Project : PXD000532

PRIDE Assigned Tags:
Biological Dataset
View in PRIDE Inspector
Download Project Files

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

    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

Accession Title Protein Count Peptide Count Unique Peptide Count Spectrum Count Identified Spectrum Count
31652 e.g. Control sample - Technical replicate #3 378 989 631 2423 648
31653 e.g. Control sample - Technical replicate #3 269 584 365 2259 379
31654 e.g. Control sample - Technical replicate #3 301 814 467 2509 463

You are about to run PRIDE Inspector via Java Web Start. Double click on the JNLP file downloaded if it didn't start automatically.

Note: Due to Oracle's recent Java update, you may experience security related problems with Java Web Start. Please add "http://www.ebi.ac.uk" to the URLs listed in the Security tab of your Java Control Panel.