메뉴 건너뛰기




Volumn 15, Issue 3, 2016, Pages 1094-1104

A study into the collision-induced dissociation (CID) behavior of cross-linked peptides

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE; PEPTIDE; PEPTIDE FRAGMENT; PROTEIN; SERINE; THREONINE; TYROSINE; CROSS LINKING REAGENT; PROTEIN BINDING;

EID: 84962542122     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M115.049296     Document Type: Article
Times cited : (64)

References (44)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 67651173106 scopus 로고    scopus 로고
    • Proteomics by mass spectrometry: Approaches, advances, and applications
    • Yates, J. R., Ruse, C. I., and Nakorchevsky, A. (2009) Proteomics by mass spectrometry: Approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11, 49-79
    • (2009) Annu. Rev. Biomed. Eng. , vol.11 , pp. 49-79
    • Yates, J.R.1    Ruse, C.I.2    Nakorchevsky, A.3
  • 4
    • 62349106992 scopus 로고    scopus 로고
    • Mass spectrometry detection and characterization of noncovalent protein complexes
    • Clifton, NJ: Springer
    • Yin, S., and Loo, J. A. (2009) Mass spectrometry detection and characterization of noncovalent protein complexes. Mass Spectrometry of Proteins and Peptides, Clifton, NJ: Springer. pp 273-282
    • (2009) Mass Spectrometry of Proteins and Peptides , pp. 273-282
    • Yin, S.1    Loo, J.A.2
  • 5
    • 33745742438 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
    • Sinz, A. (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682
    • (2006) Mass Spectrom. Rev. , vol.25 , pp. 663-682
    • Sinz, A.1
  • 7
    • 78149438179 scopus 로고    scopus 로고
    • Crosslinking combined with mass spectrometry for structural proteomics
    • Petrotchenko, E. V., and Borchers, C. H. (2010) Crosslinking combined with mass spectrometry for structural proteomics. Mass Spectrom. Rev. 29, 862-876
    • (2010) Mass Spectrom. Rev. , vol.29 , pp. 862-876
    • Petrotchenko, E.V.1    Borchers, C.H.2
  • 8
    • 79851513173 scopus 로고    scopus 로고
    • The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes
    • Rappsilber, J. (2011) The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J. Struct. Biol. 173, 530-540 doi: 10.1016/j.jsb.2010.10.014
    • (2011) J. Struct. Biol. , vol.173 , pp. 530-540
    • Rappsilber, J.1
  • 10
    • 84857966803 scopus 로고    scopus 로고
    • Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography
    • Leitner, A., Reischl, R., Walzthoeni, T., Herzog, F., Bohn, S., Förster, F., and Aebersold, R. (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol. Cell. Proteomics 11, M111.014126
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. M111014126
    • Leitner, A.1    Reischl, R.2    Walzthoeni, T.3    Herzog, F.4    Bohn, S.5    Förster, F.6    Aebersold, R.7
  • 11
    • 77955636430 scopus 로고    scopus 로고
    • Cleavable cross-linker for protein structure analysis: Reliable identification of cross-linking products by tandem MS
    • Müller, M. Q., Dreiocker, F., Ihling, C. H., Schäfer, M., and Sinz A. (2010) Cleavable cross-linker for protein structure analysis: Reliable identification of cross-linking products by tandem MS. Anal. Chem. 82, 6958-68
    • (2010) Anal. Chem. , vol.82 , pp. 6958-6968
    • Müller, M.Q.1    Dreiocker, F.2    Ihling, C.H.3    Schäfer, M.4    Sinz, A.5
  • 12
    • 78651092959 scopus 로고    scopus 로고
    • Development of a novel cross-linking strategy for fast and accurate identification of crosslinked peptides of protein complexes
    • Kao, A., Chiu, C., Vellucci, D., Yang, Y., Patel, V. R., Guan, S., Randall, A., Baldi, P., Rychnovsky, S. D., and Huang, L. (2011) Development of a novel cross-linking strategy for fast and accurate identification of crosslinked peptides of protein complexes. Mol. Cell. Proteomics 10, M110.002212
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. M110002212
