Quantitative Proteomics in Plants: Choices in Abundance

The field of proteomics is evolving from cataloguing proteins under static conditions to comparative analyses. Defining proteins that change in abundance, form, location, or activity may indicate which proteins are involved in developmental changes or responses to alterations in environmental conditions. Such studies are facilitated by an increasing number of complementary technical options for performing quantitative proteomic comparisons. As with any developing field, however, rapid expansion in new techniques introduces concerns about choosing the appropriate approach. The goals of this perspective essay, therefore, are both to introduce the various options that are available (or nearly so) for quantitative proteomics and to discuss considerations related to applying these methods in the laboratory. Proteomics is well into its second decade as a field of study, so referring to proteomics as a new or recent area of science no longer seems applicable. However, the majority of the first decade was dominated by two-dimensional gel electrophoresis and traditional protein staining techniques (described below) as the primary means of performing comparative experiments. Two-dimensional gels coupled with conventional staining methods have been (and continue to be) productive in providing relevant information about biological systems. However, problems with sensitivity, throughput, and reproducibility of this method place limitations on comparative proteomic studies. The advent of a number of powerful and complementary technologies for performing quantitative comparisons greatly expands the depth and breadth of reliable information that can be obtained about the dynamic proteome. Therefore, the goals of this essay are to provide an overview of these new technologies and to serve as a starting point for those seeking to incorporate quantitative proteomics into their research programs.