|short question absolute peptide/protein quantification with internal heavy labeled||Tobi||2019-01-03|
Dear all, wish you a good start into to the new year.
Is there a way to average peptide quantification results directly within skyline into protein quantification results? I can imagine this beeing troublesome in cases where peptides belong to several proteins, but when working with preselected representative peptides this might be helpful to quickly get to a complete results report. Do you have plans to implement something in this direction or do you want to stay on the peptide level?
Question on internal standard based absolute quantification.
Is it possible to do internal absolute quantification with different amounts in each replicate/file? So far I only get no or messed up quantitative results based on some regressions which I might not be able to avoid if I want the quantification result at all.
I would like to set to Replicate/Analyte Concentration to values ranging from 115-140 fmol, meaning in replicate 01_1 all heavy labeled peptides are present at an amount of 115fmol, while in replicate 04_01 the value is 140 fmol etc. All light peptides should be quantified against heavy but only within the same file.
As far as I can see I don't get the expected output for Quantification in Peptide Ratio Results. All light BSA peptides should have around 100 fmol for all replicates, while spectrin peptides should have ca. 20 fmol in replicate 02_01 and 02_02 but close to 0 fmol in other replicates.
I know this might not be the usual approach but it is for comparisons and it would be nice to know if it is technically possible or not.