Quantitative plant proteomics

Abstract

Quantitation is an inherent requirement in comparative proteomics and there is no exception to this for plant proteomics. Quantitative proteomics has high demands on the experimental workflow, requiring a thorough design and often a complex multi-step structure. It has to include sufficient numbers of biological and technical replicates and methods that are able to facilitate a quantitative signal read-out. Quantitative plant proteomics in particular poses many additional challenges but because of the nature of plants it also offers some potential advantages. In general, analysis of plants has been less prominent in proteomics. Low protein concentration, difficulties in protein extraction, genome multiploidy, high Rubisco abundance in green tissue, and an absence of well-annotated and completed genome sequences are some of the main challenges in plant proteomics. However, the latter is now changing with several genomes emerging for model plants and crops such as potato, tomato, soybean, rice, maize and barley. This review discusses the current status in quantitative plant proteomics (MS-based and non-MS-based) and its challenges and potentials. Both relative and absolute quantitation methods in plant proteomics from DIGE to MS-based analysis after isotope labeling and label-free quantitation are described and illustrated by published studies. In particular, we describe plant-specific quantitative methods such as metabolic labeling methods that can take full advantage of plant metabolism and culture practices, and discuss other potential advantages and challenges that may arise from the unique properties of plants.

Quantitative proteomics analysis reveals that S-nitrosoglutathione reductase (GSNOR) and nitric oxide signaling enhance poplar defense against chilling stress

“…Widely used quantitative proteomics techniques include classical gelbased methods (2DE, DIGE) and liquid chromatographymass spectrometry-based methods such as isotopic labeling and the relatively new label-free methods. Among these methods, isobaric tags for relative and absolute quantification (iTRAQ) can be used to analyze up to eight different samples within the same experiment (Bindschedler and Cramer 2011;Alexandersson et al 2013). As fast growing trees, poplars play an important role in forestry and as energy crops.…”

Impairment in Sulfite Reductase Leads to Early Leaf Senescence in Tomato Plants

“…S4B). Rubisco, the most abundant protein in green tissue (Bindschedler and Cramer, 2011), was decreased in the lower leaves compared with the wild type ( Fig. 2B; Supplemental Fig.…”

Uncovering plant-pathogen crosstalk through apoplastic proteomic studies

“…However, the absence of one of the actors in these simplified models underestimates the complexity of the events occurring during the plant-pathogen crosstalk. The large dynamic range of protein abundance present in plant-pathogen samples, such as pathogen-infected leaves represents an additional difficulty (Bindschedler and Cramer, 2011). In fact, many important proteins are present at low level and are thus difficult to isolate from complex mixtures containing more highly abundant proteins.…”