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Volumn 13, Issue 2, 2014, Pages 527-535

"out-gel" tryptic digestion procedure for chemical cross-linking studies with mass spectrometric detection

Author keywords

cross linking; extraction and digestion; protein complexes; proteins; SDS PAGE

Indexed keywords

CROSS-LINKING REAGENTS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HIV REVERSE TRANSCRIPTASE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 84893828096     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400710q     Document Type: Article
Times cited : (7)

References (42)
  • 2
    • 0028915465 scopus 로고
    • Electrophoretic recovery of proteins from polyacrylamide gel
    • Shoji, M.; Kato, M.; Hashizume, S. Electrophoretic recovery of proteins from polyacrylamide gel J. Chromatogr. A 1995, 698, 145-162
    • (1995) J. Chromatogr. A , vol.698 , pp. 145-162
    • Shoji, M.1    Kato, M.2    Hashizume, S.3
  • 3
    • 46249102561 scopus 로고    scopus 로고
    • Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels
    • Seelert, H.; Krause, F. Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels Electrophoresis 2008, 29, 2617-2636
    • (2008) Electrophoresis , vol.29 , pp. 2617-2636
    • Seelert, H.1    Krause, F.2
  • 4
    • 0035498813 scopus 로고    scopus 로고
    • A method for the quantitative recovery of proteins from polyacrylamide gels
    • Scheer, J. M.; Ryan, C. A. A method for the quantitative recovery of proteins from polyacrylamide gels Anal. Biochem. 2001, 298, 130-132
    • (2001) Anal. Biochem. , vol.298 , pp. 130-132
    • Scheer, J.M.1    Ryan, C.A.2
  • 5
    • 0001752671 scopus 로고
    • Preparative methods for disk electrophoresis with special reference to the isolation of pituitary hormones
    • Lewis, U. J.; Clark, M. O. Preparative methods for disk electrophoresis with special reference to the isolation of pituitary hormones Anal. Biochem. 1963, 6, 303-315
    • (1963) Anal. Biochem. , vol.6 , pp. 303-315
    • Lewis, U.J.1    Clark, M.O.2
  • 6
    • 0031148680 scopus 로고    scopus 로고
    • Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels
    • Cohen, S. L.; Chait, B. T. Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels Anal. Biochem. 1997, 247, 257-267
    • (1997) Anal. Biochem. , vol.247 , pp. 257-267
    • Cohen, S.L.1    Chait, B.T.2
  • 7
    • 51649122509 scopus 로고    scopus 로고
    • Electroelution of proteins from polyacrylamide gels
    • In; Walker, J. M. Humana Press: Totowa, NJ
    • Jeno, P.; Horst, M. Electroelution of proteins from polyacrylamide gels. In The Protein Protocols Handbook; Walker, J. M., Ed.; Humana Press: Totowa, NJ, 1996; pp 207-214.
    • (1996) The Protein Protocols Handbook , pp. 207-214
    • Jeno, P.1    Horst, M.2
  • 8
    • 0022481284 scopus 로고
    • Electroelution of fixed and stained membrane proteins from preparative sodium dodecyl-sulfate-polyacrylamide gels into a membrane trap
    • Jacobs, E.; Clad, A. Electroelution of fixed and stained membrane proteins from preparative sodium dodecyl-sulfate-polyacrylamide gels into a membrane trap Anal. Biochem. 1986, 154, 583-589
    • (1986) Anal. Biochem. , vol.154 , pp. 583-589
    • Jacobs, E.1    Clad, A.2
  • 9
    • 0025233342 scopus 로고
    • Elution of proteins from gels
    • Harrington, M. G. Elution of proteins from gels Methods Enzymol. 1990, 182, 488-495
    • (1990) Methods Enzymol. , vol.182 , pp. 488-495
    • Harrington, M.G.1
  • 10
    • 0030905461 scopus 로고    scopus 로고
