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Volumn 6, Issue 8, 2011, Pages 829-836

Isotopic signature transfer and mass pattern prediction (IsoStamp): An enabling technique for chemically-directed proteomics

Author keywords

[No Author keywords available]

Indexed keywords

ISOTOPE; PEPTIDE; PEPTIDE FRAGMENT;

EID: 80051967494     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb100338x     Document Type: Article
Times cited : (48)

References (47)
  • 1
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon, B. and Aebersold, R. (2006) Mass spectrometry and protein analysis Science 312, 212-217
    • (2006) Science , vol.312 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 2
    • 0141502007 scopus 로고    scopus 로고
    • Shotgun proteomics: Integrating technologies to answer biological questions
    • McDonald, W. H. and Yates, J. R., 3rd. (2003) Shotgun proteomics: integrating technologies to answer biological questions Curr. Opin. Mol. Ther. 5, 302-309 (Pubitemid 37185350)
    • (2003) Current Opinion in Molecular Therapeutics , vol.5 , Issue.3 , pp. 302-309
    • McDonald, W.H.1    Yates III, J.R.2
  • 3
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K., McCormack, A. L., and Yates, J. R., 3rd. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 5, 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 4
    • 0028575316 scopus 로고
    • Error-tolerant identification of peptides in sequence databases by peptide sequence tags
    • Mann, M. and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags Anal. Chem. 66, 4390-4399 (Pubitemid 124006101)
    • (1994) Analytical Chemistry , vol.66 , Issue.24 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 5
    • 0028824080 scopus 로고
    • Mass spectrometric approaches for the identification of gel-separated proteins
    • Patterson, S. D. and Aebersold, R. (1995) Mass spectrometric approaches for the identification of gel-separated proteins Electrophoresis 16, 1791-1814
    • (1995) Electrophoresis , vol.16 , pp. 1791-1814
    • Patterson, S.D.1    Aebersold, R.2
  • 6
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: History, character, and diagnostic prospects
    • Anderson, N. L. and Anderson, N. G. (2002) The human plasma proteome: history, character, and diagnostic prospects Mol. Cell. Proteomics 1, 845-867
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 7
    • 34848903890 scopus 로고    scopus 로고
    • The implications of proteolytic background for shotgun proteomics
    • DOI 10.1074/mcp.M700029-MCP200
    • Picotti, P., Aebersold, R., and Domon, B. (2007) The implications of proteolytic background for shotgun proteomics Mol. Cell. Proteomics 6, 1589-1598 (Pubitemid 47506169)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.9 , pp. 1589-1598
    • Picott, P.1    Aebersold, R.2    Domont, B.3
  • 8
    • 70549084975 scopus 로고    scopus 로고
    • Directed mass spectrometry: Towards hypothesis-driven proteomics
    • Schmidt, A., Claassen, M., and Aebersold, R. (2009) Directed mass spectrometry: towards hypothesis-driven proteomics Curr. Opin. Chem. Biol. 13, 510-517
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 510-517
    • Schmidt, A.1    Claassen, M.2    Aebersold, R.3
  • 9
    • 77956836941 scopus 로고    scopus 로고
    • Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays
    • Savitski, M. M., Fischer, F., Mathieson, T., Sweetman, G., Lang, M., and Bantscheff, M. (2010) Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays J. Am. Soc. Mass Spectrom. 21, 1668-1679
    • (2010) J. Am. Soc. Mass Spectrom. , vol.21 , pp. 1668-1679
    • Savitski, M.M.1    Fischer, F.2    Mathieson, T.3    Sweetman, G.4    Lang, M.5    Bantscheff, M.6
  • 10
    • 70549113220 scopus 로고    scopus 로고
    • Perspectives of targeted mass spectrometry for protein biomarker verification
