PXD000308

PXD000308 is an original dataset announced via ProteomeXchange.

Title	Shotgun label-free quantitative proteomics of water-deficit stressed mid-mature peanut (Arachis hypogaea L.) seed
Description	Legume seeds and peanuts, in particular, are an inexpensive source of plant proteins and edible oil. Owing to their importance in global food security, it is necessary to understand the genetic, biochemical, and physiological mechanisms involved in controlling seed quality and nutritive attributes. A comprehensive understanding of seed development and the effects of water-deficit stress on the incorporation of the main storage reserves in seeds, such as proteins, fatty acids, starch, and secondary metabolites will enhance our ability to improve seed quality and yield through molecular breeding programs. In the present study we employed a label-free quantitative proteomics approach to study the functional proteins altered in the mid mature peanut seed during water-deficit stress. The RAW files of LC-MS/MS runs were converted to mzXML format and searched using GPM (Global Proteome Machine, version 2.1.1) software. Each mzXML spectra file was also searched against a reversed sequence database to calculate the false discovery rate (FDR). The 16 output files for each replicate were combined to create a single merged result file and only proteins with FDR less than 1% were used for the analysis. The following parameters were used for the search: Enzyme: trypain, [RK]|{P}; allowed missed cleavage: 2; variable modification: methionine oxidation; fixed modification: carbamidomethylation of cysteine; MS and MS/MS mass tolerance: ±2 Da and ±0.2 Da respectively. For the comparative analysis, the normalized spectral abundance factors (NSAFs) was used to study protein abundance as described earlier. For each identified protein, k, in sample i, the number of spectral counts was divided by length of the identified protein. NSAFi values for each sample i were obtained by normalizing SpCk/Lengthk values to the total by dividing by the sum (SpCk/Lengthk) over all proteins.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:16:51.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Masoud zabet-moghaddam
SpeciesList	scientific name: Arachis hypogaea (Peanut); NCBI TaxID: 3818;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-01 03:35:25	ID requested
1	2013-10-17 07:36:49	announced
1	2013-10-17 07:41:19	announced
⏵ 2	2014-07-25 01:16:52	announced	Updated project metadata.

Dataset with its publication pending

submitter keyword: Peanut

Masoud zabet-moghaddam
contact affiliation	Center for Biotechnology and Genomics
contact email	masoud.zabet@ttu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000308
     1. Label: PRIDE project
     2. Name: Shotgun label-free quantitative proteomics of water-deficit stressed mid-mature peanut (Arachis hypogaea L.) seed