Project PXD000308



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


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.

Sample Processing Protocol

See details in reference(s) : 24094305

Data Processing Protocol

See details in reference(s) : 24094305


Masoud zabet-moghaddam, Center for Biotechnology and Genomics

Submission Date


Publication Date



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Experiment Type

Bottom-up proteomics


    Kottapalli KR, Zabet-Moghaddam M, Rowland D, Faircloth W, Mirzaei M, Haynes PA, Payton P; Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed., J Proteome Res, 2013 Nov 1, 12, 11, 5048-57, PubMed: 24094305