Fig. 4: Comparison of HarmonizR and iRS for the batch effect reduction in Multiplex TMT experiments at the peptide and protein level. | Nature Communications

Fig. 4: Comparison of HarmonizR and iRS for the batch effect reduction in Multiplex TMT experiments at the peptide and protein level.

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

Fig. 4

a Experimental design. b Batch count distribution of 12615 peptides quantified. c Batch count distribution of 2579 proteins quantified. d Scatter plot distribution of samples across PC1 and PC3 in NIPALS-PCA, based on 8877 peptides found in 50% of all samples and corresponding sample specific CV/means for each TMT batch for unnormalized data, after iRS normalization and after HarmonizR (ComBat). (All batches represented n = 8 biologically independent samples. (Control: n = 3; Cetuximab 24 h: n = 1; Cetuximab 0–3 h: n = 3; Internal reference: n = 2). 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 Scatter plot distribution of samples across PC1 and PC3 in NIPALS-PCA, based on 2152 proteins found in 50% of all samples and corresponding; sample specific CV/means for each TMT batch for unnormalized data, after iRS normalization and after HarmonizR (ComBat). (All batches represented n = 8 biologically independent samples. (Control: n = 3; Cetuximab 24 h: n = 1; Cetuximab 0–3 h: n = 3; Internal reference: n = 2). 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. f Overall and batch-specific variation of specific peptides for the housekeeping protein NUDT21 for unnormalized data, after iRS normalization, and after HarmonizR (ComBat). g Overall and batch-specific variation of NUDT21 for unnormalized data, after iRS normalization and after HarmonizR (ComBat) at protein level. Source data are provided as a Source Data file.

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