Dear Skyline team,
I am working with DDA results and have 12 samples that I am trying to compare and see differences between. I have been noticing that my protein list changes depending upon how many samples I choose to search or display in skyline at a time. Is there a reason for this? I find it curious, because if I search my serum sample independently I only observe ~70 proteins while if I search it with all of my other samples I see 200 proteins and I still see strong protein abundances for the other ~130 proteins that I did not originally observe when individually searching these samples. Is there something I am missing here and a correct way I should be grouping these samples if they are not replicates or very similar?
Best Regards,
Karsten Poulsen