How to get Skyline to produce different molecule calibration curves in a single instance?

How to get Skyline to produce different molecule calibration curves in a single instance? manesh chand  2024-02-14 15:46

I have 115 molecules that I want to calculate concentrations for using Skyline. We have ran a calibration curve of all 115 molecules pooled together at varying concentrations and performed a serial dilution that we ran on our SCIEX 6500 QTrap, files are labelled inslicht 753884 cal 0-9. I followed the tutorial steps for the small molecule quantification and I am able to input the analyte concentration values for one of the 115 molecules on the document grid view and get a calibration curve for. However, this does not allow me to add the other 114 molecules that have different concentrations inside those cal 0-9 files that I want to calculate concentrations for using a singular Skyline instance. Is there a way I can format the document grid view in Skyline to where I can input the other 114 molecule known concentrations into the analyte concentration column without having Skyline auto filling those values down. I have attached pictures of the molecule setting and document grid view, skyline files, and raw data. Thank you for the help!

manesh chand responded:  2024-02-14 15:48

Here are the screenshots of the molecule settings and document grid view.

Nick Shulman responded:  2024-02-14 15:55
If your dilution series involves taking some high concentration mixture and diluting it with a solvent, then you should set the "Analyte Concentration" of the highest concentration Replicate to a simple number like "1" and then set the "Concentration Multiplier" on each of your different molecules to the right number so that the Concentration Multiplier multiplied by the Replicate Concentration gives you the concentration of that molecule in that replicate.

If your dilution series is something more complicated, such as mixing a high concentration pool with a low concentration pool then the "Concentration Multiplier" will not be sufficient for you to specify the concentration of each molecule in each replicate.
If you have a dilution series like that then you will need to set the "Explicit Analyte Concentration" on each of your molecules and replicates.
The Explicit Analyte Concentration can be found in the available columns of the Report Editor in the Document Grid at "Molecule Lists > Molecules > Molecule Results".

More information about the Document Grid can be found in the Custom Reports tutorial:
-- Nick