Protein Inference and Protein Quantification: Two Sides of the Same Coin
In this paper, the authors investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference is to determine whether each candidate protein is present in the sample or not. Protein quantification is to calculate the abundance of each protein. Naturally, the absent proteins should have zero abundances. Thus, they argue that the protein inference problem can be viewed as a special case of protein quantification problem: present proteins are those proteins with non-zero abundances. Based on this idea, their paper tries to use three very simple protein quantification methods to solve the protein inference problem effectively.