Small molecule (non-global) standard concentrations

Small molecule (non-global) standard concentrations jrenders  2020-09-01

Hi there,
Thanks so much for adding the ion ratio features to skyline - we are currently rebuilding all of our small molecule methods in skyline and have unfortunately hit a snag. I think you previously made mention of (in the future) adding the ability to assign calibration curve regression and weighting on a per-analyte basis. Right now, via the "Document grid --> Reports --> Replicates" report we can assign analyte concentrations, but only globally. However, we have methods where our calibrators do not have all analytes at the same concentration. Is there plans to allow for a per-analyte concentration assignment as well in the future? Or perhaps there is already a way to handle this via the document grid or pivot table? Thanks for any guidance you can suggest.

Nick Shulman responded:  2020-09-01
In Skyline-Daily, there is a new feature where you can set the concentration of each molecule in each replicate independently.

The column in the Document Grid is called "Explicit Analyte Concentration" and it can be found on the "Molecule Result":
Molecule Lists > Molecules > Molecule Results
Proteins > Peptides > Peptide Results

-- Nick
jrenders responded:  2020-09-01
Thanks Nick! I probably should have been able to figure that one out on my own, but I appreciate the help!
abrell responded:  2021-01-15
Hi, is there a way to extend the concept of explicit analyte concentration to heavy standards?

Not all of our calibrators have the same amount of IS. I've tried using "Concentration Multiplier", as well as treating the labeled- and un-labeled calibrants as separate spp (i.e. not heavy and light) and thus far I've been unable to handle this situation. Thanks.
Nick Shulman responded:  2021-01-15

Do you have a calibration curve (even if it's a single point calibration curve with one external standard)?
If your different calibrators have external standards in addition to the samples, and you would like certain samples to use certain external standards, you can set the "Batch Name" column on the Replicates in the Document Grid. A particular replicate will only use the external standards with the same Batch Name.

Otherwise, it might be that you need to have your different replicates be in separate Skyline documents.
-- Nick