I have two replications of a bait-prey mass spec. experiment (trtA-Exp1, control and trtB-Exp2, control). For each experiment, I have a list of identified proteins along with their uniprot IDs, #Peptides, #PSMs, and #Unique Peptides for each protein. My goal is to detect the important proteins which are connected to the bait protein through creating protein-protein interaction network.
I'd like to compare trtA-Exp1 and trtA-Exp2 datasets/replications. There are some proteins which are common and some are unique to only one of the samples. I was wondering if you could advice me how should I compare the proteins between these two samples? Should I only keep the proteins that were identified in both replicates? What about unique proteins? How can I calculate fold change of each protein while I only have #Peptides, #PSMs, and #Unique Peptides of each protein?
I would highly appreciate if you could help and advice me in this regards.