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Volumn 9, Issue 1, 2010, Pages 585-594

MS/MS/MS reveals false positive identification of histone serine methylation

Author keywords

C terminal elimination; Charge dependence; False positive identification; Histone modifications; Loss of C terminal; MS MS MS analysis; Protein methylation; Side chain assisted C terminal rearrangement

Indexed keywords

CARBOXYL GROUP; HISTONE; SERINE; SYNTHETIC PEPTIDE;

EID: 73649107630     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900864s     Document Type: Article
Times cited : (15)

References (45)
  • 1
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • Strahl, B. D.; Allis, C. D. The language of covalent histone modifications. Nature 2000, 403 (6765), 41-45.
    • (2000) Nature , vol.403 , Issue.6765 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 2
    • 59349100985 scopus 로고    scopus 로고
    • Dynamic protein methylation in chromatin biology
    • Ng, S. S.; Yue, W. W.; Oppermann, U.; Klose, R. J. Dynamic protein methylation in chromatin biology. Cell. Mol. Life Sci. 2009, 66 (3), 407-422.
    • (2009) Cell. Mol. Life Sci , vol.66 , Issue.3 , pp. 407-422
    • Ng, S.S.1    Yue, W.W.2    Oppermann, U.3    Klose, R.J.4
  • 3
    • 27644589675 scopus 로고    scopus 로고
    • The diverse functions of histone lysine methylation
    • Martin, C.; Zhang, Y. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 2005, 6 (11), 838-849.
    • (2005) Nat. Rev. Mol. Cell Biol , vol.6 , Issue.11 , pp. 838-849
    • Martin, C.1    Zhang, Y.2
  • 4
    • 38349035858 scopus 로고    scopus 로고
    • Arginine methylation at a glance
    • Bedford, M. T. Arginine methylation at a glance. J. Cell Sci. 2007, 120 (24), 4243-4246.
    • (2007) J. Cell Sci , vol.120 , Issue.24 , pp. 4243-4246
    • Bedford, M.T.1
  • 5
    • 28044433451 scopus 로고    scopus 로고
    • Protein posttranslational modifications: The chemistry of proteome diversifications
    • Walsh, C. T.; Garneau-Tsodikova, S.; Gatto, G. J. Protein posttranslational modifications: The chemistry of proteome diversifications. Angew. Chem., Int. Ed. 2005, 44 (45), 7342-7372.
    • (2005) Angew. Chem., Int. Ed , vol.44 , Issue.45 , pp. 7342-7372
    • Walsh, C.T.1    Garneau-Tsodikova, S.2    Gatto, G.J.3
  • 6
    • 44449117052 scopus 로고    scopus 로고
    • Identification and validation of eukaryotic aspartate and glutamate methylation in proteins
    • Sprung, R.; Chen, Y.; Zhang, K.; Cheng, D.; Zhang, T.; Peng, J.; Zhao, Y. Identification and validation of eukaryotic aspartate and glutamate methylation in proteins. J. Proteome Res. 2008, 7 (3), 1001-1006.
    • (2008) J. Proteome Res , vol.7 , Issue.3 , pp. 1001-1006
    • Sprung, R.1    Chen, Y.2    Zhang, K.3    Cheng, D.4    Zhang, T.5    Peng, J.6    Zhao, Y.7
  • 7
    • 0027494347 scopus 로고
    • Protein methylation
    • Clarke, S. Protein methylation. Curr. Opin. Cell Biol. 1993, 5 (6), 977-983.
    • (1993) Curr. Opin. Cell Biol , vol.5 , Issue.6 , pp. 977-983
    • Clarke, S.1
  • 8
    • 48849107682 scopus 로고    scopus 로고
    • Identifying and quantifying sites of protein methylation by heavy methyl SILAC
    • Chapter 14, Unit 14.9
    • Ong, S.-E.; Mann, M., Identifying and quantifying sites of protein methylation by heavy methyl SILAC. Curr. Protoc. Protein Sci. 2006, Chapter 14, Unit 14.9.
    • (2006) Curr. Protoc. Protein Sci
    • Ong, S.-E.1    Mann, M.2
  • 9
    • 20844457100 scopus 로고    scopus 로고
    • Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra
    • Chen, Y.; Kwon, S. W.; Kim, S. C.; Zhao, Y. M. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J. Proteome Res. 2005, 4 (3), 998-1005.
