Generate protein expression profiles of the developing mouse cerebral cortex using tandem mass spectrometry (MS/MS).

<p>(A) A flow chart showing protein identification process using MS/MS. Protein expression was analyzed by MS/MS. To identify proteins with significant expression levels in the cortex, the ‘protein score’ with the threshold > 35 was applied. As a result, 1351, 1380, and 1327 proteins were identified in cortices at E13.5, E15.5 and P1, respectively. (B) Diagram summarizing the pattern of proteins found in mouse cortices at three developmental stages. Each sphere indicates proteins expressed at one stage. The overlapping part of the spheres indicates proteins identified at both stages. The numbers of proteins identified are labeled accordingly. (C) Frequency distribution of identified proteins by MS/MS. Identified proteins by MS/MS were assigned into different bins (from < -2 to > 8) by their protein expression value (see details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125608#sec002" target="_blank">Materials and Methods</a> for the definition of protein expression value). Briefly, protein matches were normalized and log2-transformed to generate protein expression value. The number of protein ID in each bin was summed as the frequency of this bin. (D) Proportional frequency distribution of identified proteins by MS/MS. Identified proteins by MS/MS were assigned into different bins by their protein expression value and the number of protein ID in each bin divided by the number of the total protein ID was summed as the proportional frequency of this bin.