    • Comparison of in-gel and on-membrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry
    • Courchesne, P. L.; Luethy, R.; Patterson, S. D. Comparison of in-gel and on-membrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry Electrophoresis 1997, 18, 369-381
    • (1997) Electrophoresis , vol.18 , pp. 369-381
    • Courchesne, P.L.1    Luethy, R.2    Patterson, S.D.3
  • 11
    • 71549165472 scopus 로고    scopus 로고
    • Elution of proteins from gels
    • Burgess, R. R. Elution of proteins from gels Methods Enzymol. 2009, 463, 565-572
    • (2009) Methods Enzymol. , vol.463 , pp. 565-572
    • Burgess, R.R.1
  • 12
    • 84893818375 scopus 로고    scopus 로고
    • Trace analysis of proteins by SDS-PAGE, in-gel digestion and mass spectrometry
    • Montgomery, H. V.; Gaskell, S. J.; Gilbert, P. Trace analysis of proteins by SDS-PAGE, in-gel digestion and mass spectrometry Adv. Mass Spectrom. 1998, 14, C014230/1-C014230/11
    • (1998) Adv. Mass Spectrom. , vol.14
    • Montgomery, H.V.1    Gaskell, S.J.2    Gilbert, P.3
  • 13
    • 0031214574 scopus 로고    scopus 로고
    • Identification of proteins by matrix-assisted laser desorption ionization-mass spectrometry following in-gel digestion in low-salt, nonvolatile buffer and simplified peptide recovery
    • Fountoulakis, M.; Langen, H. Identification of proteins by matrix-assisted laser desorption ionization-mass spectrometry following in-gel digestion in low-salt, nonvolatile buffer and simplified peptide recovery Anal. Biochem. 1997, 250, 153-156
    • (1997) Anal. Biochem. , vol.250 , pp. 153-156
    • Fountoulakis, M.1    Langen, H.2
  • 15
    • 34548178909 scopus 로고    scopus 로고
    • In-gel digestion for mass spectrometric characterization of proteins and proteomes
    • Shevchenko, A.; Tomas, H.; Havli, J.; Olsen, J. V.; Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes Nat. Protoc. 2007, 1, 2856-2860
    • (2007) Nat. Protoc. , vol.1 , pp. 2856-2860
    • Shevchenko, A.1    Tomas, H.2    Havli, J.3    Olsen, J.V.4    Mann, M.5
  • 16
    • 0017613305 scopus 로고
    • Peptide mapping by limited proteolysis in sodium dodecyl sulfate and analysis by gel electrophoresis
    • Cleveland, D. W.; Fischer, S. G.; Kirschner, M. W.; Laemmli, U. K. Peptide mapping by limited proteolysis in sodium dodecyl sulfate and analysis by gel electrophoresis J. Biol. Chem. 1977, 252, 1102-1106
    • (1977) J. Biol. Chem. , vol.252 , pp. 1102-1106
    • Cleveland, D.W.1    Fischer, S.G.2    Kirschner, M.W.3    Laemmli, U.K.4
  • 17
    • 0029927505 scopus 로고    scopus 로고
    • Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels
    • Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels Anal. Chem. 1996, 68, 850-858
    • (1996) Anal. Chem. , vol.68 , pp. 850-858
    • Shevchenko, A.1    Wilm, M.2    Vorm, O.3    Mann, M.4
  • 18
    • 0016304913 scopus 로고
    • The isolation and properties of a rabbit liver binding protein specific for asialoglycoproteins
    • Hudgin, R. L.; Pricer, W. E.; Ashwell, G.; Stockert, R. J.; Morell, A. G. The isolation and properties of a rabbit liver binding protein specific for asialoglycoproteins J. Biol. Chem. 1974, 249, 5536-43
    • (1974) J. Biol. Chem. , vol.249 , pp. 5536-5543
    • Hudgin, R.L.1    Pricer, W.E.2    Ashwell, G.3    Stockert, R.J.4    Morell, A.G.5
  • 19
    • 0021355340 scopus 로고
    • A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids
    • Wessel, D.; Flugge, U. I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids Anal. Biochem. 1984, 138, 141-143
