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Volumn 26, Issue 7, 2015, Pages 1128-1142

Large-scale examination of factors influencing phosphopeptide neutral loss during collision induced dissociation

Author keywords

Collision induced dissociation; Neutral loss; Phosphopeptide; Phosphorylation

Indexed keywords

AMINO ACIDS; MASS SPECTROMETRY; PEPTIDES; PHOSPHORYLATION;

EID: 84934999520     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-015-1109-y     Document Type: Article
Times cited : (12)

References (43)
  • 1
    • 0034797512 scopus 로고    scopus 로고
    • The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lectur
    • 1:CAS:528:DC%2BD3MXns1els70%3D
    • Cohen, P.: The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lectur. Eur. J. Biochem. 268, 5001-5010 (2001)
    • (2001) Eur. J. Biochem. , vol.268 , pp. 5001-5010
    • Cohen, P.1
  • 2
    • 27744563093 scopus 로고    scopus 로고
    • State-of-the-art in phosphoproteomics
    • 1:CAS:528:DC%2BD2MXht1GrtbzI
    • Reinders, J., Sickmann, A.: State-of-the-art in phosphoproteomics. Proteomics. 5, 4052-4061 (2005)
    • (2005) Proteomics , vol.5 , pp. 4052-4061
    • Reinders, J.1    Sickmann, A.2
  • 4
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high-throughput protein phosphorylation analysis and site localization
    • 1:CAS:528:DC%2BD28XhtVGgsrjF
    • Beausoleil, S.A., Villen, J., Gerber, S.A., Rush, J., Gygi, S.P.: A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285-1292 (2006)
    • (2006) Nat. Biotechnol , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villen, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 5
    • 55849122284 scopus 로고    scopus 로고
    • Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis
    • 1:CAS:528:DC%2BD1cXhsVCjtrrJ
    • Villen, J., Beausoleil, S.A., Gygi, S.P.: Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics. 8, 4444-4452 (2008)
    • (2008) Proteomics. , vol.8 , pp. 4444-4452
    • Villen, J.1    Beausoleil, S.A.2    Gygi, S.P.3
  • 6
    • 61849182590 scopus 로고    scopus 로고
    • Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification
    • 1:CAS:528:DC%2BD1cXhsV2hur%2FK
    • Ulintz, P.J., Yocum, A.K., Bodenmiller, B., Aebersold, R., Andrews, P.C., Nesvizhskii, A.I.: Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J. Proteome Res. 8, 887-899 (2009)
    • (2009) J. Proteome Res. , vol.8 , pp. 887-899
    • Ulintz, P.J.1    Yocum, A.K.2    Bodenmiller, B.3    Aebersold, R.4    Andrews, P.C.5    Nesvizhskii, A.I.6
  • 7
    • 55849104839 scopus 로고    scopus 로고
    • Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications
    • 1:CAS:528:DC%2BD1cXhsVCjtrrL
    • Wiesner, J., Premsler, T., Sickmann, A.: Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics. 8, 4466-4483 (2008)
    • (2008) Proteomics. , vol.8 , pp. 4466-4483
    • Wiesner, J.1    Premsler, T.2    Sickmann, A.3
  • 8
    • 34547167007 scopus 로고    scopus 로고
    • Neutral loss-based phosphopeptide recognition: A collection of caveats
    • 1:CAS:528:DC%2BD2sXmsVKmtrk%3D
    • Lehmann, W.D., Kruger, R., Salek, M., Hung, C.W., Wolschin, F., Weckwerth, W.: Neutral loss-based phosphopeptide recognition: a collection of caveats. J. Proteome Res. 6, 2866-2873 (2007)
    • (2007) J. Proteome Res. , vol.6 , pp. 2866-2873
    • Lehmann, W.D.1    Kruger, R.2    Salek, M.3    Hung, C.W.4    Wolschin, F.5    Weckwerth, W.6
  • 9
    • 0032237775 scopus 로고    scopus 로고
