TABLE 2.
Summary of recent large-scale proteomics studies highlighting enrichment types and data analysis software used for the identification or site-specific localization of ADP-ribosylation
| Enrichment type | Samples analyzed | Activation | Data analysis | Sites searched | # Sites identified | # Proteins | References |
|---|---|---|---|---|---|---|---|
|
| |||||||
| Peptide level Afl521 | H2O2 treated HeLa cells and mouse liver digest | HCD | MaxQuant (+541.0611) | Lys, Arg, Glu, Asp | >900 | >500 | Martello et al. (2016) |
| Boronate, HA elution | Breast cancer cells | CID | SEQUEST (+15.0109) | Asp, Glu | 503 | 322 | Zhen et al. (2017) |
| Peptide level Afl521 | Mouse C2C12 cell line (myotubes), Mouse skeletal muscle (SM), Mouse heart muscle (HM) | HCD-PP- EThcD, HCD | Mascot (+541.0611) | Ser, Arg, Lys, Asp, Glu | Mostly Arg in WT; Ser, Lys, Asp, Glu in ARTC1KO | NAD+: 80C2C12 Control: 7C2C12 WT: 558SM ARTC1KO:29SM WT: 127HM ARTC1KO:23HM | Leutert et al. (2018) |
| Peptide level Afl521 | H2O2 treated HeLa cells | ETD | MaxQuant (+541.0611) | Cys, Asp, Glu, His, Lys, Arg, Ser, Thr, Tyr | 3450 3090 at Ser | 1370 1283 at Ser | Larsen et al. (2018) |
| Peptide level Afl521 | H2O2 treated HeLa cells | ETD, EThcD | MaxQuant (+541.0611) | Cys, Asp, Glu, His, Lys, Arg, Ser, Thr, Tyr | 7040 sites | 2149 | Hendriks et al. (2019) |
| Protein level Afl521 IP | PAPR7 overexpressed lung cancer cells | CID | Scaffold | Not specified | Not reported | 954 | Lu et al. (2019) |
| Peptide level; WT and eAfl521 | H2O2 treated and control HeLa cells | HCD-PP-EThcD | Mascot (+541.0611) | Ser, Arg, Lys, Asp, Glu, Tyr | Control: 5WT Treated: 118WT Control: 24e Treated: 327e | Control: 3WT Treated: 89WT Control: 19e Treated: 245e | Nowak et al. (2020) |
| Peptide level Afl521 | H2O2 treated and control HeLa cells | AI-ETD | MaxQuant (+541.0611) | Cys, Asp, Glu, His, Lys, Arg, Ser, Thr, Tyr | Control: 450; Treated: 5206 | Control: 295; Treated: 1800 | Buch-Larsen et al. (2020) |
| Peptide level Afl521 | H2O2 and methyl methanesulfonate treated U20S cells | EThcD | MaxQuant (+541.0611) | Cys, Asp, Glu, His, Lys, Arg, Ser, Thr, Tyr | Control: 268 Total: 1681 | Control: 168 Total: 716 | Buch-Larsen et al. (2021) |
| Peptide level Afl521; high pH fractionation | WT, HPF1 KO, and ARH3 KO U20S cells with or without H2O2 | EThcD | MaxQuant (+541.0611) | Cys, Asp, Glu, His, Lys, Arg, Ser, Thr, Tyr | 1596 | 799 | Hendriks et al. (2021, p. 3) |
| Peptide level Afl521 | Whole blood and plasma | HCD, EThcD | Mascot (+541.0611) | Asp, Glu, His, Lys, Arg, Ser, Tyr | Not reported | 60 in blood 17 in plasma | Lüthi et al. (2021) |
| Peptide level Afl521 | Spleen T-cells treated with NAD+ | HCD | Mascot (+541.0611) | Ser, Arg, Lys, Asp, Glu, Thr, Tyr | 36 (Arg, Ser) | 67 | Leutert, Duan, et al. (2021) |
| Peptide level Afl521 | HEK 293T cell lysate | EThcD | MaxQuant (+541.0611) | Cys, Asp, Glu, His, Lys, Arg, Ser, Thr, Tyr | 939 sites; 471 sites at Cys | 490; 374 Cys modified | Rodriguez et al. (2021) |
| Metabolic labeling (DTB-NAD+ analog) | HeLa cells treated with H2O2 and Olaparib | HCD | MaxQuant | Not specified | Not reported | Control: 35 H2O2: 120 Olaparib: 259 Both: 206 | Lehner et al. (2022) |
Abbreviations: DTB, desthiobiotin; e, engineered; HA, hydroxylamine; KO, knockout; Olaparib, PARP inhibitor; WT, wild type.