Evaluation of label-free quantitative proteomics in a plant matrix: A case study of the night-to-day transition in corn leaf

Abstract

The application of a label-free, LC-MS/MS based proteomics method for analysis of plant tissues was evaluated using both a spike study and case study in corn (Zea mays) leaf tissue. The spike study was utilized to establish a label-free proteomics protocol for corn leaf tissue, with focus on the assessment of sensitivity and accuracy. The data from this spike study indicated that this protocol had quantitative accuracy within ±20% of the true values and was able to differentiate 1.5 fold changes in protein abundance in a corn leaf matrix. Furthermore, the applicability of this protocol as a useful tool for answering biologically relevant questions was tested in a case study of the response of the proteome to night-to-day transition in corn leaf tissue. The label-free proteomics approach detected 136 differentially abundant proteins (FDR = 0.01 with an absolute log fold change ≥ 0.8) and 313 proteins whose abundance did not change in response to the diurnal cycle using ANOVA fixed effects model analysis. Identified proteins were mapped to their Gene Ontology (GO) biological processes and compared with expected diurnal biology. Many observed changes, including an increase in photosynthetic processes, were consistent with anticipated biological responses to the night-to-day transition. The results from the spike and case studies show that the label-free method can reliably provide a means to detect changes in protein abundance in plant tissue.