    • (2005) J. Proteome Res , vol.4 , Issue.3 , pp. 998-1005
    • Chen, Y.1    Kwon, S.W.2    Kim, S.C.3    Zhao, Y.M.4
  • 10
    • 67049132397 scopus 로고    scopus 로고
    • Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra
    • Chen, Y.; Zhang, J.; Xing, G.; Zhao, Y. Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra. J. Proteome Res. 2009, 8, 3141-3147.
    • (2009) J. Proteome Res , vol.8 , pp. 3141-3147
    • Chen, Y.1    Zhang, J.2    Xing, G.3    Zhao, Y.4
  • 11
    • 4544370533 scopus 로고    scopus 로고
    • Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation
    • Olsen, J. V.; Mann, M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (37), 13417-13422.
    • (2004) Proc. Natl. Acad. Sci. U.S.A , vol.101 , Issue.37 , pp. 13417-13422
    • Olsen, J.V.1    Mann, M.2
  • 12
    • 51449083131 scopus 로고    scopus 로고
    • Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
    • Bandeira, N.; Olsen, J. V.; Mann, J. V.; Mann, M.; Pevzner, P. A. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics 2008, 24 (13), i416-23.
    • (2008) Bioinformatics , vol.24 , Issue.13 I416-23
    • Bandeira, N.1    Olsen, J.V.2    Mann, J.V.3    Mann, M.4    Pevzner, P.A.5
  • 13
    • 58149489223 scopus 로고    scopus 로고
    • In-depth, high-accuracy proteomics of sea urchin tooth organic matrix
    • Mann, K.; Poustka, A. J.; Mann, M. In-depth, high-accuracy proteomics of sea urchin tooth organic matrix. Proteome Sci. 2008, 6.
    • (2008) Proteome Sci , pp. 6
    • Mann, K.1    Poustka, A.J.2    Mann, M.3
  • 14
    • 73649142265 scopus 로고    scopus 로고
    • Schenk, S.; Schoenhals, G. J.; de Souza, G.; Mann, M. A high confidence, manually validated human blood plasma protein reference set. BMC Med. Genomics 2008, 1, 41.
    • Schenk, S.; Schoenhals, G. J.; de Souza, G.; Mann, M. A high confidence, manually validated human blood plasma protein reference set. BMC Med. Genomics 2008, 1, 41.
  • 15
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127 (3), 635-648.
    • (2006) Cell , vol.127 , Issue.3 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5    Mortensen, P.6    Mann, M.7
  • 16
    • 34247383227 scopus 로고    scopus 로고
    • Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS
    • Lee, J.; Xu, Y. D.; Chen, Y.; Sprung, R.; Kim, S. C.; Xie, S. H.; Zhao, Y. M. Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol. Cell. Proteomics 2007, 6 (4), 669-676.
    • (2007) Mol. Cell. Proteomics , vol.6 , Issue.4 , pp. 669-676
    • Lee, J.1    Xu, Y.D.2    Chen, Y.3    Sprung, R.4    Kim, S.C.5    Xie, S.H.6    Zhao, Y.M.7
  • 18
    • 33646899550 scopus 로고    scopus 로고
    • Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer
    • Macek, B.; Waanders, L. F.; Olsen, J. V.; Mann, M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell. Proteomics 2006, 5 (5), 949-958.
    • (2006) Mol. Cell. Proteomics , vol.5 , Issue.5 , pp. 949-958
    • Macek, B.1    Waanders, L.F.2    Olsen, J.V.3    Mann, M.4
  • 19
    • 34250782684 scopus 로고    scopus 로고
    • Extraction, purification and analysis of histones
    • Shechter, D.; Dormann, H. L.; Allis, C. D.; Hake, S. B. Extraction, purification and analysis of histones. Nat. Protoc. 2007, 2 (6), 1445-1457.
    • (2007) Nat. Protoc , vol.2 , Issue.6 , pp. 1445-1457
    • Shechter, D.1    Dormann, H.L.2    Allis, C.D.3    Hake, S.B.4
  • 20
    • 41149159170 scopus 로고    scopus 로고
    • Complications in the assignment of 14 and 28 Da mass shift detected by mass spectrometry as in vivo methylation from endogenous proteins
    • Jung, S. Y.; Li, Y. H.; Wang, Y.; Chen, Y.; Zhao, Y. M.; Qin, J. Complications in the assignment of 14 and 28 Da mass shift detected by mass spectrometry as in vivo methylation from endogenous proteins. Anal. Chem. 2008, 80 (5), 1721-1729.
