Dataset Information

Shotgun label-free quantitative proteomics of water-deficit stressed mid-mature peanut (Arachis hypogaea L.) seed

ABSTRACT: 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.

INSTRUMENT(S): LTQ

ORGANISM(S): Arachis Hypogaea (peanut)

SUBMITTER: Masoud zabet-moghaddam

PROVIDER: PXD000308 | Pride | 2013-10-17

REPOSITORIES: Pride

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Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed.

Kottapalli Kameswara Rao KR Zabet-Moghaddam Masoud M Rowland Diane D Faircloth Wilson W Mirzaei Mehdi M Haynes Paul A PA Payton Paxton P

Journal of proteome research 20131014 11

Legume seeds and peanuts, in particular, are an inexpensive source of plant proteins and edible oil. A comprehensive understanding of seed metabolism 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 ...[more]

PMID: 24094305

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			Action	DRS
	ContolR1.xml	Xml
	Control-R1-mzXML.zip	Other
	Control-R1.zip	Other
	Control-R2-mzXML.zip	Other
	Control-R2.zip	Other