    • Kao, A.1    Chiu, C.2    Vellucci, D.3    Yang, Y.4    Patel, V.R.5    Guan, S.6    Randall, A.7    Baldi, P.8    Rychnovsky, S.D.9    Huang, L.10
  • 15
    • 73649112404 scopus 로고    scopus 로고
    • New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra
    • Choi, S., Jeong, J., Na, S., Lee, H. S., Kim, H. Y., Lee, K. J., and Paek, E. (2010) New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra. J. Proteome Res. 9, 626-635
    • (2010) J. Proteome Res. , vol.9 , pp. 626-635
    • Choi, S.1    Jeong, J.2    Na, S.3    Lee, H.S.4    Kim, H.Y.5    Lee, K.J.6    Paek, E.7
  • 16
    • 79952430498 scopus 로고    scopus 로고
    • Xlink-Identifier: An automated data analysis platform for confident identifications of chemically crosslinked peptides using tandem mass spectrometry
    • Du, X., Chowdhury, S. M., Manes, N. P., Wu, S., Mayer, M. U., Adkins, J. N., Anderson, G. A., and Smith, R. D. (2011) Xlink-Identifier: An automated data analysis platform for confident identifications of chemically crosslinked peptides using tandem mass spectrometry. J. Proteome Res. 10, 923-931
    • (2011) J. Proteome Res. , vol.10 , pp. 923-931
    • Du, X.1    Chowdhury, S.M.2    Manes, N.P.3    Wu, S.4    Mayer, M.U.5    Adkins, J.N.6    Anderson, G.A.7    Smith, R.D.8
  • 19
    • 84890084967 scopus 로고    scopus 로고
    • Hekate: Software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples
    • Holding, A. N., Lamers, M. H., Stephens, E., and Skehel, J. M. (2013). Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. Journal of Proteome Research, 12, 5923-5933
    • (2013) Journal of Proteome Research , vol.12 , pp. 5923-5933
    • Holding, A.N.1    Lamers, M.H.2    Stephens, E.3    Skehel, J.M.4
  • 20
    • 82555186441 scopus 로고    scopus 로고
    • Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links
    • Mayne, S. L. N., and Patterton, H.-G. (2011) Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links. Brief Bioinform. 12, 660-71
    • (2011) Brief Bioinform. , vol.12 , pp. 660-671
    • Mayne, S.L.N.1    Patterton, H.-G.2
  • 23
    • 76649135167 scopus 로고    scopus 로고
    • Finding chimeras: A bioinformatics strategy for identification of cross-linked peptides
    • Chu, F., Baker, P. R., Burlingame, A. L., and Chalkley, R. J. (2010) Finding chimeras: A bioinformatics strategy for identification of cross-linked peptides. Mol. Cell. Proteomics 9, 25-31
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 25-31
    • Chu, F.1    Baker, P.R.2    Burlingame, A.L.3    Chalkley, R.J.4
  • 24
    • 84898766201 scopus 로고    scopus 로고
    • Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra
    • Wang, J., Anania, V. G., Knott, J., Rush, J., Lill, J. R., Bourne, P. E., and Bandeira, N. (2014). Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Molecular & Cellular Proteomics 13, 1128-1136
    • (2014) Molecular & Cellular Proteomics , vol.13 , pp. 1128-1136
    • Wang, J.1    Anania, V.G.2    Knott, J.3    Rush, J.4    Lill, J.R.5    Bourne, P.E.6    Bandeira, N.7
  • 25
    • 26244461164 scopus 로고    scopus 로고
    • Development and application of diazirines in biological and synthetic macromolecular systems
    • Blencowe, A., and Hayes, W. (2005) Development and application of diazirines in biological and synthetic macromolecular systems. Soft Matter 1, 178
    • (2005) Soft Matter , vol.1 , pp. 178
    • Blencowe, A.1    Hayes, W.2
  • 26
    • 0037353846 scopus 로고    scopus 로고
    • Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides
    • Tabb, D. L., Smith, L. L., Breci, L. A., Wysocki, V. H., Lin, D., and Yates, J. R. 3rd (2003) Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 75, 1155-1163
    • (2003) Anal. Chem. , vol.75 , pp. 1155-1163
    • Tabb, D.L.1    Smith, L.L.2    Breci, L.A.3    Wysocki, V.H.4    Lin, D.5    Yates, J.R.6
  • 27
  • 28
    • 84893048557 scopus 로고    scopus 로고
    • MS2PIP: A tool for MS/MS peak intensity prediction