    • (2008) Anal. Chem , vol.80 , Issue.5 , pp. 1721-1729
    • Jung, S.Y.1    Li, Y.H.2    Wang, Y.3    Chen, Y.4    Zhao, Y.M.5    Qin, J.6
  • 21
    • 58849092421 scopus 로고    scopus 로고
    • PTMap-A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites
    • Chen, Y.; Chen, W.; Cobb, M. H.; Zhao, Y. M. PTMap-A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (3), 761-766.
    • (2009) Proc. Natl. Acad. Sci. U.S.A , vol.106 , Issue.3 , pp. 761-766
    • Chen, Y.1    Chen, W.2    Cobb, M.H.3    Zhao, Y.M.4
  • 22
    • 55549131141 scopus 로고    scopus 로고
    • Mass spectrometry analysis of phosphopeptides after peptide carboxy group derivatization
    • Xu, Y. W.; Zhang, L. J.; Lu, H. J.; Yang, P. Y. Mass spectrometry analysis of phosphopeptides after peptide carboxy group derivatization. Anal. Chem. 2008, 80 (21), 8324-8328.
    • (2008) Anal. Chem , vol.80 , Issue.21 , pp. 8324-8328
    • Xu, Y.W.1    Zhang, L.J.2    Lu, H.J.3    Yang, P.Y.4
  • 23
    • 0033535961 scopus 로고    scopus 로고
    • Accurate quantitation of protein expression and site-specific phosphorylation
    • Oda, Y.; Huang, K.; Cross, F. R.; Cowburn, D.; Chait, B. T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (12), 6591-6596.
    • (1999) Proc. Natl. Acad. Sci. U.S.A , vol.96 , Issue.12 , pp. 6591-6596
    • Oda, Y.1    Huang, K.2    Cross, F.R.3    Cowburn, D.4    Chait, B.T.5
  • 24
    • 18744375196 scopus 로고    scopus 로고
    • Identifying and quantifying in vivo methylation sites by heavy methyl SILAC
    • Ong, S. E.; Mittler, G.; Mann, M. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat. Methods 2004, 1 (2), 119-126.
    • (2004) Nat. Methods , vol.1 , Issue.2 , pp. 119-126
    • Ong, S.E.1    Mittler, G.2    Mann, M.3
  • 25
    • 0036428393 scopus 로고    scopus 로고
    • Amino acid residue specific stable isotope labeling for quantitative proteomics
    • Zhu, H. N.; Pan, S. Q.; Gu, S.; Bradbury, E. M.; Chen, X. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 2002, 16 (22), 2115-2123.
    • (2002) Rapid Commun. Mass Spectrom , vol.16 , Issue.22 , pp. 2115-2123
    • Zhu, H.N.1    Pan, S.Q.2    Gu, S.3    Bradbury, E.M.4    Chen, X.5
  • 26
    • 47949130351 scopus 로고    scopus 로고
    • Identifying differences in protein expression levels by spectral counting and feature selection
    • Carvalho, P. C.; Hewel, J.; Barbosa, V. C.; Yates, J. R. Identifying differences in protein expression levels by spectral counting and feature selection. Genetics Mol. Res. 2008, 7 (2), 342-356.
    • (2008) Genetics Mol. Res , vol.7 , Issue.2 , pp. 342-356
    • Carvalho, P.C.1    Hewel, J.2    Barbosa, V.C.3    Yates, J.R.4
  • 28
    • 65549106401 scopus 로고    scopus 로고
    • Methyl group migration during the fragmentation of singly charged ions of trimethyllysine-containing peptides: Precaution of using MS/MS of singly charged ions for interrogating peptide methylation
    • Xiong, L.; Ping, L.; Yuan, B.; Wang, Y. Methyl group migration during the fragmentation of singly charged ions of trimethyllysine-containing peptides: precaution of using MS/MS of singly charged ions for interrogating peptide methylation. J. Am. Soc. Mass Spectrom. 2009, 20 (6), 1172-1181.
    • (2009) J. Am. Soc. Mass Spectrom , vol.20 , Issue.6 , pp. 1172-1181
    • Xiong, L.1    Ping, L.2    Yuan, B.3    Wang, Y.4
  • 29
    • 0030861687 scopus 로고    scopus 로고
    • Novel peptide dissociation: Gas-phase intramolecular rearrangement of internal amino acid residues
    • Vachet, R. W.; Bishop, B. M.; Erickson, B. W.; Glish, G. L. Novel peptide dissociation: Gas-phase intramolecular rearrangement of internal amino acid residues. J. Am. Chem. Soc. 1997, 119 (24), 5481-5488.
