SOD cambium Proteomics Data - OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants

Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. The MS raw data files were converted to mzXML files using massWolf (version 4.3.1). The MS mzXML and MASCOT xml files were parsed and processed with a program developed in-house. Briefly, each scan was subjected to smoothing using Savitzky-Golay filtering (second order polynomial, five data points, two iterations) and peak areas were calculated after noise reduction. Peak mass was set to the average of the three highest data points for each peak. Unique peptides identified with MASCOT were matched to the parsed MS data using the parameters detected m/z, charge state and retention time, using a retention time window of ± 1.0 min. Charge states were calculated by using the first three isotopic peaks of a peptide and the same mass tolerances for detecting the mono isotopic peak as in the MASCOT search.