    • Fragmentation of phosphopeptides in an ion trap mass spectrometer
    • 1:CAS:528:DyaK1cXmvF2quro%3D
    • DeGnore, J.P., Qin, J.: Fragmentation of phosphopeptides in an ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 9, 1175-1188 (1998)
    • (1998) J. Am. Soc. Mass Spectrom. , vol.9 , pp. 1175-1188
    • Degnore, J.P.1    Qin, J.2
  • 11
    • 0034501099 scopus 로고    scopus 로고
    • Mobile and localized protons: A framework for understanding peptide dissociation
    • 1:CAS:528:DC%2BD3MXltFWrtQ%3D%3D
    • Wysocki, V.H., Tsaprailis, G., Smith, L.L., Breci, L.A.: Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 35, 1399-1406 (2000)
    • (2000) J. Mass Spectrom. , vol.35 , pp. 1399-1406
    • Wysocki, V.H.1    Tsaprailis, G.2    Smith, L.L.3    Breci, L.A.4
  • 12
    • 0032995789 scopus 로고    scopus 로고
    • Electrospray tandem mass spectrometric studies of phosphopeptides and phosphopeptide analogues
    • 1:CAS:528:DyaK1MXhvFyhu7o%3D
    • Tholey, A., Reed, J., Lehmann, W.D.: Electrospray tandem mass spectrometric studies of phosphopeptides and phosphopeptide analogues. J. Mass Spectrom. 34, 117-123 (1999)
    • (1999) J. Mass Spectrom. , vol.34 , pp. 117-123
    • Tholey, A.1    Reed, J.2    Lehmann, W.D.3
  • 13
    • 0034582658 scopus 로고    scopus 로고
    • Leaving group and gas phase neighboring group effects in the side chain losses from protonated serine and its derivatives
    • 1:CAS:528:DC%2BD3cXot1Onsr8%3D
    • Reid, G.E., Simpson, R.J., O'Hair, R.A.: Leaving group and gas phase neighboring group effects in the side chain losses from protonated serine and its derivatives. J. Am. Soc. Mass Spectrom. 11, 1047-1060 (2000)
    • (2000) J. Am. Soc. Mass Spectrom. , vol.11 , pp. 1047-1060
    • Reid, G.E.1    Simpson, R.J.2    O'Hair, R.A.3
  • 14
    • 39749196893 scopus 로고    scopus 로고
    • Mechanistic insights into the multistage gas-phase fragmentation behavior of phosphoserine- and phosphothreonine-containing peptides
    • 1:CAS:528:DC%2BD1cXksV2hug%3D%3D
    • Palumbo, A.M., Tepe, J.J., Reid, G.E.: Mechanistic insights into the multistage gas-phase fragmentation behavior of phosphoserine- and phosphothreonine-containing peptides. J. Proteome Res. 7, 771-779 (2008)
    • (2008) J. Proteome Res. , vol.7 , pp. 771-779
    • Palumbo, A.M.1    Tepe, J.J.2    Reid, G.E.3
  • 15
    • 58149116970 scopus 로고    scopus 로고
    • Evaluation of gas-phase rearrangement and competing fragmentation reactions on protein phosphorylation site assignment using collision induced dissociation-MS/MS and MS3
    • 1:CAS:528:DC%2BD1cXhtlyisbnK
    • Palumbo, A.M., Reid, G.E.: Evaluation of gas-phase rearrangement and competing fragmentation reactions on protein phosphorylation site assignment using collision induced dissociation-MS/MS and MS3. Anal. Chem. 80, 9735-9747 (2008)
    • (2008) Anal. Chem. , vol.80 , pp. 9735-9747
    • Palumbo, A.M.1    Reid, G.E.2
  • 16
    • 80052798356 scopus 로고    scopus 로고
    • Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides
    • 1:CAS:528:DC%2BC3MXhtFOls77P
    • Rozman, M.: Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides. J. Mass Spectrom. 46, 949-955 (2011)
    • (2011) J. Mass Spectrom. , vol.46 , pp. 949-955
    • Rozman, M.1
  • 17
  • 18
    • 84874992573 scopus 로고    scopus 로고
    • Examining factors that influence erroneous phosphorylation site localization via competing fragmentation and rearrangement reactions during ion trap CID-MS/MS and -MS(3.)
