Comparison and validation of SOD and CAT by iTRAQ profiling and enzyme activity assays.

<p>iTRAQ analysis showed quantitative changes of SOD and CAT during three developmental stages (A). Activity assays for SOD and CAT were conducted to validate the iTRAQ results (B and C, respectively). Bars represent standard errors (n = 3). Significantly different groups are indicated by different lowercase letters (<i>P</i> < 0.05).</p

Functional classification on differential proteins with iTRAQ ratios > or < 1.2-fold.

<p>^<i>a</i> Protein accession numbers in Swiss-prot</p><p>^<i>b</i> The iTRAQ ratios for PEM, GE and CE using PEM as control</p><p>^<i>c</i> The clusters (expression pattern) that proteins are ascribed</p><p>^<i>d</i> Proteins that have no GO annotations</p><p>Functional classification on differential proteins with iTRAQ ratios > or < 1.2-fold.</p

The development of cultured somatic embryos in <i>L</i>. <i>principis-rupprechtii</i>.

<p>Samples were imaged at three developmental stages: PEM (A, bar = 500μm; B, bar = 100μm), GE (C, bar = 200μm) and CE (D, bar = 500μm).</p

Cluster analysis of proteins differentially expressed during SE.

<p>Four clusters were generated to classify proteins during three time points: PEM stage, GE stage and CE stage. The membership values are used to assess how well a given entry fits the consensus profile and allows color coding cluster graph items according to their goodness of fit to the cluster consensus profile.</p

Experimental design and iTRAQ workflow used in this study.

<p>Samples were analyzed by iTRAQ coupling with nanoLC-MS/MS for examining the proteome changes during SE in <i>L</i>. <i>principis-rupprechtii</i>. Proteins were identified using MASCOT software.</p

Cluster profiles of protein functional clusters during somatic embryo development.

<p>A heat map of the log 2 relative abundance of proteins during SE in relation to the PEM stage was created with the iTRAQ-derived quantitative data. Proteins were grouped according to their known or putative biological functions. For each protein, accession number and protein description are provided. Yellow indicates upregulation, blue denotes downregulation, and black signifies zero difference. The grading represents the ratios of protein expression levels.</p

Functional categorization of differentially expressed proteins during SE.

<p>Ninety-six differentially expressed proteins during three developmental stages (PEM, GE and CE) were categorized based on “Cellular Component,” “Molecular Function,” and “Biological Process” using WEGO.</p