    • Degroeve, S., and Martens, L. (2013) MS2PIP: A tool for MS/MS peak intensity prediction. Bioinformatics 29, 3199-3203
    • (2013) Bioinformatics , vol.29 , pp. 3199-3203
    • Degroeve, S.1    Martens, L.2
  • 29
    • 84867315928 scopus 로고    scopus 로고
    • SQID-XLink: Implementation of an intensity-incorporated algorithm for cross-linked peptide identification
    • Li, W., O'Neill, H. A., and Wysocki, V. H. (2012) SQID-XLink: Implementation of an intensity-incorporated algorithm for cross-linked peptide identification. Bioinformatics 28, 2548-2550
    • (2012) Bioinformatics , vol.28 , pp. 2548-2550
    • Li, W.1    O'Neill, H.A.2    Wysocki, V.H.3
  • 31
    • 84891758507 scopus 로고    scopus 로고
    • Quantitative crosslinking/mass spectrometry using isotope-labelled cross-linkers
    • Fischer, L., Chen, Z. A., and Rappsilber, J. (2013) Quantitative crosslinking/mass spectrometry using isotope-labelled cross-linkers. J. Proteomics 88, 120-128
    • (2013) J. Proteomics , vol.88 , pp. 120-128
    • Fischer, L.1    Chen, Z.A.2    Rappsilber, J.3
  • 32
    • 84923677327 scopus 로고    scopus 로고
    • Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by crosslinking and molecular modelling
    • Barysz, H., Kim, J. H., Chen, Z. A., Hudson, D. F., Rappsilber, J., Gerloff, D. L., and Earnshaw, W. C. (2015) Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by crosslinking and molecular modelling. Open Biol. 5, 150005
    • (2015) Open Biol. , vol.5 , pp. 150005
    • Barysz, H.1    Kim, J.H.2    Chen, Z.A.3    Hudson, D.F.4    Rappsilber, J.5    Gerloff, D.L.6    Earnshaw, W.C.7
  • 33
    • 84923073621 scopus 로고    scopus 로고
    • Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules
    • Trowitzsch, S., Viola, C., Scheer, E., Conic, S., Chavant, V., Fournier, M.,... Berger, I. (2015). Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules. Nature Communications 6, 6011
    • (2015) Nature Communications , vol.6 , pp. 6011
    • Trowitzsch, S.1    Viola, C.2    Scheer, E.3    Conic, S.4    Chavant, V.5    Fournier M....6    Berger, I.7
  • 35
    • 79960196834 scopus 로고    scopus 로고
    • Spectrum-tospectrum searching using a proteome-wide spectral library
    • Yen, C.-Y., Houel, S., Ahn, N. G., and Old, W. M. (2011) Spectrum-tospectrum searching using a proteome-wide spectral library. Mol. Cell. Proteomics 10, M111.007666
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. M111007666
    • Yen, C.-Y.1    Houel, S.2    Ahn, N.G.3    Old, W.M.4
  • 36
    • 84962525355 scopus 로고    scopus 로고
    • Serum albumin domain structures in human blood serum by mass spectrometry and computational biology
    • Belsom, A., Schneider, M., Fischer, L., Brock, O., and Rappsilber, J. (2015) Serum albumin domain structures in human blood serum by mass spectrometry and computational biology. Mol. Cell. Proteomics 3, 1105-1116
    • (2015) Mol. Cell. Proteomics , vol.3 , pp. 1105-1116
    • Belsom, A.1    Schneider, M.2    Fischer, L.3    Brock, O.4    Rappsilber, J.5
  • 40
    • 84870658462 scopus 로고    scopus 로고
    • Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry
    • Lauber, M. A., Rappsilber, J., and Reilly, J. P. (2012). Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Molecular & Cellular Proteomics 11, 1965-1976
    • (2012) Molecular & Cellular Proteomics , vol.11 , pp. 1965-1976
    • Lauber, M.A.1    Rappsilber, J.2    Reilly, J.P.3
  • 41
    • 84891758507 scopus 로고    scopus 로고
    • Quantitative crosslinking/mass spectrometry using isotope-labelled cross-linkers
    • Fischer, L., Chen, Z. A., and Rappsilber, J. (2013). Quantitative crosslinking/mass spectrometry using isotope-labelled cross-linkers. Journal of Proteomics, 88, 120-128
    • (2013) Journal of Proteomics , vol.88 , pp. 120-128
    • Fischer, L.1    Chen, Z.A.2    Rappsilber, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.