I have got a list of Mass Spec data from 2 different in-solution digested samples and I would like to compare them and make a statement about the different protein present. In sample#1 137 proteins could have been identified and in sample#2 228. I numbered the proteins, which I call ranking. The proteins are pretty much all the same, but in different positions with different scores. I ranked the proteins by just numbering them from 1 to n. What does it means if Protein A is at Rank 7 in Sample#1 and Rank 27 in Sample#2, but is scored with 83.2 in Sample#1 and 103.36 in Sample#2. Can I tell anything about it's abundance in sample#1 vs #2 by looking at Rank and Score? What do the Scores exactely tell me?
Would be sooo great if anyone could give me a hint