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Protein identification and data analysis

GZ Guofang Zhang
LL Libo Liu
CL Chun Li
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The raw mass spectrometry data were submitted to Mascot 2.2 software (Matrix Science, London, UK) through Proteome Discoverer 1.4, and searches were performed against the L. bulgaricus database, which contains 24,177 protein sequences, for protein identification and quantification. The screening conditions for the trusted proteins included a false discovery rate of no more than 1%, which was calculated with a decoy database model, and the protein ratios were quantified based on the median of only unique peptide ratios in Mascot. The t-test was used to evaluate statistical significance. Proteins with the fold-change of ≥ 1.5 or ≤ −1.5 and P-value < 0.05 were considered significantly up-regulated or down-regulated, respectively. The Blast2GO program was used to annotate the molecular function, biological process and cellular component information for the target proteins. Metabolic pathway analysis of the differentially expressed proteins was performed using KEGG.

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