Increasing Confidence of Proteomics Data Regarding the Identification of Stress-Responsive Proteins in Crop Plants

Numerous stresses caused by complex environmental conditions, e.g., drought, heat, cold, salinity, strong light, UV, and heavy metals, negatively affect plant growth and lead to substantial crop losses worldwide. It is estimated that up to 50–70% of declines in crop productivity can be attributed to abiotic stress (Mittler, 2006). Abiotic stress, particularly drought and extreme temperatures, will be more frequent and severe in the near future because of global climate change (Horton et al., 2015). Understanding the abiotic stress response in plants has attracted substantial attention within the plant proteomics community. Quantitative proteomic comparisons are particularly useful in defining proteins that change in abundance, form, location, activity, and these comparisons may indicate involvement in responses to alterations in environmental conditions (Thelen and Peck, 2007). Such analyses can detect proteins involved in the mechanisms underlying plant stress resistance to various abiotic stresses. These proteins can potentially serve as molecular markers in marker-assisted selection by possibly speeding up the identification of relevant targets for stress breeding. Considering the 2DE and/or iTRAQ analysis methods of proteomics as an example, we briefly analyzed the methodological defects in detecting stress-responsive proteins in plants and propose our opinions for addressing these defects in future plant stress proteomics. The intended audiences of this opinion paper are novice rather than experienced scientists in the plant proteomics research community.