Averaging across multiple proteomic experiments

Question

[bhumm]

I am fairly new to proteomic analyses so apologies if this is a silly question.

We have performed two separate aptamer based proteomic experiments. We have analyzed these datasets individually but would like to average across this to increase our N. How does one typically go about doing this? Do we average across all raw values? Or do we average across the averages of the individual experiments?

Any insight, opinions, or literature on this topic would be deeply appreciated.

[ATpoint]

How does averaging increase N? Say you have a study of 3 vs 3 and average with another 3 vs 3 it is still 3 vs 3. What is the setup here? Is it the same exact specimen again (technical replicate) or new material (biological replicates)?

[bhumm]

It is two biological replicates. I reasoned it as increasing N=2. For both biological replicates, it is ~13 controls vs ~13 disease condition.