Gel-based and gel-free quantitative proteomics approaches at a glance
2012
Abdallah, Cosette | Dumas-Gaudot, Eliane | Renaut, Jenny | Sergeant, Kjell
Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, t he shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without draw backs. T he burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein ext r action, some protein abundance in green tissue, and the absence of well-annotated and complete d genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and - free methods and their application to plants. The latest t rends in peptide fractionation amenable to MS analysis are as well discussed.
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