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Volumn 14, Issue 9, 2015, Pages 4072-4079

Optimization of LTQ-orbitrap mass spectrometer parameters for the identification of ADP-ribosylation sites

Author keywords

ADP ribosylation; electron transfer dissociation; ETD; HCD; higher energy collisional dissociation; histone; LTQ Orbitrap; mass spectrometry; PARP

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSE; PROTEIN;

EID: 84941081849     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00432     Document Type: Article
Times cited : (44)

References (31)
  • 1
    • 33749260519 scopus 로고    scopus 로고
    • Nuclear ADP-ribosylation reactions in mammalian cells: Where are we today and where are we going?
    • Hassa, P. O.; Haenni, S.; Elser, M.; Hottiger, M. O. Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol. Mol. Biol. Rev. 2006, 70 (3) 789-829 10.1128/MMBR.00040-05
    • (2006) Microbiol. Mol. Biol. Rev. , vol.70 , Issue.3 , pp. 789-829
    • Hassa, P.O.1    Haenni, S.2    Elser, M.3    Hottiger, M.O.4
  • 2
    • 77951023118 scopus 로고    scopus 로고
    • Toward a unified nomenclature for mammalian ADP-ribosyltransferases
    • Hottiger, M. O.; Hassa, P. O.; Luscher, B.; Schuler, H.; Koch-Nolte, F. Toward a unified nomenclature for mammalian ADP-ribosyltransferases Trends Biochem. Sci. 2010, 35 (4) 208-19 10.1016/j.tibs.2009.12.003
    • (2010) Trends Biochem. Sci. , vol.35 , Issue.4 , pp. 208-219
    • Hottiger, M.O.1    Hassa, P.O.2    Luscher, B.3    Schuler, H.4    Koch-Nolte, F.5
  • 4
    • 70349935191 scopus 로고    scopus 로고
    • Identification of the ADP-ribosylation sites in the PARP-1 automodification domain: Analysis and implications
    • Tao, Z.; Gao, P.; Liu, H. Identification of the ADP-ribosylation sites in the PARP-1 automodification domain: analysis and implications J. Am. Chem. Soc. 2009, 131 (40) 14258-14260 10.1021/ja906135d
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.40 , pp. 14258-14260
    • Tao, Z.1    Gao, P.2    Liu, H.3
  • 5
    • 67649888368 scopus 로고    scopus 로고
    • Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites
    • Altmeyer, M.; Messner, S.; Hassa, P. O.; Fey, M.; Hottiger, M. O. Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites Nucleic Acids Res. 2009, 37 (11) 3723-38 10.1093/nar/gkp229
    • (2009) Nucleic Acids Res. , vol.37 , Issue.11 , pp. 3723-3738
    • Altmeyer, M.1    Messner, S.2    Hassa, P.O.3    Fey, M.4    Hottiger, M.O.5
  • 6
    • 84875939839 scopus 로고    scopus 로고
    • Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry
    • 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 J. Proteome Res. 2013, 12, 1868 10.1021/pr301219h
    • (2013) J. Proteome Res. , vol.12 , pp. 1868
    • Chapman, J.D.1    Gagne, J.P.2    Poirier, G.G.3    Goodlett, D.R.4
  • 7
    • 33644850114 scopus 로고    scopus 로고
    • The expanding role of poly(ADP-ribose) metabolism: Current challenges and new perspectives
    • Gagne, J. P.; Hendzel, M. J.; Droit, A.; Poirier, G. G. The expanding role of poly(ADP-ribose) metabolism: current challenges and new perspectives Curr. Opin. Cell Biol. 2006, 18 (2) 145-51 10.1016/j.ceb.2006.02.013
    • (2006) Curr. Opin. Cell Biol. , vol.18 , Issue.2 , pp. 145-151
    • Gagne, J.P.1    Hendzel, M.J.2    Droit, A.3    Poirier, G.G.4
  • 8
    • 38449088040 scopus 로고    scopus 로고
    • The diverse biological roles of mammalian PARPs, a small but powerful family of poly-ADP-ribose polymerases
    • Hassa, P. O.; Hottiger, M. O. The diverse biological roles of mammalian PARPs, a small but powerful family of poly-ADP-ribose polymerases Front. Biosci., Landmark Ed. 2008, 13, 3046-82 10.2741/2909
    • (2008) Front. Biosci., Landmark Ed. , vol.13 , pp. 3046-3082
    • Hassa, P.O.1    Hottiger, M.O.2
  • 9
    • 77954274504 scopus 로고    scopus 로고
    • The PARP side of the nucleus: Molecular actions, physiological outcomes, and clinical targets
    • Krishnakumar, R.; Kraus, W. The PARP side of the nucleus: Molecular actions, physiological outcomes, and clinical targets Mol. Cell 2010, 39 (1) 8-24 10.1016/j.molcel.2010.06.017
