batches of 20-96 samples. The data are imported and analyzed using Skyline in batches. The quantities are then generated using a common report.
Batch correction can be done a number of ways. Skyline itself can perform calibration, either single point or multiple point calibration. We have used a single reference material to minimize batch effects. https://pubmed.ncbi.nlm.nih.gov/30350613/
We have also made use of both ComBat and SVA for batch correction from a report that has been generated by Skyline.
I hope this helps,