Can we do LFQ analysis in Skyline? shelkarmicrobio23591  2021-06-14

Dear Skyline,
Can we do LFQ analysis in Skyline?

Please suggest workflow.

Nick Shulman responded:  2021-06-14
Yes, Skyline can be used for label free quantification.

Often, when you are doing quantification, what you really want to be doing is comparing peak areas between different sets of replicates.
If you want to learn about comparing groups of replicates, you should look at the Group Comparison tutorial:

I believe all (or maybe most) of the "Full-Scan Acquisition Data" tutorials on the Skyline Tutorials page deal with label free quantification:

-- Nick
Brendan MacLean responded:  2021-06-14
Note, however, that LFQ is often used in the field as a synonym for MS1 chromatogram extraction from DDA data, because it was one of the earliest methods for doing "label-free quantification" (as opposed to SILAQ, ITRAQ or TMT which are label based technologies for DDA).

The answer to that question, is also, yes, you can do label free quantification with DDA data in Skyline, but you will want to start more specifically with the MS1 filtering tutorial:

And the DDA Search tutorial:

If you were not thinking DDA, then Nick's more general answer still applies.

shelkarmicrobio23591 responded:  2021-06-15
Thank you Dr. Nick and Dr. Brendan.