Fig. S1. PCA of the relative abundance profiles of each protein, with any protein not detected at any growth temperature excluded. By scoring the non-detected data as zero (Fig. 1) or eliminating from the input data matrix all proteins that were non-detected in at least one condition (Fig. S1), we evaluated the overall effects of not detecting a protein and found that the trends were similar. This additional assessment was included in view of the proteomics changes occurring at −2°C that reflect physiological changes leading to aggregation. A. Heat-map showing the clustering of individual data sets from six temperatures (−2°C, 1°C, 4°C, 10°C, 16°C, 28°C), with 23°C used as the reference for normalization. Biological and technical replicates were combined to give weighted average abundance ratios for each protein. The average Pearson distance metrics were used to define the column clustering. The legend represents the relative scaled abundance of each individual protein at the different temperatures. B. PCA line-plot of proteins differentially expressed shown as a 12 × 12 grid. The Cartesian space of the first 2 principal components loadings and rotations was divided in a 12 × 12 cell grid. The scale for the loadings is reported on the top (PC1) and right (PC2) side of the figure. The scale for the rotations is reported on the bottom (PC1) and left (PC2) side of the figure. Each protein and temperature was assigned to a cell based on its loading and rotation score respectively. The line graphs in each cell represent the relative abundance profiles at −2°C, 1°C, 4°C, 10°C, 16°C, 28°C (from left to right). The first principal component (PC1) explained 46.3% of the variance while PC2 explained 19.2%. Locus tag is provided for proteins with the highest PC loadings. Proteins inferred to be secreted or cell surface proteins are labelled in blue. A spot for 23°C is provided (as a reference) at the axis origin for the rotations. Abbreviations: sol, soluble fraction; sup, supernatant fraction; insol, insoluble fraction.

Fig. S2. Flow chart outlining the use of multiplex iTRAQ with biological and technical replicates of fractionated samples for M. burtonii grown at seven different temperatures.

Table S1. Abundance ratios of selected differentially abundant proteins in M. burtonii at different growth temperatures.

Table S2. Abundance ratios of all differentially abundant proteins in M. burtonii at different growth temperatures.

Table S3. All M. burtonii proteins identified using iTRAQ post-incorporation labelling and LC/LC–MS/MS.

Table S4. Numbers of proteins, peptides and spectra applying a false discovery rate (FDR) of 1%.

EMI_2467_sm_FigS1-2-TableS1_S3-4.pdf1242KSupporting info item
EMI_2467_sm_tS2.xls157KSupporting info item

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