Project PXD000532

PRIDE Assigned Tags:
Biological Dataset
Download Project Files
Project Protein Table
Project Peptide Table
Visualize in PRIDE Inspector
Follow the next three steps to open your selected project or assay in PRIDE Inspector:

  • 1.

    Download, uncompress and open PRIDE Inspector
  • 2.

    Click in the magnifier on the left top corner, paste the project or assay that you would like to open in the search box, and hit search
  • 3.

    Click in the corresponding "Download" button to download the files and visualize them

Summary

Title

SOD cambium Proteomics Data

Description

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.

Sample Processing Protocol

See details in reference PMID : 24341908

Data Processing Protocol

See details in reference PMID : 24341908

Contact

Joakim Bygdell, Forest Genetics and Plant Physiology

Submission Date

21/10/2013

Publication Date

17/04/2014

Publication

    Srivastava V, Obudulu O, Bygdell J, Löfstedt T, Rydén P, Nilsson R, Ahnlund M, Johansson A, Jonsson P, Freyhult E, Qvarnström J, Karlsson J, Melzer M, Moritz T, Trygg J, Hvidsten TR, Wingsle G. OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. BMC Genomics. 2013 Dec 17;14:893 PubMed(s) : 24341908

Assay

Showing 1 - 3 of 3 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 31652 e.g. Control sample - Technical replicate #3 378 989 631 2423 648
2 31653 e.g. Control sample - Technical replicate #3 269 584 365 2259 379
3 31654 e.g. Control sample - Technical replicate #3 301 814 467 2509 463