    • 1:CAS:528:DC%2BC3sXjslKrsL4%3D
    • Cui, L., Reid, G.E.: Examining factors that influence erroneous phosphorylation site localization via competing fragmentation and rearrangement reactions during ion trap CID-MS/MS and -MS(3.). Proteomics. 13, 964-973 (2013)
    • (2013) Proteomics. , vol.13 , pp. 964-973
    • Cui, L.1    Reid, G.E.2
  • 19
    • 79959988139 scopus 로고    scopus 로고
    • Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment
    • 1:CAS:528:DC%2BC3MXltlGhsbc%3D
    • Kelstrup, C.D., Hekmat, O., Francavilla, C., Olsen, J.V.: Pinpointing phosphorylation sites: quantitative filtering and a novel site-specific x-ion fragment. J. Proteome Res. 10, 2937-2948 (2011)
    • (2011) J. Proteome Res. , vol.10 , pp. 2937-2948
    • Kelstrup, C.D.1    Hekmat, O.2    Francavilla, C.3    Olsen, J.V.4
  • 20
    • 84862564417 scopus 로고    scopus 로고
    • Formation of y∈+∈10 and y∈+∈11 ions in the collision-induced dissociation of peptide ions
    • 1:CAS:528:DC%2BC38XltVahtL4%3D
    • Kilpatrick, L.E., Neta, P., Yang, X., Simon-Manso, Y., Liang, Y., Stein, S.E.: Formation of y∈+∈10 and y∈+∈11 ions in the collision-induced dissociation of peptide ions. J. Am. Soc. Mass Spectrom. 23, 655-663 (2012)
    • (2012) J. Am. Soc. Mass Spectrom. , vol.23 , pp. 655-663
    • Kilpatrick, L.E.1    Neta, P.2    Yang, X.3    Simon-Manso, Y.4    Liang, Y.5    Stein, S.E.6
  • 21
    • 84856178935 scopus 로고    scopus 로고
    • Pathways for water loss from doubly protonated peptides containing serine or threonine
    • 1:CAS:528:DC%2BC38XltVaitLw%3D
    • Harrison, A.G.: Pathways for water loss from doubly protonated peptides containing serine or threonine. J. Am. Soc. Mass Spectrom. 23, 116-123 (2012)
    • (2012) J. Am. Soc. Mass Spectrom. , vol.23 , pp. 116-123
    • Harrison, A.G.1
  • 22
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • 1:CAS:528:DC%2BD1MXks12ksb0%3D
    • Wisniewski, J.R., Zougman, A., Nagaraj, N., Mann, M.: Universal sample preparation method for proteome analysis. Nat. Methods. 6, 359-362 (2009)
    • (2009) Nat. Methods. , vol.6 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 23
    • 41149110237 scopus 로고    scopus 로고
    • Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides
    • 1:CAS:528:DC%2BD2sXhtlaktLbK
    • Alpert, A.J.: Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal. Chem. 80, 62-76 (2008)
    • (2008) Anal. Chem. , vol.80 , pp. 62-76
    • Alpert, A.J.1
  • 24
    • 34248640261 scopus 로고    scopus 로고
    • Highly selective enrichment of phosphorylated peptides using titanium dioxide
    • 1:CAS:528:DC%2BD2sXhtFagt77N
    • Thingholm, T.E., Jorgensen, T.J., Jensen, O.N., Larsen, M.R.: Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat. Protoc. 1, 1929-1935 (2006)
    • (2006) Nat. Protoc. , vol.1 , pp. 1929-1935
    • Thingholm, T.E.1    Jorgensen, T.J.2    Jensen, O.N.3    Larsen, M.R.4
  • 26
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • 1:CAS:528:DC%2BD2sXjs1Kls70%3D
    • Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., King, N., Stein, S.E., Aebersold, R.: Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics. 7, 655-667 (2007)
