Table 2.

Summary of the different MS methodologies for the analysis of the ADP-ribosylated proteome. (site) indicates the studies where ADP-ribosylation site information is obtained. CID, collision-induced dissociation; HCD, higher-energy collisional dissociation; ETD, electron transfer dissociation; ETcaD, electron-transfer dissociation with supplemental collisional activation; EThcD, electron-transfer/higher-energy collision dissociation.

Affinity purification	Binding Specificity	Fragmentation MS2	Reference
Af1521 macrodomain	Bind to both mono- and poly-ADP-ribose	CID	Dani et al., 2009
Af1521 macrodomain	Bind to both mono- and poly-ADP-ribose	HCD	Jungmichel et al., 2009
10H antibody	Bind to poly-ADP-ribose (only units >10)	CID	Gagné et al., 2008
PARG-DEAD (catalytically inactive PARG)	Bind to poly-ADP-ribose	CID	Gagné et al., 2012
IMAC	For phosphopeptide enrichment	CID (site)	Chapman et al., 2013
IMAC	For phosphopeptide enrichment	CID/HCD (site)	Daniels et al., 2014
Boronate affinity chromatography	Boron forms ester bonds with the 1,2-cis-diol moiety in ADP-ribose; Asp-/Glu-ADP-ribose converted to hydroxamic acid	CID (site)	Zhang et al., 2013
IMAC	For phosphopeptide enrichment	ETD (site)	Leidecker et al., 2016
Af1521 macrodomain	Bind to both mono- and poly-ADP-ribose	HCD/ETD (site)	Martello et al., 2016
Af1521 macrodomain	Bind to both mono- and poly-ADP-ribose	HCD/ETcaD/EThcD (site)	Bilan et al., 2017