    • Huttenhain, R., Malmstrom, J., Picotti, P., and Aebersold, R. (2009) Perspectives of targeted mass spectrometry for protein biomarker verification Curr. Opin. Chem. Biol. 13, 518-525
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 518-525
    • Huttenhain, R.1    Malmstrom, J.2    Picotti, P.3    Aebersold, R.4
  • 11
    • 70249130836 scopus 로고    scopus 로고
    • Methods for proteomic analysis of transcription factors
    • Jiang, D., Jarrett, H. W., and Haskins, W. E. (2009) Methods for proteomic analysis of transcription factors J. Chromatogr. A 1216, 6881-6889
    • (2009) J. Chromatogr. A , vol.1216 , pp. 6881-6889
    • Jiang, D.1    Jarrett, H.W.2    Haskins, W.E.3
  • 13
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • DOI 10.1038/13690
    • Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 17, 994-999 (Pubitemid 29474856)
    • (1999) Nature Biotechnology , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 16
    • 76249116706 scopus 로고    scopus 로고
    • Getting a chemical handle on protein post-translational modification
    • Heal, W. P. and Tate, E. W. (2010) Getting a chemical handle on protein post-translational modification Org. Biomol. Chem. 8, 731-738
    • (2010) Org. Biomol. Chem. , vol.8 , pp. 731-738
    • Heal, W.P.1    Tate, E.W.2
  • 17
    • 0034677879 scopus 로고    scopus 로고
    • Cell surface engineering by a modified Staudinger reaction
    • DOI 10.1126/science.287.5460.2007
    • Saxon, E. and Bertozzi, C. R. (2000) Cell surface engineering by a modified Staudinger reaction Science 287, 2007-2010 (Pubitemid 30158675)
    • (2000) Science , vol.287 , Issue.5460 , pp. 2007-2010
    • Saxon, E.1    Bertozzi, C.R.2
  • 20
    • 77949822323 scopus 로고    scopus 로고
    • Bioorthogonal chemical reporters for monitoring protein acetylation
    • Yang, Y. Y., Ascano, J. M., and Hang, H. C. (2010) Bioorthogonal chemical reporters for monitoring protein acetylation J. Am. Chem. Soc. 132, 3640-3641
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 3640-3641
    • Yang, Y.Y.1    Ascano, J.M.2    Hang, H.C.3
  • 22
    • 77951805919 scopus 로고    scopus 로고
    • Inflammatory stimuli regulate caspase substrate profiles
    • Agard, N. J., Maltby, D., and Wells, J. A. (2010) Inflammatory stimuli regulate caspase substrate profiles Mol. Cell. Proteomics 9, 880-893
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 880-893
    • Agard, N.J.1    Maltby, D.2    Wells, J.A.3
  • 23
    • 79851510345 scopus 로고    scopus 로고
    • Chemical 'omics' approaches for understanding protein cysteine oxidation in biology
    • Leonard, S. E. and Carroll, K. S. (2011) Chemical 'omics' approaches for understanding protein cysteine oxidation in biology Curr. Opin. Chem. Biol. 15, 88-102
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 88-102
    • Leonard, S.E.1    Carroll, K.S.2
  • 24
    • 73449131845 scopus 로고    scopus 로고
    • An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis
    • Meier, J. L., Niessen, S., Hoover, H. S., Foley, T. L., Cravatt, B. F., and Burkart, M. D. (2009) An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis ACS Chem. Biol. 4, 948-957
    • (2009) ACS Chem. Biol. , vol.4 , pp. 948-957
    • Meier, J.L.1    Niessen, S.2    Hoover, H.S.3    Foley, T.L.4    Cravatt, B.F.5    Burkart, M.D.6
  • 25
    • 76149136920 scopus 로고    scopus 로고
    • Use of a combination of isotopically coded cross-linkers and isotopically coded N-terminal modification reagents for selective identification of inter-peptide crosslinks
    • Petrotchenko, E. V., Serpa, J. J., and Borchers, C. H. (2010) Use of a combination of isotopically coded cross-linkers and isotopically coded N-terminal modification reagents for selective identification of inter-peptide crosslinks Anal. Chem. 82, 817-823
    • (2010) Anal. Chem. , vol.82 , pp. 817-823
    • Petrotchenko, E.V.1    Serpa, J.J.2    Borchers, C.H.3