    • (2007) Proteomics. , vol.7 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6    Aebersold, R.7
  • 27
    • 53249098366 scopus 로고    scopus 로고
    • Building consensus spectral libraries for peptide identification in proteomics
    • 1:CAS:528:DC%2BD1cXhtFKktLfM
    • Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., Stein, S.E., Aebersold, R.: Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods. 5, 873-875 (2008)
    • (2008) Nat. Methods. , vol.5 , pp. 873-875
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    Stein, S.E.5    Aebersold, R.6
  • 29
    • 84947402121 scopus 로고
    • Rectangular confidence regions for means of multivariate normal distributions
    • Sidak, Z.: Rectangular confidence regions for means of multivariate normal distributions. J. Am. Stat. Assoc. 62, 626-633 (1967)
    • (1967) J. Am. Stat. Assoc. , vol.62 , pp. 626-633
    • Sidak, Z.1
  • 30
    • 53049084796 scopus 로고    scopus 로고
    • Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis
    • 1:CAS:528:DC%2BD1cXntlKrt7s%3D
    • Payne, S.H., Yau, M., Smolka, M.B., Tanner, S., Zhou, H., Bafna, V.: Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J. Proteome Res. 7, 3373-3381 (2008)
    • (2008) J. Proteome Res. , vol.7 , pp. 3373-3381
    • Payne, S.H.1    Yau, M.2    Smolka, M.B.3    Tanner, S.4    Zhou, H.5    Bafna, V.6
  • 31
    • 38649116302 scopus 로고    scopus 로고
    • Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra
    • 1:CAS:528:DC%2BD2sXhsVOntbnP
    • Sun, S., Yu, C., Qiao, Y., Lin, Y., Dong, G., Liu, C., Zhang, J., Zhang, Z., Cai, J., Zhang, H., Bu, D.: Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra. J. Proteome Res. 7, 202-208 (2008)
    • (2008) J. Proteome Res. , vol.7 , pp. 202-208
    • Sun, S.1    Yu, C.2    Qiao, Y.3    Lin, Y.4    Dong, G.5    Liu, C.6    Zhang, J.7    Zhang, Z.8    Cai, J.9    Zhang, H.10    Bu, D.11
  • 33
    • 56949103268 scopus 로고    scopus 로고
    • Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation
    • 1:CAS:528:DC%2BD1cXhsVyrtrjO
    • Savitski, M.M., Falth, M., Fung, Y.M., Adams, C.M., Zubarev, R.A.: Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation. J. Am. Soc. Mass Spectrom. 19, 1755-1763 (2008)
    • (2008) J. Am. Soc. Mass Spectrom. , vol.19 , pp. 1755-1763
    • Savitski, M.M.1    Falth, M.2    Fung, Y.M.3    Adams, C.M.4    Zubarev, R.A.5
  • 34
    • 27844510036 scopus 로고    scopus 로고
    • Manipulating the fragmentation patterns of phosphopeptides via gas-phase boron derivatization: Determining phosphorylation sites in peptides with multiple serines
    • 1:CAS:528:DC%2BD2MXht1Cmsb7L
    • Gronert, S., Li, K.H., Horiuchi, M.: Manipulating the fragmentation patterns of phosphopeptides via gas-phase boron derivatization: determining phosphorylation sites in peptides with multiple serines. J. Am. Soc. Mass Spectrom. 16, 1905-1914 (2005)
    • (2005) J. Am. Soc. Mass Spectrom. , vol.16 , pp. 1905-1914
    • Gronert, S.1    Li, K.H.2    Horiuchi, M.3
  • 35
    • 0038034116 scopus 로고    scopus 로고
    • Cleavage N-terminal to proline: Analysis of a database of peptide tandem mass spectra
    • 1:CAS:528:DC%2BD3sXitlGlsLo%3D
