I have a curiosity. Imagine I have a A Vs B experiment and a number of proteins are changing in the two conditions. Ok.
Now, I have protein X, in which I am particularly interested in. X is low abundance in condition A, but visible (identified in DDA & 5 SWATH peaks visible in the microapp). The same protein X is totally absent in B (this is a known fact, so I am expecting this).
How can I make SWATH to report protein X as having a certain area in all A replicates and area zero (or close to) in all B replicates? In all the tests I did, protein X was totally ignored in all SWATH reports after the search.
Any trick I am missing?