Figure 2

Identification of variation in SWATH-MS data associated with biological and technical factors. (A) Experimental design showing 6 CLL patients samples (3 UM-CLL and 3 M-CLL) with replicate sample preparations (n = 3), each analysed in triplicate by SWATH-MS, resulting in 54 acquisitions and quantitative information for 5179 proteins across all samples. (B) PCA plot of uncorrected protein expression data showing sample clustering based on sample preparation day. (C) Results of ANOVA, limma and partial correlation analysis, highlighting the number of differentially expressed proteins identified (≤ 10% FDR) which are associated with technical variables (SWATH-MS run and sample preparation day) or biological variables (IGHV mutational subgroup (UM-CLL/M-CLL) and % of IGHV mutation). (D) Venn diagram showing overlap of proteins found to be differentially expressed between UM-CLL and M-CLL by ANOVA and limma and proteins correlating with the percentage of IGHV mutation by partial correlation analysis.