    • Breci, L.A., Tabb, D.L., Yates III, J.R., Wysocki, V.H.: Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal. Chem. 75, 1963-1971 (2003)
    • (2003) Anal. Chem. , vol.75 , pp. 1963-1971
    • Breci, L.A.1    Tabb, D.L.2    Yates, J.R.3    Wysocki, V.H.4
  • 36
    • 0033757177 scopus 로고    scopus 로고
    • Studies on the dephosphorylation of phosphotyrosine-containing peptides during post-source decay in matrix-assisted laser desorption/ionization
    • 1:CAS:528:DC%2BD3cXotFWlurk%3D
    • Metzger, S., Hoffmann, R.: Studies on the dephosphorylation of phosphotyrosine-containing peptides during post-source decay in matrix-assisted laser desorption/ionization. J. Mass Spectrom. 35, 1165-1177 (2000)
    • (2000) J. Mass Spectrom. , vol.35 , pp. 1165-1177
    • Metzger, S.1    Hoffmann, R.2
  • 37
    • 66349108979 scopus 로고    scopus 로고
    • Gas-phase intramolecular phosphate shift in phosphotyrosine-containing peptide monoanions
    • 1:CAS:528:DC%2BD1MXlt1SgsLY%3D
    • Edelson-Averbukh, M., Shevchenko, A., Pipkorn, R., Lehmann, W.D.: Gas-phase intramolecular phosphate shift in phosphotyrosine-containing peptide monoanions. Anal. Chem. 81, 4369-4381 (2009)
    • (2009) Anal. Chem. , vol.81 , pp. 4369-4381
    • Edelson-Averbukh, M.1    Shevchenko, A.2    Pipkorn, R.3    Lehmann, W.D.4
  • 38
    • 0345547409 scopus 로고    scopus 로고
    • Neutral loss of amino acid residues from protonated peptides in collision-induced dissociation generates N- or C-terminal sequence ladders
    • 1:CAS:528:DC%2BD3sXpslGktbc%3D
    • Salek, M., Lehmann, W.D.: Neutral loss of amino acid residues from protonated peptides in collision-induced dissociation generates N- or C-terminal sequence ladders. J. Mass Spectrom. 38, 1143-1149 (2003)
    • (2003) J. Mass Spectrom. , vol.38 , pp. 1143-1149
    • Salek, M.1    Lehmann, W.D.2
  • 39
    • 0032366914 scopus 로고    scopus 로고
    • Evaluated gas phase basicities and proton affinities of molecules: An update
    • 1:CAS:528:DyaK1cXjvVKgtLs%3D
    • Hunter, E.P.L., Lias, S.G.: Evaluated gas phase basicities and proton affinities of molecules: an update. J. Phys. Chem. Ref. Data. 27, 413-656 (1998)
    • (1998) J. Phys. Chem. Ref. Data. , vol.27 , pp. 413-656
    • Hunter, E.P.L.1    Lias, S.G.2
  • 40
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • 1:CAS:528:DC%2BD2cXktlWmtLs%3D
    • Zhang, Z.: Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 3908-3922 (2004)
    • (2004) Anal. Chem. , vol.76 , pp. 3908-3922
    • Zhang, Z.1
  • 41
    • 26444607864 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges
    • 1:CAS:528:DC%2BD2MXptVCnsbw%3D
    • Zhang, Z.: Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 77, 6364-6373 (2005)
    • (2005) Anal. Chem. , vol.77 , pp. 6364-6373
    • Zhang, Z.1
  • 42
    • 81255146358 scopus 로고    scopus 로고
    • Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications
    • 1:CAS:528:DC%2BC3MXhtlOqu77F
    • Zhang, Z.: Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications. Anal. Chem. 83, 8642-8651 (2011)
    • (2011) Anal. Chem. , vol.83 , pp. 8642-8651
    • Zhang, Z.1


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