Setting different analyte concentrations for different peptides

Setting different analyte concentrations for different peptides lee julie  2019-11-12

Hi, I am trying to define the analyte concentration for samples defined as QCs in the Document Grid under replicates. I am unable to define separate analyte concentrations for different peptides - it applies the last defined concentration to all peptides. Any advice on how to correctly approach this?

Thanks in advance

Nick Shulman responded:  2019-11-12
Skyline allows you to fill in two different numbers in the Document Grid to specify the spiked in concentrations of peptides.

One setting is on the Replicate and is called "Analyte Concentration".
The other setting is on the Peptide and is called "Concentration Multiplier".

You should choose numbers for these two values so that the Analyte Concentration times the Concentration Multiplier is equal to the spiked in concentratrion of that peptide.

This works so long as your samples where the ratio of the spiked in peptides to each other did not vary relative to each other.

If you have a more complicated way of spiking peptides into your samples, then that is not something that is currently supported by Skyline. So far, we have not found anyone who actually needed calibration curves to enable specifying the "full matrix" of spike in quantities across peptides and replicates.

You can find more information about this in this support request:
-- Nick
lee julie responded:  2019-11-12
Thanks for the quick response Nick.

It seems that what I'm trying to set up is currently not supported by Skyline. I have concentration multiplier values defined for my peptides according which correlate with my calibration curves set at different concentrations. However I am using a biological sample as my QC which has varying conc. of each peptide that are not proportional to the concentration multiplier values and I am trying to define the expected peptide conc. of the QCs across multiple batches. Could you think of an alternative method to do this on either Skyline or Panorama? I was thinking of setting up a Guide Set on AutoQC with my QCs but analyte conc. is not an available metric.