Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

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  • Cosette Abdallah
    Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
  • Eliane Dumas-Gaudot
    UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
  • Jenny Renaut
    Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
  • Kjell Sergeant
    Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg

Description

<jats:p>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, the 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 drawbacks. The 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 extraction, some protein abundance in green tissue, and the absence of well-annotated and completed 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 trends in peptide fractionation amenable to MS analysis are as well discussed.</jats:p>

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