    • (2010) Mol. Cell , vol.39 , Issue.1 , pp. 8-24
    • Krishnakumar, R.1    Kraus, W.2
  • 13
    • 84886719040 scopus 로고    scopus 로고
    • PARP-1 and gene regulation: Progress and puzzles
    • Kraus, W. L.; Hottiger, M. O. PARP-1 and gene regulation: progress and puzzles Mol. Aspects Med. 2013, 34 (6) 1109-23 10.1016/j.mam.2013.01.005
    • (2013) Mol. Aspects Med. , vol.34 , Issue.6 , pp. 1109-1123
    • Kraus, W.L.1    Hottiger, M.O.2
  • 14
    • 84857891632 scopus 로고    scopus 로고
    • On PAR with PARP: Cellular stress signaling through poly(ADP-ribose) and PARP-1
    • Luo, X.; Kraus, W. L. On PAR with PARP: cellular stress signaling through poly(ADP-ribose) and PARP-1 Genes Dev. 2012, 26 (5) 417-432 10.1101/gad.183509.111
    • (2012) Genes Dev. , vol.26 , Issue.5 , pp. 417-432
    • Luo, X.1    Kraus, W.L.2
  • 15
    • 79957572693 scopus 로고    scopus 로고
    • ADP-ribosylation of histones by ARTD1: An additional module of the histone code?
    • Hottiger, M. O. ADP-ribosylation of histones by ARTD1: an additional module of the histone code? FEBS Lett. 2011, 585 (11) 1595-9 10.1016/j.febslet.2011.03.031
    • (2011) FEBS Lett. , vol.585 , Issue.11 , pp. 1595-1599
    • Hottiger, M.O.1
  • 16
    • 80052172007 scopus 로고    scopus 로고
    • Histone ADP-ribosylation in DNA repair, replication and transcription
    • Messner, S.; Hottiger, M. O. Histone ADP-ribosylation in DNA repair, replication and transcription Trends Cell Biol. 2011, 21 (9) 534-42 10.1016/j.tcb.2011.06.001
    • (2011) Trends Cell Biol. , vol.21 , Issue.9 , pp. 534-542
    • Messner, S.1    Hottiger, M.O.2
  • 17
    • 60649085333 scopus 로고    scopus 로고
    • Tandem mass spectrometry investigation of ADP-ribosylated kemptide
    • Hengel, S. M.; Shaffer, S. A.; Nunn, B. L.; Goodlett, D. R. Tandem mass spectrometry investigation of ADP-ribosylated kemptide J. Am. Soc. Mass Spectrom. 2009, 20 (3) 477-483 10.1016/j.jasms.2008.10.025
    • (2009) J. Am. Soc. Mass Spectrom. , vol.20 , Issue.3 , pp. 477-483
    • Hengel, S.M.1    Shaffer, S.A.2    Nunn, B.L.3    Goodlett, D.R.4
  • 18
    • 80054717097 scopus 로고    scopus 로고
    • Identification of distinct amino acids as ADP-ribose acceptor sites by mass spectrometry
    • Rosenthal, F.; Messner, S.; Roschitzki, B.; Gehrig, P.; Nanni, P.; Hottiger, M. O. Identification of distinct amino acids as ADP-ribose acceptor sites by mass spectrometry Methods Mol. Biol. 2011, 780, 57-66 10.1007/978-1-61779-270-0-4
    • (2011) Methods Mol. Biol. , vol.780 , pp. 57-66
    • Rosenthal, F.1    Messner, S.2    Roschitzki, B.3    Gehrig, P.4    Nanni, P.5    Hottiger, M.O.6
  • 19
    • 84870772480 scopus 로고    scopus 로고
    • Identification of ADP-ribosylation sites of CD38 mutants by precursor ion scanning mass spectrometry
    • Jiang, H.; Sherwood, R.; Zhang, S.; Zhu, X.; Liu, Q.; Graeff, R.; Kriksunov, I. A.; Lee, H. C.; Hao, Q.; Lin, H. Identification of ADP-ribosylation sites of CD38 mutants by precursor ion scanning mass spectrometry Anal. Biochem. 2013, 433 (2) 218-226 10.1016/j.ab.2012.10.029
    • (2013) Anal. Biochem. , vol.433 , Issue.2 , pp. 218-226
    • Jiang, H.1    Sherwood, R.2    Zhang, S.3    Zhu, X.4    Liu, Q.5    Graeff, R.6    Kriksunov, I.A.7    Lee, H.C.8    Hao, Q.9    Lin, H.10
  • 20
    • 68349128504 scopus 로고    scopus 로고
    • Precursor ion scanning and sequencing of arginine-ADP-ribosylated peptide by mass spectrometry
    • Osago, H.; Yamada, K.; Shibata, T.; Yoshino, K.-i.; Hara, N.; Tsuchiya, M. Precursor ion scanning and sequencing of arginine-ADP-ribosylated peptide by mass spectrometry Anal. Biochem. 2009, 393 (2) 248-54 10.1016/j.ab.2009.06.028
    • (2009) Anal. Biochem. , vol.393 , Issue.2 , pp. 248-254
    • Osago, H.1    Yamada, K.2    Shibata, T.3    Yoshino, K.-I.4    Hara, N.5    Tsuchiya, M.6
  • 21
    • 84857062060 scopus 로고    scopus 로고
    • A Review of Tandem Mass Spectrometry Characterization of Adenosine Diphosphate-Ribosylated Peptides
