Optimization of LTQ-Orbitrap Mass Spectrometer Parameters for the Identification of ADP-Ribosylation Sites

Rosenthal, Florian; Nanni, Paolo; Barkow-Oesterreicher, Simon; Hottiger, Michael O.

doi:10.1021/acs.jproteome.5b00432

Cited by 49 publications

(88 citation statements)

References 31 publications

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“…Although the use of ETD alone yielded fewer peptides carrying an ADP-ribose moiety compared with HCD, the ETD fragmentation did allow for the detection of certain unique peptides not present in the HCD subset (Rosenthal et al 2015). Moreover, a combinatorial approach using the two techniques together was more robust in the identification of ADP-ribosylated peptides (Rosenthal et al 2015). The benefits and drawbacks of each of the approaches mentioned here must be considered when designing experiments to detect ADP-ribosylated proteins.…”

Section: Ms Methods For the Detection Of Adp-ribosylationmentioning

confidence: 98%

“…The use of these MS techniques may lead to a loss of the labile ADP-ribose units from amino acid residues, resulting in a reduced number of sites identified. The use of electron transfer dissociation (ETD) has been suggested as an alternative that allows the ADP-ribose chains to remain intact, thus providing wider coverage (Rosenthal et al 2015). Although the use of ETD alone yielded fewer peptides carrying an ADP-ribose moiety compared with HCD, the ETD fragmentation did allow for the detection of certain unique peptides not present in the HCD subset (Rosenthal et al 2015).…”

Section: Ms Methods For the Detection Of Adp-ribosylationmentioning

confidence: 99%

“…The use of electron transfer dissociation (ETD) has been suggested as an alternative that allows the ADP-ribose chains to remain intact, thus providing wider coverage (Rosenthal et al 2015). Although the use of ETD alone yielded fewer peptides carrying an ADP-ribose moiety compared with HCD, the ETD fragmentation did allow for the detection of certain unique peptides not present in the HCD subset (Rosenthal et al 2015). Moreover, a combinatorial approach using the two techniques together was more robust in the identification of ADP-ribosylated peptides (Rosenthal et al 2015).…”

Section: Ms Methods For the Detection Of Adp-ribosylationmentioning

confidence: 99%

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PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

2017

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The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field.ADP-ribosylation is a reversible post-translational modification (PTM) of proteins resulting in the covalent attachment of a single ADP-ribose unit [i.e., mono(ADP-ribose) (MAR)] or polymers of ADP-ribose units [i.e., poly(ADP-ribose) (PAR)] on a variety of amino acid residues on target proteins (Gibson and Kraus 2012;Daniels et al. 2015a). This modification is mediated by a diverse group of ADPribosyl transferase (ADPRT) enzymes that use ADP-ribose units derived from β-NAD + to catalyze the ADP-ribosylation reaction. These enzymes include bacterial ADPRTs (e.g., cholera toxin and diphtheria toxin) as well as members of three different protein families in yeast and animals: (1) arginine-specific ecto-enzymes (ARTCs), (2) sirtuins, and (3) PAR polymerases (PARPs) . Surprisingly, a recent study showed that the bacterial toxin DarTG can ADP-ribosylate DNA . How this fits into the broader picture of cellular ADP-ribosylation has yet to be determined.In this review, we focus on the mono(ADP-ribosyl)ation (MARylation) and poly(ADP-ribosyl)ation (PARylation) of glutamate, aspartate, and lysine residues by PARP family members. While many reviews have been written on PARPs in the past decade, we highlight the current trends and ideas in the field, in particular those discoveries that have been published in the past 2-3 years.

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Section: Ms Methods For the Detection Of Adp-ribosylationmentioning

confidence: 98%

Section: Ms Methods For the Detection Of Adp-ribosylationmentioning

confidence: 99%

Section: Ms Methods For the Detection Of Adp-ribosylationmentioning

confidence: 99%

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PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

2017

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“…2,6,17–20 In order to elucidate how histone ADP-ribosylation is involved in DNA damage response and repair, it is important to first understand where the modifications occur during this process. However, ADP-ribosylation is a particularly challenging PTM to identify for several reasons: (1) it is highly heterogeneous, i.e.…”

Section: Introductionmentioning

confidence: 99%

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage

et al. 2017

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ADP-ribosylation is a protein post-translational modification catalyzed by ADP-ribose transferases (ARTs). ART activity is critical in mediating many cellular processes, and is required for DNA damage repair. All five histone proteins are extensively ADP-ribosylated by ARTs upon induction of DNA damage. However, how these modifications aid in repair processes is largely unknown, primarily due to lack of knowledge about where they site-specifically occur on histones. Here, we conduct a comprehensive analysis of histone Asp/Glu ADP-ribosylation sites upon DNA damage induced by dimethyl sulfate (DMS). We also demonstrate that incubation of cell nuclei with NAD+, as has been done previously in the literature, leads to spurious ADP-ribosylation levels of histone proteins. Altogether, we were able to identify 30 modification sites, 20 of which are novel. We also quantify the abundance of these modification sites during the course of DNA damage insult to identify which sites are critical for mediating repair. We found that every quantifiable site increases in abundance over time and that each identified ADP-ribosylation site is located on the surface of the nucleosome. Together, the data suggest specific Asp/Glu residues are unlikely to be critical for DNA damage repair and rather that this process is likely dependent on ADP-ribosylation of the nucleosomal surface in general.

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“…As a post-translational modification (PTM), the study of ADP-ribosylation is best aided by the global assessment of the PTM attachment sites by mass spectrometry (MS). Recent advances within the field have allowed for endogenous ADP-ribosylation site identification by MS [13–23]. Three major methods have been described to identify ADP-ribosylation sites (reviewed recently in [16,24])—progress which will aid the ADP-ribosylation field for years to come.…”

Section: Introductionmentioning

confidence: 99%

ADP-Ribosylated Peptide Enrichment and Site Identification: The Phosphodiesterase-Based Method

Daniels

Ong

Leung

2017

Methods in Molecular Biology

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Protein ADP-ribosylation is a post-translational modification (PTM) that plays an important role in all major cellular processes, including DNA repair, cellular signaling, and RNA metabolism. Site identification for this PTM has recently become possible through the development of several mass spectrometry based methods, a critical step in understanding the regulatory role played by mono(ADP-ribose) (MAR), poly(ADP-ribose) (PAR), and the enzymes which make these modifications: Poly(ADP-ribose) Polymerases (PARPs), best known for their role in DNA repair and as targets for chemotherapeutic PARP inhibitors. Here, we have described our method for enriching and identifying ADP-ribosylation events through the use of a phosphodiesterase to digest protein-conjugated ADP-ribose down to its attachment structure, phosphoribose. We also include here a guide to choosing between Collision-induced dissociation (CID), Higher-energy collisional dissociation (HCD) and Electron-transfer dissociation (ETD) based peptide fragmentation for the identification of phosphoribosylated peptides.

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Optimization of LTQ-Orbitrap Mass Spectrometer Parameters for the Identification of ADP-Ribosylation Sites

Cited by 49 publications

References 31 publications

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage

ADP-Ribosylated Peptide Enrichment and Site Identification: The Phosphodiesterase-Based Method

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