Bringing proteomics discovery studies towards clinical application requirements: guidelines and practical suggestions

Proteomics is the study of proteome which encompasses the nature and amounts of all the proteins present in a cell, or tissue at a given time and in a given condition. Differential proteomics refers to the determination of quantitative maps of protein expression from different biological where two or more conditions are compared (relative quantification). One of the main areas of research in quantitative differential proteomics is the discovery of biomarkers. At the biomolecular level, a biomarker is a molecule present at levels significantly different when a change of specific condition of health occurs. Differential quantitative proteomics generates a large list of proteins along with their relative abundances between different conditions and allows the identification of biomarker candidates. However, the approach is not straightforward and not all of the many differentially abundant proteins identified in proteomics studies become biomarkers used in clinical practice. The bottleneck is the reliability of the results of proteomics studies.
The objectives of this work were therefore to develop and optimize methods using liquid chromatography hyphenated to mass spectrometry to obtain reliable results from proteomics discovery studies. These reliable results could be better leveraged for future clinical use. Based on the expertise gained, all relevant information is gather in a synthetic manner to draw guidelines, recommendations and practical advices to get reliable proteomics results.