In this work we have critically revised and updated the literature dealing with wine quality control based on protein or peptide mass spectrometry-based fingerprinting. A number of pitfalls in the experimental design of most work dealing with this subject are highlighted along with recommendations on how to circumvent them. As a general trend, the conclusions reported to date in the literature of the topic are inconclusive mainly due to the (i) low number of representative samples, (ii) lack of basic analytical concepts, and (iii) lack of adequate statistical and software tools. In addition, we have critically revised the sample treatments commonly used to separate proteins from wines, emphasizing that the majority of literature is devoted to white wines, probably because of difficulties in isolating the protein content in red wines.