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Figure 1. Pearson correlation plot of replicate M1 and M2, and M1 and M3. The Pearson correlation R was approximately 0.90 for both replicates.

Figure 2. Protein ratio correlation between the five biologicial cell line replicates (4-mix and 5-mix).

Figure 3. Protein abundance indexes in the different cell lines. The protein abundance index contribution of the cell line (red crosses) estimated using the Normalized Abundance Factor (NSAF) and the normalized SILAC ratio obtained from MaxQuant is compared to the contribution of the Internal Standard (IS, green dots) for the five cell lines studied: (A) Molm-13, (B) MV4-11, (C) NB4, (D) OCI-AML3, and (E) THP-1. Protein abundance indexes are plotted against the average abundance index of the IS, only proteins quantified in at least three replicates with two or more unique peptides are considered here.

Figure 4. Protein expression pattern for Heat shock protein beta (HSPB1).

Table 1. Proteins quantified with two or more peptides were used to calculate the %CV of the triplicate analysis. Normalization was performed on the protein ratios by subtracting the median of all protein ratios in the column. M1 corresponds to run 1 (the values presented along with the other cell lines), M2 to technical replicate 2 and M3 to technical replicate 3.

Table 2.

Table 3.

Table 4. Example of how the four cell line-experiment was back-calculated in order to get protein ratios corresponding to the five cell line-experiment. R1 is protein ratio from the 5-mix, R2 is protein ratio from the 4-mix. R'1 is back calculated R2 (see supplementary Information, section 2.3 for details).

Table 5. The relative contributions of the mix and the different cell lines to the total protein abundance index is estimated from the MaxQuant results. This table contains the information used to create Supplementary Figure 3 and Supplementary Table II.

Table 6. Proteins linked to AML by the Kyoto Encyclopedia of Genes and Genomes (KEGG), found in pools from AML blast cell from time of diagnosis (E1) and during relapse (E2). The data was normalized based on the entire dataset (n=4253 proteins), and the fold change (FC) is displayed. Number of unique peptides from E1 and E2 is also listed, in addition to gene ontology annotation.

Table I. The table displays the 2.5% and 97.5% percentiles and Pearson R value for the biological replicates of the five cell lines (5-mix versus 4-mix) and technical replicates (M2 and M3 versus M1) of Molm-13.

Table II. The ratio of the abundance index obtained from the mix or the cell line relatively to the average of the abundance index in the mix (deviation to the y=x line in Supplementary Figure 3) was computed for every protein in every cell line. This table lists the interquartile distance (50% range) and the 2.5 to 97.5 percentiles distance (95% range) of this ratio for all cell lines replicates using the 5-mix IS. The value is given in log2 scale, the regulation it corresponds to is given in parenthesis when relevant. For example, when measured together with the Molm-13 cell line, 50% of the mix ratios were comprised in a deviation range of 0.44 in log2 scale which corresponds to ratios ranging from 0.86:1 to 1.16:1. 95% were comprised in a deviation range of 1.68 which corresponds to ratios ranging from 0.56:1 to 1.79:1. In comparison, for the cell line ratios, 50% were comprised in a deviation range of 0.71 in log scale which corresponds to ratios ranging from 0.78:1 to 1.28:1. 95% were comprised in a deviation range of 2.79 which corresponds to ratios ranging from 0.38:1 to 2.63:1.

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