Fig. 2: Evaluation of different erasers and enrichers for the purification of ADPr.

a Overview of the experimental design. HeLa cells were cultured, H₂O₂-treated at 1 mM for 10 min, lysed, and either mock treated, PARG-treated, or ARH3-treated. Quadruplicate (n = 4) ADPr peptide purifications were performed using either Af1521 macrodomain, E6F6A antibody (AB1), or D9P7Z antibody (AB2). ADPr peptides were analyzed using ETD-based high-resolution MS. b Overview of the number of ADPr sites identified and localized (>90% probability). Data are presented as mean values ± SD, n = 4 purification replicates. “C”; control, “P”; PARG, “A”; ARH3, “MBR”; matching between runs. c Visualization of the abundance fraction of ADPr as distributed across different amino acid residue types. d Scatter plot analysis demonstrating the correlation between mock-treated and PARG-treated ADPr sites. “R” indicates Pearson correlation, p-value determined via linear regression t test. e Volcano plot analysis comparing ARH3-treated versus mock-treated Af1521-enriched ADPr sites. Red and blue dots indicate significantly down- and upregulated sites, respectively. Significance was determined via two-tailed Student’s t testing, with permutation-based FDR-control applied with an s0 fuzz factor of 0.5 and 2500 rounds of randomization, to ensure a corrected p-value of <1%. f As e, but comparing PARG-treated versus mock-treated Af1521-enriched ADPr sites. Source data are provided as a Source Data file.