Extended Data Fig. 2: Correlation coefficients and imputation strategy for mass spectrometry data.
From: Outlining cardiac ion channel protein interactors and their signature in the human electrocardiogram
a) Heat map visualizing Pearson correlation coefficients for all measured protein intensities across all experiments. The experiments were carried out in quadruplicates (named as _01, _02, _03, _04) and the figure shows the Pearson correlation values between all the baits and their replicates calculated from the log2 transformed raw intensities of all identified proteins. The darker shade of blue indicates a higher Pearson correlation. The numbers in blue on the right side depict the mean Pearson correlation coefficient for each set of four replicates per bait IP. b) Distributions showing the source of protein intensities used in the comparative analysis of each control. As seen, most data come from the median of all measured IP experiments. If no value was present in the median value, a value was used from control IgG pulldown experiments. If no value was available from both the above sources, a scaled proteome measurement was imputed. And in the few cases where no value was obtainable from the proteome either, the value was imputed from a left shifted normal distribution.