  • 26
    • 70549102769 scopus 로고    scopus 로고
    • Halogenated peptides as internal standards (H-PINS): Introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry
    • Mirzaei, H., Brusniak, M. Y., Mueller, L. N., Letarte, S., Watts, J. D., and Aebersold, R. (2009) Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry Mol. Cell. Proteomics 8, 1934-1946
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 1934-1946
    • Mirzaei, H.1    Brusniak, M.Y.2    Mueller, L.N.3    Letarte, S.4    Watts, J.D.5    Aebersold, R.6
  • 27
    • 37549027670 scopus 로고    scopus 로고
    • Enrichment tags for enhanced-resolution profiling of the polar metabolome
    • Carlson, E. E. and Cravatt, B. F. (2007) Enrichment tags for enhanced-resolution profiling of the polar metabolome J. Am. Chem. Soc. 129, 15780-15782
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 15780-15782
    • Carlson, E.E.1    Cravatt, B.F.2
  • 28
    • 0038111843 scopus 로고    scopus 로고
    • Structural analysis of oligosaccharides by a combination of electrospray mass spectrometry and bromine isotope tagging of reducing-end sugars with 2-amino-5-bromopyridine
    • DOI 10.1002/rcm.1064
    • Li, M. and Kinzer, J. A. (2003) Structural analysis of oligosaccharides by a combination of electrospray mass spectrometry and bromine isotope tagging of reducing-end sugars with 2-amino-5-bromopyridine Rapid Commun. Mass Spectrom. 17, 1462-1466 (Pubitemid 36791153)
    • (2003) Rapid Communications in Mass Spectrometry , vol.17 , Issue.13 , pp. 1462-1466
    • Li, M.1    Kinzer, J.A.2
  • 29
    • 33744458765 scopus 로고    scopus 로고
    • Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry
    • DOI 10.1021/cc0501460
    • Paulick, M. G., Hart, K. M., Brinner, K. M., Tjandra, M., Charych, D. H., and Zuckermann, R. N. (2006) Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry J. Comb. Chem. 8, 417-426 (Pubitemid 43798307)
    • (2006) Journal of Combinatorial Chemistry , vol.8 , Issue.3 , pp. 417-426
    • Paulick, M.G.1    Hart, K.M.2    Brinner, K.M.3    Tjandra, M.4    Charych, D.H.5    Zuckermann, R.N.6
  • 30
    • 0001180208 scopus 로고
    • Partial structure elucidation of the most abundant octa and nonachlorotoxaphene congeners in marine mammals by using conventional electron ionization mass spectrometry and mass spectrometry/mass spectrometry
    • Buser, H., Oehme, M., Vetter, W., and Luckas, B. (1993) Partial structure elucidation of the most abundant octa and nonachlorotoxaphene congeners in marine mammals by using conventional electron ionization mass spectrometry and mass spectrometry/mass spectrometry Fresenius J. Anal. Chem. 347, 502-512
    • (1993) Fresenius J. Anal. Chem. , vol.347 , pp. 502-512
    • Buser, H.1    Oehme, M.2    Vetter, W.3    Luckas, B.4
  • 31
    • 0036756784 scopus 로고    scopus 로고
    • Utilization of charge and mass labeling for the structural identification of heterocyclic quaternary salts by mass spectrometry
    • Enjalbal, C., Sanches, P., Martinez, J., Aubagnac, J., Sanz, D., Claramunt, R. M., and Elguero, J. (2002) Utilization of charge and mass labeling for the structural identification of heterocyclic quaternary salts by mass spectrometry Int. J. Mass Spectrom. 219, 391-401
    • (2002) Int. J. Mass Spectrom. , vol.219 , pp. 391-401
    • Enjalbal, C.1    Sanches, P.2    Martinez, J.3    Aubagnac, J.4    Sanz, D.5    Claramunt, R.M.6    Elguero, J.7
  • 32
    • 0034653646 scopus 로고    scopus 로고
    • Protein identification with a single accurate mass of a cysteine- containing peptide and constrained database searching
    • DOI 10.1021/ac9913210
    • Goodlett, D. R., Bruce, J. E., Anderson, G. A., Rist, B., Pasa-Tolic, L., Fiehn, O., Smith, R. D., and Aebersold, R. (2000) Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching Anal. Chem. 72, 1112-1118 (Pubitemid 30163763)
