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Volumn 11, Issue 7, 2012, Pages 3753-3765

Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments

Author keywords

bioinformatics; phosphopeptide isomers; phosphoproteomics; tandem mass spectrometry

Indexed keywords

AMINO ACID; CELL EXTRACT; PHOSPHOPEPTIDE; RIBONUCLEOPROTEIN;

EID: 84863615204     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300229m     Document Type: Article
Times cited : (25)

References (41)
  • 1
    • 33750456519 scopus 로고    scopus 로고
    • Vivo, and site-specific phosphorylation dynamics in signaling networks
    • DOI 10.1016/j.cell.2006.09.026, PII S0092867406012748
    • 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) 635-48 (Pubitemid 44647421)
    • (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    Global, M.8
  • 3
    • 63049113651 scopus 로고    scopus 로고
    • Analytical strategies for phosphoproteomics
    • Thingholm, T. E.; Jensen, O. N.; Larsen, M. R. Analytical strategies for phosphoproteomics Proteomics 2009, 9 (6) 1451-68
    • (2009) Proteomics , vol.9 , Issue.6 , pp. 1451-1468
    • Thingholm, T.E.1    Jensen, O.N.2    Larsen, M.R.3
  • 6
    • 79959733666 scopus 로고    scopus 로고
    • ProteoConnections: A bioinformatics platform to facilitate proteome and phosphoproteome analyses
    • Courcelles, M.; Lemieux, S.; Voisin, L.; Meloche, S.; Thibault, P. ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses Proteomics 2011, 11 (13) 2654-71
    • (2011) Proteomics , vol.11 , Issue.13 , pp. 2654-2671
    • Courcelles, M.1    Lemieux, S.2    Voisin, L.3    Meloche, S.4    Thibault, P.5
  • 8
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high-throughput protein phosphorylation analysis and site localization
    • DOI 10.1038/nbt1240, PII NBT1240
    • 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. 2006, 24 (10) 1285-92 (Pubitemid 44564776)
    • (2006) Nature Biotechnology , vol.24 , Issue.10 , pp. 1285-1292
    • Beausoleil, S.A.1    Villen, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 9
    • 51649090664 scopus 로고    scopus 로고
    • PhosphoScore: An open-source phosphorylation site assignment tool for MSn data
    • Ruttenberg, B. E.; Pisitkun, T.; Knepper, M. A.; Hoffert, J. D. PhosphoScore: an open-source phosphorylation site assignment tool for MSn data J. Proteome Res. 2008, 7 (7) 3054-9
    • (2008) J. Proteome Res. , vol.7 , Issue.7 , pp. 3054-3059
    • Ruttenberg, B.E.1    Pisitkun, T.2    Knepper, M.A.3    Hoffert, J.D.4
  • 10
    • 49849092381 scopus 로고    scopus 로고
    • PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information
    • Wan, Y.; Cripps, D.; Thomas, S.; Campbell, P.; Ambulos, N.; Chen, T.; Yang, A. PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information J. Proteome Res. 2008, 7 (7) 2803-11
    • (2008) J. Proteome Res. , vol.7 , Issue.7 , pp. 2803-2811
    • Wan, Y.1    Cripps, D.2    Thomas, S.3    Campbell, P.4    Ambulos, N.5    Chen, T.6    Yang, A.7
  • 11
    • 63349105962 scopus 로고    scopus 로고
    • PhosCalc: A tool for evaluating the sites of peptide phosphorylation from mass spectrometer data
    • MacLean, D.; Burrell, M. A.; Studholme, D. J.; Jones, A. M. PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data BMC Res. Notes 2008, 1, 30
    • (2008) BMC Res. Notes , vol.1 , pp. 30
    • MacLean, D.1    Burrell, M.A.2    Studholme, D.J.3    Jones, A.M.4
  • 13
    • 59049086847 scopus 로고    scopus 로고
    • Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry
    • Swaney, D. L.; Wenger, C. D.; Thomson, J. A.; Coon, J. J. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (4) 995-1000
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , Issue.4 , pp. 995-1000
    • Swaney, D.L.1    Wenger, C.D.2    Thomson, J.A.3    Coon, J.J.4
  • 15
    • 0025711355 scopus 로고
    • Reversed-phase high-performance liquid chromatographic separation of synthetic phosphopeptide isomers
    • Otvos, L., Jr; Tangoren, I. A.; Wroblewski, K.; Hollosi, M.; Lee, V. M. Reversed-phase high-performance liquid chromatographic separation of synthetic phosphopeptide isomers J. Chromatogr. 1990, 512, 265-72
    • (1990) J. Chromatogr. , vol.512 , pp. 265-272
    • Otvos Jr., L.1    Tangoren, I.A.2    Wroblewski, K.3    Hollosi, M.4    Lee, V.M.5
  • 16
    • 0030731064 scopus 로고    scopus 로고
    • Separation of sets of mono- and diphosphorylated peptides by reversed- phase high performance liquid chromatography