    • (1997) J. Am. Chem. Soc , vol.119 , Issue.24 , pp. 5481-5488
    • Vachet, R.W.1    Bishop, B.M.2    Erickson, B.W.3    Glish, G.L.4
  • 30
    • 56949085455 scopus 로고    scopus 로고
    • Peptide sequence scrambling through cyclization of b(5) ions
    • Harrison, A. G. Peptide sequence scrambling through cyclization of b(5) ions. J. Am. Soc. Mass Spectrom. 2008, 19 (12), 1776-1780.
    • (2008) J. Am. Soc. Mass Spectrom , vol.19 , Issue.12 , pp. 1776-1780
    • Harrison, A.G.1
  • 31
    • 0037444731 scopus 로고    scopus 로고
    • Peptide rearrangement during quadrupole ion trap fragmentation: Added complexity to MS/MS spectra
    • Yague, J.; Paradela, A.; Ramos, M.; Ogueta, S.; Marina, A.; Barahona, F.; de Castro, J. A. L.; Vazquez, J. Peptide rearrangement during quadrupole ion trap fragmentation: Added complexity to MS/MS spectra. Anal. Chem. 2003, 75 (6), 1524-1535.
    • (2003) Anal. Chem , vol.75 , Issue.6 , pp. 1524-1535
    • Yague, J.1    Paradela, A.2    Ramos, M.3    Ogueta, S.4    Marina, A.5    Barahona, F.6    de Castro, J.A.L.7    Vazquez, J.8
  • 32
    • 0024689648 scopus 로고
    • Elucidation of some fragmentations of small peptides using sequential mass spectrometry on a hybrid instrument
    • Thorne, G. C.; Gaskell, S. J. Elucidation of some fragmentations of small peptides using sequential mass spectrometry on a hybrid instrument. Rapid Commun. Mass Spectrom. 1989, 3 (7), 217-21.
    • (1989) Rapid Commun. Mass Spectrom , vol.3 , Issue.7 , pp. 217-221
    • Thorne, G.C.1    Gaskell, S.J.2
  • 33
    • 0000590005 scopus 로고
    • + ions via rearrangement involving loss of the c-terminal amino-acid residue
    • + ions via rearrangement involving loss of the c-terminal amino-acid residue. J. Am. Soc. Mass Spectrom. 1990, 1 (3), 249-257.
    • (1990) J. Am. Soc. Mass Spectrom , vol.1 , Issue.3 , pp. 249-257
    • Thorne, G.C.1    Ballard, K.D.2    Gaskell, S.J.3
  • 34
    • 0026570099 scopus 로고
    • Intramolecular oxygen-18 isotopic exchange in the gas-phase observed during the tandem mass-spectrometric analysis of peptides
    • Ballard, K. D.; Gaskell, S. J. Intramolecular oxygen-18 isotopic exchange in the gas-phase observed during the tandem mass-spectrometric analysis of peptides. J. Am. Chem. Soc. 1992, 114 (1), 64-71.
    • (1992) J. Am. Chem. Soc , vol.114 , Issue.1 , pp. 64-71
    • Ballard, K.D.1    Gaskell, S.J.2
  • 35
    • 0030063262 scopus 로고    scopus 로고
    • Effect of the position of a basic amino acid on C-terminal rearrangement of protonated peptides upon collision-induced dissociation
    • Gonzalez, J.; Besada, V.; Garay, H.; Reyes, O.; Padron, G.; Tambara, Y.; Takao, T.; Shimonishi, Y. Effect of the position of a basic amino acid on C-terminal rearrangement of protonated peptides upon collision-induced dissociation. J. Mass Spectrom. 1996, 31 (2), 150-158.
    • (1996) J. Mass Spectrom , vol.31 , Issue.2 , pp. 150-158
    • Gonzalez, J.1    Besada, V.2    Garay, H.3    Reyes, O.4    Padron, G.5    Tambara, Y.6    Takao, T.7    Shimonishi, Y.8
  • 37
    • 0030037157 scopus 로고    scopus 로고
    • Secondary interactions affecting the dissociation patterns of arginine-containing peptide ions
    • Vachet, R. W.; Asam, M. R.; Glish, G. L. Secondary interactions affecting the dissociation patterns of arginine-containing peptide ions. J. Am. Chem. Soc. 1996, 118 (26), 6252-6256.