    • Hengel, S. M.; Goodlett, D. R. A Review of Tandem Mass Spectrometry Characterization of Adenosine Diphosphate-Ribosylated Peptides Int. J. Mass Spectrom. 2012, 312, 114-121 10.1016/j.ijms.2011.06.003
    • (2012) Int. J. Mass Spectrom. , vol.312 , pp. 114-121
    • Hengel, S.M.1    Goodlett, D.R.2
  • 22
    • 84905366697 scopus 로고    scopus 로고
    • Phosphoproteomic Approach to Characterize Protein Mono- and Poly(ADP-ribosyl)ation Sites from Cells
    • Daniels, C. M.; Ong, S. E.; Leung, A. K. Phosphoproteomic Approach to Characterize Protein Mono- and Poly(ADP-ribosyl)ation Sites from Cells J. Proteome Res. 2014, 13 (8) 3510-22 10.1021/pr401032q
    • (2014) J. Proteome Res. , vol.13 , Issue.8 , pp. 3510-3522
    • Daniels, C.M.1    Ong, S.E.2    Leung, A.K.3
  • 23
    • 84886246082 scopus 로고    scopus 로고
    • Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses
    • Jungmichel, S.; Rosenthal, F.; Altmeyer, M.; Lukas, J.; Hottiger, M. O.; Nielsen, M. L. Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses Mol. Cell 2013, 52 (2) 272-85 10.1016/j.molcel.2013.08.026
    • (2013) Mol. Cell , vol.52 , Issue.2 , pp. 272-285
    • Jungmichel, S.1    Rosenthal, F.2    Altmeyer, M.3    Lukas, J.4    Hottiger, M.O.5    Nielsen, M.L.6
  • 24
    • 78149391462 scopus 로고    scopus 로고
    • H-score, a mass accuracy driven rescoring approach for improved peptide identification in modification rich samples
    • Savitski, M. M.; Mathieson, T.; Becher, I.; Bantscheff, M. H-score, a mass accuracy driven rescoring approach for improved peptide identification in modification rich samples J. Proteome Res. 2010, 9 (11) 5511-5516 10.1021/pr1006813
    • (2010) J. Proteome Res. , vol.9 , Issue.11 , pp. 5511-5516
    • Savitski, M.M.1    Mathieson, T.2    Becher, I.3    Bantscheff, M.4
  • 26
    • 84881232861 scopus 로고    scopus 로고
    • PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications
    • Nanni, P.; Panse, C.; Gehrig, P.; Mueller, S.; Grossmann, J.; Schlapbach, R. PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications Proteomics 2013, 13 (15) 2251-5 10.1002/pmic.201300036
    • (2013) Proteomics , vol.13 , Issue.15 , pp. 2251-2255
    • Nanni, P.1    Panse, C.2    Gehrig, P.3    Mueller, S.4    Grossmann, J.5    Schlapbach, R.6
  • 27
    • 80052472260 scopus 로고    scopus 로고
    • Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment
    • Zhao, P.; Viner, R.; Teo, C. F.; Boons, G. J.; Horn, D.; Wells, L. Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment J. Proteome Res. 2011, 10 (9) 4088-104 10.1021/pr2002726
    • (2011) J. Proteome Res. , vol.10 , Issue.9 , pp. 4088-4104
    • Zhao, P.1    Viner, R.2    Teo, C.F.3    Boons, G.J.4    Horn, D.5    Wells, L.6
  • 28
    • 84866084330 scopus 로고    scopus 로고
    • Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins
    • Singh, C.; Zampronio, C. G.; Creese, A. J.; Cooper, H. J. Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins J. Proteome Res. 2012, 11 (9) 4517-25 10.1021/pr300257c
    • (2012) J. Proteome Res. , vol.11 , Issue.9 , pp. 4517-4525
    • Singh, C.1    Zampronio, C.G.2    Creese, A.J.3    Cooper, H.J.4
  • 29
    • 79959682385 scopus 로고    scopus 로고
    • Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity
    • Mayampurath, A. M.; Wu, Y.; Segu, Z. M.; Mechref, Y.; Tang, H. Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity Rapid Commun. Mass Spectrom. 2011, 25 (14) 2007-19 10.1002/rcm.5059
    • (2011) Rapid Commun. Mass Spectrom. , vol.25 , Issue.14 , pp. 2007-2019
    • Mayampurath, A.M.1    Wu, Y.2    Segu, Z.M.3    Mechref, Y.4    Tang, H.5
  • 30
    • 84884906084 scopus 로고    scopus 로고
    • Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome
    • Zhang, Y.; Wang, J.; Ding, M.; Yu, Y. Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome Nat. Methods 2013, 10, 981 10.1038/nmeth.2603
    • (2013) Nat. Methods , vol.10 , pp. 981
    • Zhang, Y.1    Wang, J.2    Ding, M.3    Yu, Y.4


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