Fig. 3: Low technical noise allows for analysis of hPTM biological cell-to-cell variability. | Nature Communications

Fig. 3: Low technical noise allows for analysis of hPTM biological cell-to-cell variability.

From: Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity

Fig. 3: Low technical noise allows for analysis of hPTM biological cell-to-cell variability.

A, B CV of histone peptidoform relative abundances for histone standard technical replicates within each batch (intra-) (A) and across the batches 1–3 (inter-) (B). For results using raw MS1 intensities see Supplementary Fig. 8A, B. Statistics: for number of injections analyzed in each group per batch see Supplementary Fig. 5B. Boxplots show the median (center), the 25th and 75th percentiles (bounds), and whiskers extending to the most extreme data points within 1.5× IQR; points beyond whiskers are plotted individually as outliers. C CV of histone peptidoform relative abundances for 10 pg histone standard technical replicates across batches 1–3 compared to bulk technical replicates of HeLa cells (Sidoli et al. A49; Sidoli et al. B50) and processing replicates of cell lines treated with DMSO in the NIH LINCS (Dele-Oni et al.33). Histone peptidoforms were filtered to match those quantified in each respective study (Supplementary Table 2). Statistics: histone standard 10 pg (all panels) n = 12, Sidoli et al. A49 Hela n = 5, Sidoli et al. B49 Hela n = 4, Dele-Oni et al. (LINCS)33 n = 3; boxplots show the median (center), the 25th and 75th percentiles (bounds), and whiskers extending to the most extreme data points within 1.5× IQR; points beyond whiskers are plotted individually as outliers. D CV of histone peptidoform relative abundances for 10 pg histone standard compared to single cells across batches 1-3 and matched by 39 peptidoforms. Statistics: histone standard 10 pg n = 12, single cells n = 22; two-sided paired Wilcoxon test, ****p ≤ 0.0001; boxplots show the median (center), the 25th and 75th percentiles (bounds), and whiskers extending to the most extreme data points within 1.5× IQR. E, F CV of histone peptidoform relative abundances ranked from highest to lowest amongst single-cells from batches 1–3, shown with technical noise (E) and after removal of technical noise (i.e., cell-to-cell variation) (F). Source data are provided as a Source Data file.

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