    • (1996) J. Am. Chem. Soc , vol.118 , Issue.26 , pp. 6252-6256
    • Vachet, R.W.1    Asam, M.R.2    Glish, G.L.3
  • 38
    • 0031106849 scopus 로고    scopus 로고
    • A mechanism for the loss of 60 u from peptides containing an arginine residue at the C-terminus
    • Deery, M. J.; Summerfield, S. G.; Buzy, A.; Jennings, K. R. A mechanism for the loss of 60 u from peptides containing an arginine residue at the C-terminus. J. Am. Soc. Mass Spectrom. 1997, 8 (3), 253-261.
    • (1997) J. Am. Soc. Mass Spectrom , vol.8 , Issue.3 , pp. 253-261
    • Deery, M.J.1    Summerfield, S.G.2    Buzy, A.3    Jennings, K.R.4
  • 39
    • 0031444782 scopus 로고    scopus 로고
    • Improving mass spectrometric sequencing of arginine-containing peptides by derivatization with acetylacetone
    • Dikler, S.; Kelly, J. W.; Russell, D. H. Improving mass spectrometric sequencing of arginine-containing peptides by derivatization with acetylacetone. J. Mass Spectrom. 1997, 32 (12), 1337-1349.
    • (1997) J. Mass Spectrom , vol.32 , Issue.12 , pp. 1337-1349
    • Dikler, S.1    Kelly, J.W.2    Russell, D.H.3
  • 40
    • 0034582526 scopus 로고    scopus 로고
    • Novel rearranged ions observed for protonated peptides via metastable decomposition in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
    • Fang, S. P.; Takao, T.; Satomi, Y.; Mo, W. J.; Shimonishi, Y. Novel rearranged ions observed for protonated peptides via metastable decomposition in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom. 2000, 11 (4), 345-351.
    • (2000) J. Am. Soc. Mass Spectrom , vol.11 , Issue.4 , pp. 345-351
    • Fang, S.P.1    Takao, T.2    Satomi, Y.3    Mo, W.J.4    Shimonishi, Y.5
  • 42
    • 0024083279 scopus 로고
    • Daughter ion mass-spectra from cationized molecules of small oligopeptides in a reflecting time-of-flight mass-spectrometer
    • Tang, X. J.; Ens, W.; Standing, K. G.; Westmore, J. B. Daughter ion mass-spectra from cationized molecules of small oligopeptides in a reflecting time-of-flight mass-spectrometer. Anal. Chem. 1988, 60 (17), 1791-1799.
    • (1988) Anal. Chem , vol.60 , Issue.17 , pp. 1791-1799
    • Tang, X.J.1    Ens, W.2    Standing, K.G.3    Westmore, J.B.4
  • 43
    • 0024286528 scopus 로고
    • Linked scan investigation of peptide degradation initiated by liquid secondary ion mass-spectrometry
    • Renner, D.; Spiteller, G. Linked scan investigation of peptide degradation initiated by liquid secondary ion mass-spectrometry. Biomed. Environ. Mass Spectrom. 1988, 15 (2), 75-77.
    • (1988) Biomed. Environ. Mass Spectrom , vol.15 , Issue.2 , pp. 75-77
    • Renner, D.1    Spiteller, G.2
  • 44
    • 0013619903 scopus 로고
    • Metal ion-peptide interactions in the gas phase: A tandem mass spectrometry study of alkali metal cationized peptides
    • Grese, R. P.; Cerny, R. L.; Gross, M. L. Metal ion-peptide interactions in the gas phase: a tandem mass spectrometry study of alkali metal cationized peptides. J. Am. Chem. Soc. 1989, 111 (8), 2835-42.
    • (1989) J. Am. Chem. Soc , vol.111 , Issue.8 , pp. 2835-2842
    • Grese, R.P.1    Cerny, R.L.2    Gross, M.L.3
  • 45
    • 0024997675 scopus 로고
    • Gas-phase interactions of lithium ions and dipeptides
    • Grese, R. P.; Gross, M. L. Gas-phase interactions of lithium ions and dipeptides. J. Am. Chem. Soc. 1990, 112 (13), 5098-104.
    • (1990) J. Am. Chem. Soc , vol.112 , Issue.13 , pp. 5098-5104
    • Grese, R.P.1    Gross, M.L.2


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