MSstats analysis using ratio light:heavy

MSstats analysis using ratio light:heavy Taina Marques  2019-10-11


I was wondering if is possible to use the ratio light:heavy to perform group comparison analysis using the MSstats in skyline?
As far I could see, skyline only does with the area without any ratio light:heavy. Is there a way that I can switch to ratio?

Thank you!

Nick Shulman responded:  2019-10-11
1. Are you asking about the Group Comparison that you get in Skyline from either:
Settings > Document Settings > Group Comparisons
View > Other Grid > Group Comparisons

One of the options that you can specify when you are configuing your Group Comparison in Skyline is "Normalization Method".
If you are not seeing "Ratio to Heavy" in that list, then you should go to:
Settings > Peptide Settings > Modifiications
and make sure that "Heavy" is chosen for "Internal Standard Type" at the bottom.

2. Alternatively, are you asking about the MSstats external tool?

If you're asking about the MSstats external tool, then I believe the answer is that the MSstats always does normalize to heavy if it sees any heavy precursors in the dataset. There is no way to tell MSstats not to normalize to heavy.
-- Nick