Gel-based and gel-free quantitative proteomics approaches at a glance

Cosette C. Abdallah (1) , Eliane E. Dumas-Gaudot (1) , Jenny J. Renaut (2) , Kjell K. Sergeant (2)

1 Agroécologie [Dijon]
2 Department Environment and Agro-Biotechnologies

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.

Mots clés: mass spectrometry; quantitative techniques comparaison

Domaines: Sciences agricoles

Cosette C. Abdallah, Eliane E. Dumas-Gaudot, Jenny J. Renaut, Kjell K. Sergeant. Gel-based and gel-free quantitative proteomics approaches at a glance. International Journal of Plant Genomics, 2012, 2012, 17p. ⟨10.1155/2012/494572⟩. ⟨hal-01004759⟩