Problems with relative quantification

Problems with relative quantification sarita  2023-08-02 05:42

Hi to everyone, I have to calculate the relative quantification of three proteins in five patients before and after a treatment. I have the peptide modified sequence and the PRM raw data.
I don't have any internal standard heavy peptides. I know that each peptide was added at the same amount in each sample. I have to perform the relative quantification, for each protein of interest, comparing the relative amount between the 2 conditions (pre- and post- treatment). How can I calculate the light/heavy ratios for each peptide in each sample? and how to obtain the adjusted p-value and foldchange of each comparison for the three proteins?

Nick Shulman responded:  2023-08-02 06:57
I think the Group Comparison tutorial would be helpful:
-- Nick