Project PXD000470

PRIDE Assigned Tags:
Biological Dataset



Proteome analysis of Brachypodium distachyon leaf under salt stress and recovery


Brachypodium distachyon is a new model plant for wheat, barley and several potential biofuel grasses. The Bd21 leaf was initially treated with salt concentrations ranging from 80 to 320 mM followed by a recovery process prior to proteome analysis. Leaf total protein was extracted according to the method of Wang et al. with minor modifications, followed by 2D DIGE separation as recommended by the manufacturer (GE Healthcare). The differentially expressed proteins spots were identified using ImageMaster 2D Platinum Software Version 5.0 (Amersham Biosciences). Protein identification was carried out by the ABI 4800 Proteomics Analyzer MALDI-TOF/TOF (Applied Biosystems, Foster City) operating in a result-dependent acquisition mode. Peptide mass maps were acquired in positive ion reflector mode (20 kV accelerating voltage) with 1000 laser shots per spectrum. Monoisotopic peak masses were automatically determined within the mass range 800-4000 Da with a signal to noise ratio minimum set to 10 and a local noise window width of m/z 250. Up to five of the most intense ions with minimum signal to noise ratio 50 were selected as precursors for MS/MS acquisition, excluding common trypsin autolysis peaks and matrix ion signals. In MS/MS-positive ion mode, spectra were averaged, collision energy was 2 kV, and default calibration was set. Monoisotopic peak masses were automatically determined with a signal to noise ratio minimum set to 5 and a local noise window width of m/z 250. The MS together with MS/MS spectra were searched against NCBI Brachypodium protein database (26035 entries in total, downloaded on July 16, 2011) using the software MASCOT version 2.1 (Matrix Science) with the following parameter settings: trypsin cleavage, one missed cleavage allowed, carbamidomethylation set as fixed modification, oxidation of methionines and phosphorylation of serine, threonine, and tyrosine allowed as variable modification, peptide mass tolerance set to 100 ppm and fragment tolerance set to ± 0.3 Da. All searches were evaluated based on the significant scores obtained from MASCOT. The results were creditable with Protein Score C. I. % and Total Ion Score C. I. % both above 95% and significance threshold p < 0.05 for the MS/MS.

Sample Processing Protocol

See details in reference(s) : 24335353

Data Processing Protocol

See details in reference(s) : 24335353


Dong-Wen Lv, College of Life Sciences

Submission Date


Publication Date



Not available


phosphorylated residue


Not available

Experiment Type

Bottom-up proteomics


    Lv DW, Subburaj S, Cao M, Yan X, Li X, Appels R, Sun DF, Ma W, Yan YM; Proteome and phosphoproteome characterization reveals new response and defense mechanisms of Brachypodium distachyon leaves under salt stress., Mol Cell Proteomics, 2013 Dec 11, PubMed: 24335353