Mining protein lists from proteomics studies: applications for drug discovery

Importance of the field: In recent years, proteomics has become a common technique applied to a wide spectrum of scientific problems, including the identification of diagnostic biomarkers, monitoring the effects of drug treatments or identification of chemical properties of a protein or a drug. Although being significantly different in scientific essence, the ultimate result of the majority of proteomics studies is a protein list. Thousands of independent proteomics studies have reported protein lists in various functional contexts. Areas covered in this review: We review here the spectrum of scientific problems where proteomics technology was applied recently to deliver protein lists. The available bioinformatics methods commonly used to understand the properties of the protein lists are compared. What the reader will gain: The types and common functional properties of the reported protein lists are discussed. The range of scientific problems where this knowledge could be potentially helpful with a focus on drug discovery issues is explored. Take home message: Reported protein lists represent a valuable resource which can be used for a variety of goals, ranging from biomarkers discovery to identification of novel therapeutic implications of known drugs.