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. 1. Introduction “In the wonderland of complete sequences, there is much that genomics cannot do, and so the future belongs to proteomics, the analysis of complete complements of proteins” [1] Originally coined by Wilkins et al. in 1996, proteomics by name is now over 15 years old. The term “proteome” refers to the entire PROTEin complement expressed by a genOME [2]. Proteomics is thus the large-scale analysis of proteins in a cell, tissue, or whole organism at a given time under defined conditions. The cutting-edge proteomics techniques offer several advantages over genome-based technologies as they directly deal with the functional molecules rather than genetic code or mRNA abundance. Even though there is only one definitive genome of an organism, it codes for multiple proteomes since the accumulation of a protein changes in relation to the environment and is the result of a combination of transcription, translation, protein turnover, and posttranslational modifications. The field of proteomics has grown at an astonishing rate, mainly due to tremendous improvements in the accuracy, sensitivity, speed and throughput of mass spectrometry (MS), and the development of powerful analytical
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