Hi Amir,
Thanks for your questions. I will try and respond individually.

1. 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

2. 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.

3. 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,
Mike

So, yes, we think it is worth your effort. If you try and decide to abandon your work midway, we would certainly be interested in understanding why that happened to see if we might fix any blocking issues.

You might be interested in watching this short presentation of a fully automated small molecule detection system from our 2017 Skyline User Group Meeting at ASMS:

https://skyline.ms/wiki/home/software/Skyline/events/2017 User Group Meeting at ASMS/page.view?name=zhang

Good luck. We look forward to hearing your feedback if you decide to give this a try.

--Brendan

Thanks Mike for the info. Looking at the files suggested I did not see a way to import MRM data from Sciex machine into skyline. Is there an example using Skyline with Sciex MRM files.
Thanks

Hi Amir,
You don't have to look at anything specific to a vendor as Skyline imports data from the six major instrument vendors from the RAW files in a vendor neutral way.

You need to start by building a Skyline document that has your targets and transitions to begin with. The information for building a document with your target lists and importing the results is shown in the Small Molecule tutorial .. https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule
The examples are for Thermo RAW files but you can use Sciex Wiff files the same. Likewise the examples are transitions for amino acids but they could easily be your lipid targets. Start by making a Skyline document with your transitions and importing a small set of files and see how it goes.

Cheers,
Mike

In fact, most of the small molecule examples use Waters Xevo data, but here is a tutorial that uses a multisample WIFF file from a QTRAP instrument.

And here is a dataset from CPTAC that covers triple quadrupole instruments from 4 (Agilent, SCIEX, Thermo, Waters) of the 5 (and Shimadzu) instrument vendors for which Skyline offers QqQ support.

https://panoramaweb.org/cptac_study9.url

There are many tutorials, webinars, and course videos available about working with small molecules in Skyline, and many, many people using it with SCIEX triple quadrupole instruments.

Good luck. Thanks for your interest.

--Brendan

Oops. The tutorial with multisample WIFF files is this one (second half):

https://skyline.ms/tutorial_existing_quant.url

Thank you Brendan and Mike. This has been very helpful. Wanted to know if someone has described using Skyline for quantitating small molecules based on internal standards.
And also is there is a tutorial on peak picking for small molecules? The one I found is bases on proteomics.
Thanks