    • DOI 10.1016/S0003-2670(97)00200-6, PII S0003267097002006
    • Hoffmann, R.; Segal, M.; Otvos, L. Separation of sets of mono- and diphosphorylated peptides by reversed-phase high performance liquid chromatography Anal. Chim. Acta 1997, 352 (1-3) 327-333 (Pubitemid 27522835)
    • (1997) Analytica Chimica Acta , vol.352 , Issue.1-3 , pp. 327-333
    • Hoffmann, R.1    Segal, M.2    Otvos Jr., L.3
  • 20
    • 77952037166 scopus 로고    scopus 로고
    • Differential phosphoproteomics of fibroblast growth factor signaling: Identification of Src family kinase-mediated phosphorylation events
    • Cunningham, D. L.; Sweet, S. M.; Cooper, H. J.; Heath, J. K. Differential phosphoproteomics of fibroblast growth factor signaling: identification of Src family kinase-mediated phosphorylation events J. Proteome Res. 2010, 9 (5) 2317-28
    • (2010) J. Proteome Res. , vol.9 , Issue.5 , pp. 2317-2328
    • Cunningham, D.L.1    Sweet, S.M.2    Cooper, H.J.3    Heath, J.K.4
  • 21
    • 51549119338 scopus 로고    scopus 로고
    • Targeted online liquid chromatography electron capture dissociation mass spectrometry for the localization of sites of in vivo phosphorylation in human Sprouty2
    • Sweet, S. M.; Mardakheh, F. K.; Ryan, K. J.; Langton, A. J.; Heath, J. K.; Cooper, H. J. Targeted online liquid chromatography electron capture dissociation mass spectrometry for the localization of sites of in vivo phosphorylation in human Sprouty2 Anal. Chem. 2008, 80 (17) 6650-7
    • (2008) Anal. Chem. , vol.80 , Issue.17 , pp. 6650-6657
    • Sweet, S.M.1    Mardakheh, F.K.2    Ryan, K.J.3    Langton, A.J.4    Heath, J.K.5    Cooper, H.J.6
  • 22
    • 27544503147 scopus 로고    scopus 로고
    • Separation and detection of phosphorylated and nonphosphorylated peptides in liquid chromatography-mass spectrometry using monolithic columns and acidic or alkaline mobile phases
    • DOI 10.1021/ac050538t
    • Tholey, A.; Toll, H.; Huber, C. G. Separation and detection of phosphorylated and nonphosphorylated peptides in liquid chromatography-mass spectrometry using monolithic columns and acidic or alkaline mobile phases Anal. Chem. 2005, 77 (14) 4618-25 (Pubitemid 41542286)
    • (2005) Analytical Chemistry , vol.77 , Issue.14 , pp. 4618-4625
    • Tholey, A.1    Toll, H.2    Huber, C.G.3
  • 23
    • 77955166629 scopus 로고    scopus 로고
    • Separation of multiphosphorylated peptide isomers by hydrophilic interaction chromatography on an aminopropyl phase
    • Singer, D.; Kuhlmann, J.; Muschket, M.; Hoffmann, R. Separation of multiphosphorylated peptide isomers by hydrophilic interaction chromatography on an aminopropyl phase Anal. Chem. 2010, 82 (15) 6409-14
    • (2010) Anal. Chem. , vol.82 , Issue.15 , pp. 6409-6414
    • Singer, D.1    Kuhlmann, J.2    Muschket, M.3    Hoffmann, R.4
  • 24
    • 59249084318 scopus 로고    scopus 로고
    • Separation of multiphosphorylated peptide isomers by CZE
    • Muetzelburg, M. V.; Hoffmann, R. Separation of multiphosphorylated peptide isomers by CZE Electrophoresis 2008, 29 (21) 4381-5
    • (2008) Electrophoresis , vol.29 , Issue.21 , pp. 4381-4385
    • Muetzelburg, M.V.1    Hoffmann, R.2
  • 25
    • 84856675258 scopus 로고    scopus 로고
    • Improvement of Phosphoproteome Analyses Using FAIMS and Decision Tree Fragmentation. Application to the Insulin Signaling Pathway in Drosophila melanogaster S2 Cells
    • Bridon, G.; Bonneil, E.; Muratore-Schroeder, T.; Caron-Lizotte, O.; Thibault, P. Improvement of Phosphoproteome Analyses Using FAIMS and Decision Tree Fragmentation. Application to the Insulin Signaling Pathway in Drosophila melanogaster S2 Cells J. Proteome Res. 2012, 11 (2) 927-40
    • (2012) J. Proteome Res. , vol.11 , Issue.2 , pp. 927-940
    • Bridon, G.1    Bonneil, E.2    Muratore-Schroeder, T.3    Caron-Lizotte, O.4    Thibault, P.5
  • 26
    • 67650360325 scopus 로고    scopus 로고
    • High-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high-resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides
    • Xuan, Y.; Creese, A. J.; Horner, J. A.; Cooper, H. J. High-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high-resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides Rapid Commun. Mass Spectrom. 2009, 23 (13) 1963-9
    • (2009) Rapid Commun. Mass Spectrom. , vol.23 , Issue.13 , pp. 1963-1969
    • Xuan, Y.1    Creese, A.J.2    Horner, J.A.3    Cooper, H.J.4
  • 27
    • 0034582319 scopus 로고    scopus 로고
    • Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules
    • DOI 10.1016/S1044-0305(99)00157-9, PII S1044030599001579
    • Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules J. Am. Soc. Mass Spectrom. 2000, 11 (4) 320-32 (Pubitemid 34516332)
    • (2000) Journal of the American Society for Mass Spectrometry , vol.11 , Issue.4 , pp. 320-332
    • Horn, D.M.1    Zubarev, R.A.2    McLafferty, F.W.3
  • 28
    • 84863060153 scopus 로고    scopus 로고
    • 1.2.4098; Pacific Northwest National Laboratory: Richland, WA.
    • Monroe, M. Peptide Fragmentation Modeller, 1.2.4098; Pacific Northwest National Laboratory: Richland, WA, 2011.
    • (2011) Peptide Fragmentation Modeller
    • Monroe, M.1
  • 30
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157 (1) 105-32
    • (1982) J. Mol. Biol. , vol.157 , Issue.1 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 31
    • 42649142332 scopus 로고    scopus 로고
    • Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: Application to cell signaling events of interferon-gamma-stimulated macrophages
    • DOI 10.1074/mcp.M700383-MCP200
    • Marcantonio, M.; Trost, M.; Courcelles, M.; Desjardins, M.; Thibault, P. Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages Mol. Cell. Proteomics 2008, 7 (4) 645-60 (Pubitemid 351597477)
    • (2008) Molecular and Cellular Proteomics , vol.7 , Issue.4 , pp. 645-660
    • Marcantonio, M.1    Trost, M.2    Courcelles, M.3    Desjardins, M.4    Thibault, P.5
  • 32
    • 67649729220 scopus 로고    scopus 로고
    • Separation of peptide isomers and conformers by ultra performance liquid chromatography
    • Winter, D.; Pipkorn, R.; Lehmann, W. D. Separation of peptide isomers and conformers by ultra performance liquid chromatography J. Sep. Sci. 2009, 32 (8) 1111-9
    • (2009) J. Sep. Sci. , vol.32 , Issue.8 , pp. 1111-1119
    • Winter, D.1    Pipkorn, R.2    Lehmann, W.D.3
  • 34
    • 33748788003 scopus 로고    scopus 로고
    • Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: Consequences for MALDI and HPLC-MALDI analysis
    • DOI 10.1021/ac061017o
    • Krokhin, O. V.; Antonovici, M.; Ens, W.; Wilkins, J. A.; Standing, K. G. Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: Consequences for MALDI and HPLC-MALDI analysis Anal. Chem. 2006, 78 (18) 6645-50 (Pubitemid 44413621)
    • (2006) Analytical Chemistry , vol.78 , Issue.18 , pp. 6645-6650
    • Krokhin, O.V.1    Antonovici, M.2    Ens, W.3    Wilkins, J.A.4    Standing, K.G.5
  • 35
    • 79959988139 scopus 로고    scopus 로고
    • Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment
    • 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. 2011, 10 (7) 2937-48
    • (2011) J. Proteome Res. , vol.10 , Issue.7 , pp. 2937-2948
    • Kelstrup, C.D.1    Hekmat, O.2    Francavilla, C.3    Olsen, J.V.4
  • 36
    • 37849189554 scopus 로고    scopus 로고
    • Protein tyrosine kinase-substrate interactions
    • DOI 10.1016/j.sbi.2006.10.012, PII S0959440X06001837, Catalysis and Regulation / Proteins
    • Bose, R.; Holbert, M. A.; Pickin, K. A.; Cole, P. A. Protein tyrosine kinase-substrate interactions Curr. Opin. Struct. Biol. 2006, 16 (6) 668-75 (Pubitemid 44827733)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.6 , pp. 668-675
    • Bose, R.1    Holbert, M.A.2    Pickin, K.A.3    Cole, P.A.4
  • 37
    • 78651277460 scopus 로고    scopus 로고
    • PHOSIDA 2011: The posttranslational modification database
    • Database Issue
    • Gnad, F.; Gunawardena, J.; Mann, M. PHOSIDA 2011: the posttranslational modification database Nucleic Acids Res. 2011, Database issue) 39-60
    • (2011) Nucleic Acids Res. , pp. 39-60
    • Gnad, F.1    Gunawardena, J.2    Mann, M.3
  • 39
    • 79751504755 scopus 로고    scopus 로고
    • Phosphorylation mechanism and structure of serine-arginine protein kinases
    • Ghosh, G.; Adams, J. A. Phosphorylation mechanism and structure of serine-arginine protein kinases FEBS J. 2011, 278 (4) 587-97
    • (2011) FEBS J. , vol.278 , Issue.4 , pp. 587-597
    • Ghosh, G.1    Adams, J.A.2
  • 40
    • 39149123489 scopus 로고    scopus 로고
    • Unveiling substrate RNA binding to H/ACA RNPs: One side fits all
    • Li, H. Unveiling substrate RNA binding to H/ACA RNPs: one side fits all Curr. Opin. Struct. Biol. 2008, 18 (1) 78-85
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , Issue.1 , pp. 78-85
    • Li, H.1


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