    • (1984) Anal. Biochem. , vol.138 , pp. 141-143
    • Wessel, D.1    Flugge, U.I.2
  • 22
    • 77958022947 scopus 로고    scopus 로고
    • An Isotopically-coded CID-cleavable biotinylated crosslinker for structural proteomics
    • 10.1074/mcp.M110.001420
    • Petrotchenko, E. V.; Serpa, J. J.; Borchers, C. H. An Isotopically-coded CID-cleavable biotinylated crosslinker for structural proteomics Mol. Cell. Proteomics 2010, 10.1074/mcp.M110.001420
    • (2010) Mol. Cell. Proteomics
    • Petrotchenko, E.V.1    Serpa, J.J.2    Borchers, C.H.3
  • 25
    • 84863807078 scopus 로고    scopus 로고
    • Use of proteinase K non-specific digestion for selective and comprehensive identification of interpeptide crosslinks: Application to prion proteins
    • 10.1074/mcp.M111.013524
    • Petrotchenko, E. V.; Serpa, J. J.; Berjanskii, M.; Suriyamongkol, B. P.; Wishart, D. S.; Borchers, C. H. Use of proteinase K non-specific digestion for selective and comprehensive identification of interpeptide crosslinks: application to prion proteins Mol. Cell. Proteomics 2012, 10.1074/mcp.M111. 013524
    • (2012) Mol. Cell. Proteomics
    • Petrotchenko, E.V.1    Serpa, J.J.2    Berjanskii, M.3    Suriyamongkol, B.P.4    Wishart, D.S.5    Borchers, C.H.6
  • 26
    • 77249179311 scopus 로고    scopus 로고
    • ICC-CLASS: Isotopically-coded cleavable crosslinking analysis suite
    • Petrotchenko, E. V.; Borchers, C. H. ICC-CLASS: isotopically-coded cleavable crosslinking analysis suite BMC Bioinf. 2010, 11, 64
    • (2010) BMC Bioinf. , vol.11 , pp. 64
    • Petrotchenko, E.V.1    Borchers, C.H.2
  • 27
    • 84893835994 scopus 로고    scopus 로고
    • National Diagnostics. Protein Fixation on Gels, (accessed May 27, 2013).
    • National Diagnostics. Protein Fixation on Gels, https://www. nationaldiagnostics.com/electrophoresis/article/protein-fixation-gels, 2011, (accessed May 27, 2013).
    • (2011)
  • 29
    • 0001535922 scopus 로고
    • Fragmentation of polypeptides by enzymic methods
    • In; Darbre, A. John Wiley and Sons: New York, NY.
    • Wilkinson, J. M. Fragmentation of polypeptides by enzymic methods. In Practical Protein Chemistry: A Handbook.; Darbre, A., Ed.; John Wiley and Sons: New York, NY, 1986.
    • (1986) Practical Protein Chemistry: A Handbook.
    • Wilkinson, J.M.1
  • 30
    • 84893875991 scopus 로고    scopus 로고
    • BoehringerMannheim, Trypsin sequencing grade product overview.
    • BoehringerMannheim, Trypsin sequencing grade product overview. 2004.
    • (2004)
  • 31
    • 84893832559 scopus 로고    scopus 로고
    • Promega-Corporation Trypsin Gold, mass spectrometry grade. Instructions for use of product V5280. Copyright 2002, 2004, 2006, 2009 (August).
    • Promega-Corporation Trypsin Gold, mass spectrometry grade. Instructions for use of product V5280. Copyright 2002, 2004, 2006, 2009 (August 2012).
    • (2012)
  • 32
    • 1942438572 scopus 로고    scopus 로고
    • Effects of common surfactants on protein digestion and matrix-assisted laser desorption/ionization mass spectrometric analysis of the digested peptides using two-layer sample preparation
    • Zhang, N.; Li, L. Effects of common surfactants on protein digestion and matrix-assisted laser desorption/ionization mass spectrometric analysis of the digested peptides using two-layer sample preparation Rapid Commun. Mass Spectrom. 2004, 18, 889-896
    • (2004) Rapid Commun. Mass Spectrom. , vol.18 , pp. 889-896
    • Zhang, N.1    Li, L.2
  • 33
    • 33645721632 scopus 로고    scopus 로고
    • Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins
    • Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins Mol. Cell. Proteomics 2006, 5, 573-588
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 573-588
    • Anderson, L.1    Hunter, C.L.2
  • 34
    • 77957344363 scopus 로고    scopus 로고
    • A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin
    • Proc, J. L.; Kuzyk, M. A.; Hardie, D. B.; Yang, J.; Smith, D. S.; Jackson, A. M.; Parker, C. E.; Borchers, C. H. A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin J. Proteome Res. 2010, 9, 5422-5437
    • (2010) J. Proteome Res. , vol.9 , pp. 5422-5437
    • Proc, J.L.1    Kuzyk, M.A.2    Hardie, D.B.3    Yang, J.4    Smith, D.S.5    Jackson, A.M.6    Parker, C.E.7    Borchers, C.H.8
  • 36
    • 0036558160 scopus 로고    scopus 로고
    • Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry
    • Wine, R. N.; Dial, J. M.; Tomer, K. B.; Borchers, C. H. Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry Anal. Chem. 2002, 74, 1939-1945
    • (2002) Anal. Chem. , vol.74 , pp. 1939-1945
    • Wine, R.N.1    Dial, J.M.2    Tomer, K.B.3    Borchers, C.H.4
  • 37
    • 84865647364 scopus 로고    scopus 로고
    • MeCAT peptide labeling for the absolute quantification of proteins by 2D-LC-ICP-MS
    • Esteban-Fernández, D.; Ahrends, R.; Linscheid, M. W. MeCAT peptide labeling for the absolute quantification of proteins by 2D-LC-ICP-MS J. Mass Spectrom. 2012, 47, 760-768
    • (2012) J. Mass Spectrom. , vol.47 , pp. 760-768
    • Esteban-Fernández, D.1    Ahrends, R.2    Linscheid, M.W.3
  • 38
    • 69749093506 scopus 로고    scopus 로고
    • Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes
    • Yan, F.; Che, F. Y.; Rykunov, D.; Nieves, E.; Fiser, A.; Weiss, L. M.; Hogue Angeletti, R. Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes Anal. Chem. 2009, 81, 7149-7159
    • (2009) Anal. Chem. , vol.81 , pp. 7149-7159
    • Yan, F.1    Che, F.Y.2    Rykunov, D.3    Nieves, E.4    Fiser, A.5    Weiss, L.M.6    Hogue Angeletti, R.7
  • 39
    • 67649963647 scopus 로고    scopus 로고
    • Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry
    • Chowdhury, S. M.; Du, X.; Tolić, N.; Wu, S.; Moore, R. J.; Mayer, M. U.; Smith, R. D.; Adkins, J. N. Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry Anal. Chem. 2009, 81, 5524-32
    • (2009) Anal. Chem. , vol.81 , pp. 5524-5532
    • Chowdhury, S.M.1    Du, X.2    Tolić, N.3    Wu, S.4    Moore, R.J.5    Mayer, M.U.6    Smith, R.D.7    Adkins, J.N.8
  • 41
    • 33744454670 scopus 로고    scopus 로고
    • Thermostable trypsin conjugates for high-throughput proteomics: Synthesis and performance evaluation
    • Sebela, M.; Stosová, T.; Havlis, J.; Wielsch, N.; Thomas, H.; Zdráhal, Z.; Shevchenko, A. Thermostable trypsin conjugates for high-throughput proteomics: synthesis and performance evaluation Proteomics 2006, 6, 2959-2963
    • (2006) Proteomics , vol.6 , pp. 2959-2963
    • Sebela, M.1    Stosová, T.2    Havlis, J.3    Wielsch, N.4    Thomas, H.5    Zdráhal, Z.6    Shevchenko, A.7
  • 42
    • 4644222872 scopus 로고    scopus 로고
    • Determination of pore/protein size via electrophoresis and slit sieve model
    • Sarbolouki, M. N.; Mahnam, K.; Rafiee-Pour, H.-A. Determination of pore/protein size via electrophoresis and slit sieve model Electrophoresis 2004, 25, 2907-2911
    • (2004) Electrophoresis , vol.25 , pp. 2907-2911
    • Sarbolouki, M.N.1    Mahnam, K.2    Rafiee-Pour, H.-A.3


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