Quantitative proteomics of different zones in human articular cartilage reveals unique patterns of protein distribution

Purpose: The progress in proteomics technology development during the last decade has made tissue proteomics available also for the study of extracellular matrices such as cartilage and bone. We have used quantitative proteomics used for a detailed study of different zones in articular cartilage to increase our knowledge of structure in relation to cartilage biology. Methods: Our gel-free proteomics approach includes tissue extraction, digestion by trypsin and tagging of peptides with ITRAQ for quantification followed by 2D LC-separations coupled to tandem mass spectrometry for their identification and quantification. The tissue was sliced from top to bottom in 10μm thin sections and the full thickness cartilage was divided into 9 pools including superficial, intermediate and deep zones. Results: Previous known distributions of e.g. superficial zone protein (lubricin) were confirmed but also novel findings were observed e.g. asporin which was predominantly seen in the top layers. In total approximately 200 proteins were identified and quantified showing different patterns. Conclusions: As an alternative to immunohistochemistry we used proteomics technology to study the protein abundance across full thickness articular cartilage. The advantage of this approach is that it allows multiple targets to be studied simultaneously and that it is independent of antibody availability. Other advantages include unambiguous identifications and improved quantifications as an unbiased detection of proteins and information on some of their structural qualities. The work has shown novel information on the differences of different layers of cartilage of value in understanding changes in early pathology.