Computational protocol: Differential accumulation of proteins in oil palms affected by fatal yellowing disease

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Protocol publication

[…] We compared asymptomatic and symptomatic roots of plants collected in two different areas. Datasets were analyzed separately. A comparison was also made between proteomes obtained from roots in the initial, intermediate and advanced stages (stages 1, 5 and 9, respectively) in order to identify differential accumulation throughout the progression of FY symptoms. This last experiment was performed only with the proteomes of roots of plants sampled in the first area.The peptic identification list was generated by the Protein Lynx Global Server (PLGS) 3.0.2 (Waters Corp, Milford, MA, USA) using a combination of exact mass and MSE fragment data. Processed spectra were then searched against a custom protein database compiled from Elaeis guineensis Jacq. at the website of the National Center for Biotechnology Information (NCBI:, 04/2016). Management and validation of mass spectrometry data were performed using the Scaffold Q+ (Scaffold version 4.5.1, Proteome Software Inc., Portland, OR). Protein identification was only accepted if the peptide identification probability was greater than 90% and proteins greater 95% accordingly to the peptideprophet and proteinprophet algorithms []. Differentially expressed proteins were determined by applying a permutation test with significance level grater than 95% (p < 0.05). Statistical significance (P-values) for quantitative measurements are available in , and Tables. With few exceptions, in this study we used the cutoff criterion of more or less abundant proteins of log2 fold change ≥ 1 for more abundant proteins and log2 fold change ≤ -1 for less abundant proteins. In addition, we highlighted proteins identified in at least two replicates. Functional annotation of proteins was performed with Blast2GO version 4.0 (Biobam). The heatmap with proteins involved in stress response and energy metabolism was calculated by the R statistical software, through the utilization of the heatmap.2 function available in the gplots R package. […]

Pipeline specifications

Software tools Scaffold Q+, PeptideProphet, ProteinProphet, Blast2GO, gplots
Databases JACQ
Application MS-based untargeted proteomics
Diseases Congenital Abnormalities
Chemicals Acetaldehyde, Ethanol, S-Adenosylmethionine