PXD000532

PXD000532 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:48:30.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000532
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Joakim Bygdell
SpeciesList	scientific name: Populus tremula x Populus tremuloides; NCBI TaxID: 47664;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	instrument model: Q-TOF Ultima; Q-Tof ultima

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-21 04:00:53	ID requested
1	2014-04-17 03:57:39	announced
⏵ 2	2014-07-24 03:48:31	announced	Updated project metadata.

Srivastava V, Obudulu O, Bygdell J, L, ö, fstedt T, Ryd, é, n P, Nilsson R, Ahnlund M, Johansson A, Jonsson P, Freyhult E, Qvarnstr, ö, m 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, 14():893(2013) [pubmed]

curator keyword: Biological

submitter keyword: cambium, superoxide dismutase, OnPLS, data integration

Joakim Bygdell
contact affiliation	Forest Genetics and Plant Physiology
contact email	Joakim.Bygdell@slu.se
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000532

PRIDE project URI

• PRIDE
  1. PXD000532
     1. Label: PRIDE project
     2. Name: SOD cambium Proteomics Data