Fig. 5: Data harmonization across different quantification approaches (DDA, TMT, and SILAC) for Cetuximab treated HiFi cells. | Nature Communications

Fig. 5: Data harmonization across different quantification approaches (DDA, TMT, and SILAC) for Cetuximab treated HiFi cells.

From: HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values

Fig. 5

a Scheme of the experimental design. b Batch count distribution of 6754 proteins quantified. c Batch-specific coverage of proteins, associated with the EGFR signaling network (Stepath et al., 2020). d Scatter plot distribution of samples across the top two principal components (PC) in NIPALS-PCA, based on 2368 proteins, found in 50% of all samples for unnormalized data after SILAC ratio adjustment and data after HarmonizR (ComBat). Lower panels show corresponding sample-specific CV and mean values. (DDA: n = 24 biologically independent samples (Control: n = 12; Cetuximab 24 h: n = 4; Cetuximab 0–3 h: n = 8); TMT: n = 24 biologically independent samples (Control: n = 12; Cetuximab 24 h: n = 4; Cetuximab 0–3 h: n = 8); SILAC: n = 23 biologically independent samples (Control: n = 12; Cetuximab 24 h: n = 4; Cetuximab 0–3 h: n = 7); TMT: 32 biologically independent samples (Control: n = 12; Cetuximab 24 h: n = 4; Cetuximab 0–3 h: n = 7; Internal reference: n = 8)). In boxplots, 50% of the data points are inside the box (Q1 (Quartile 1) being the lower bound of the box (25%), Q3 being the upper bound of the box (75%)). Whiskers show all values beyond the box without outliers. Outliners were defined as Q3 + 1.5 * IQR (Interquartile range) (upper outlier) and Q1-1.5 * IQR (lower outlier). IQR being Q1–Q3. e Overall and batch specific variation of the housekeeping protein NUDT21 for unnormalized data, after SILAC ratio adjustment and after HarmonizR (ComBat) usage. Source data are provided as a Source Data file.

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