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Though ADP-ribosylation is therapeutically important, investigation of this protein modification has been limited by a lack of proteomic tools for site identification. Recent work has demonstrated the potential of a tag-based pipeline in which MAR\/PAR is hydrolyzed down to phosphoribose, leaving a 212 Dalton tag at the modification site. While the pipeline has been proven effective by multiple groups, a barrier to application has become evident: the enzyme used to transform MAR\/PAR into phosphoribose must be purified from the rattlesnake <jats:italic>Crotalus adamanteus<\/jats:italic> venom, which is contaminated with proteases detrimental for proteomic applications. Here, we outline the steps necessary to purify snake venom phosphodiesterase I (SVP) and describe two alternatives to SVP\u2014the bacterial Nudix hydrolase <jats:italic>Ec<\/jats:italic>RppH and human <jats:italic>Hs<\/jats:italic>NudT16. Importantly, expression and purification schemes for these Nudix enzymes have already been proven, with high-quality yields easily attainable. We demonstrate their utility in identifying ADP-ribosylation sites on Poly(ADP-ribose) Polymerase 1 (PARP1) with mass spectrometry and discuss a structure-based rationale for this Nudix subclass in degrading protein-conjugated ADP-ribose, including both MAR and PAR.<\/jats:p>","DOI":"10.1038\/srep18271","type":"journal-article","created":{"date-parts":[[2015,12,16]],"date-time":"2015-12-16T10:34:53Z","timestamp":1450262093000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":65,"title":["Nudix hydrolases degrade protein-conjugated ADP-ribose"],"prefix":"10.1038","volume":"5","author":[{"given":"Casey M.","family":"Daniels","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Puchong","family":"Thirawatananond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shao-En","family":"Ong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra B.","family":"Gabelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony K. 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A phosphoproteomic approach to characterize protein mono and poly(ADP-ribosyl)ation sites from whole cell lysate. Journal of proteome research, 10.1021\/pr401032q (2014).","DOI":"10.1021\/pr401032q"},{"key":"BFsrep18271_CR6","doi-asserted-by":"crossref","unstructured":"Chapman, J. D., Gagne, J. P., Poirier, G. G. & Goodlett, D. R. Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry. Journal of proteome research, 10.1021\/pr301219h (2013).","DOI":"10.1021\/pr301219h"},{"key":"BFsrep18271_CR7","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1016\/j.jasms.2008.10.025","volume":"20","author":"SM Hengel","year":"2009","unstructured":"Hengel, S. M., Shaffer, S. A., Nunn, B. L. & Goodlett, D. R. Tandem mass spectrometry investigation of ADP-ribosylated kemptide. 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