Two-step normalization

Two-step normalization roman sakson  2019-10-02

Dear all,

I have a more general question concerning data analysis. Is there any possibility to have a two-step data normalization workflow implemented in Skyline? We often use spike-in SILAC experiments and normalization to heavy very nicely removes technical variance from our sample preparation workflows etc. However, it would be great if we could then use these L/H ratios and still normalize them to some housekeeping peptides to address biological variance (I realize that this can be done via global or surrogate standards but I would very much like to have it in addition to heavy normalization and not instead of it). Is something like this possible in Skyline or should I rather try working with MSstats for this purpose?

Thanks for this great piece of software!