    • (2000) Analytical Chemistry , vol.72 , Issue.6 , pp. 1112-1118
    • Goodlett, D.R.1    Bruce, J.E.2    Anderson, G.A.3    Rist, B.4    Pasa-Tolic, L.5    Fiehn, O.6    Smith, R.D.7    Aebersold, R.8
  • 33
    • 0031900241 scopus 로고    scopus 로고
    • A novel derivatization method with 5-bromonicotinic acid N-hydroxysuccinimide for determination of the amino acid sequences of peptides
    • DOI 10.1002/(SICI)1097-0231(19980529)12:10<603::AID-RCM204>3.0. CO;2-0
    • Miyagi, M., Nakao, M., Nakazawa, T., Kato, I., and Tsunasawa, S. (1998) A novel derivatization method with 5-bromonicotinic acid N-hydroxysuccinimide for determination of the amino acid sequences of peptides Rapid Commun. Mass Spectrom. 12, 603-608 (Pubitemid 28222701)
    • (1998) Rapid Communications in Mass Spectrometry , vol.12 , Issue.10 , pp. 603-608
    • Miyagi, M.1    Nakao, M.2    Nakazawa, T.3    Kato, I.4    Tsunasawa, S.5
  • 34
    • 78649357870 scopus 로고    scopus 로고
    • Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics
    • Yang, Y. Y., Grammel, M., Raghavan, A. S., Charron, G., and Hang, H. C. (2010) Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics Chem. Biol. 17, 1212-1222
    • (2010) Chem. Biol. , vol.17 , pp. 1212-1222
    • Yang, Y.Y.1    Grammel, M.2    Raghavan, A.S.3    Charron, G.4    Hang, H.C.5
  • 35
    • 14644392991 scopus 로고    scopus 로고
    • Isotope-differentiated binding energy shift tags (IDBEST™) for improved targeted biomarker discovery and validation
    • DOI 10.1586/14789450.1.4.421
    • Hall, M. P. and Schneider, L. V. (2004) Isotope-differentiated binding energy shift tags (IDBEST) for improved targeted biomarker discovery and validation Exp. Rev. Proteomics 1, 421-431 (Pubitemid 43826409)
    • (2004) Expert Review of Proteomics , vol.1 , Issue.4 , pp. 421-431
    • Hall, M.P.1    Schneider, L.V.2
  • 36
    • 33646751578 scopus 로고    scopus 로고
    • Mass defect labeling of cysteine for improving peptide assignment in shotgun proteomic analyses
    • Hernandez, H., Niehauser, S., Boltz, S. A., Gawandi, V., Phillips, R. S., and Amster, I. J. (2006) Mass defect labeling of cysteine for improving peptide assignment in shotgun proteomic analyses Anal. Chem. 78, 3417-3423
    • (2006) Anal. Chem. , vol.78 , pp. 3417-3423
    • Hernandez, H.1    Niehauser, S.2    Boltz, S.A.3    Gawandi, V.4    Phillips, R.S.5    Amster, I.J.6
  • 37
    • 46849091191 scopus 로고    scopus 로고
    • Mass defect profiles of biological matrices and the general applicability of mass defect filtering for metabolite detection
    • DOI 10.1002/rcm.3585
    • Zhang, H., Zhu, M., Ray, K. L., Ma, L., and Zhang, D. (2008) Mass defect profiles of biological matrices and the general applicability of mass defect filtering for metabolite detection Rapid Commun. Mass Spectrom. 22, 2082-2088 (Pubitemid 351956694)
    • (2008) Rapid Communications in Mass Spectrometry , vol.22 , Issue.13 , pp. 2082-2088
    • Zhang, H.1    Zhu, M.2    Ray, K.L.3    Ma, L.4    Zhang, D.5
  • 39
    • 50649090726 scopus 로고    scopus 로고
    • Software for the calculation of isotope patterns in tandem mass spectrometry
    • Ramaley, L. and Herrera, L. C. (2008) Software for the calculation of isotope patterns in tandem mass spectrometry Rapid Commun. Mass Spectrom. 22, 2707-2714
    • (2008) Rapid Commun. Mass Spectrom. , vol.22 , pp. 2707-2714
    • Ramaley, L.1    Herrera, L.C.2
  • 40
    • 77954370396 scopus 로고    scopus 로고
    • Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: A novel method to determine interresidue distances in protein structures through cross-linking
    • Zelter, A., Hoopmann, M. R., Vernon, R., Baker, D., MacCoss, M. J., and Davis, T. N. (2010) Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking J. Proteome Res. 9, 3583-3589
    • (2010) J. Proteome Res. , vol.9 , pp. 3583-3589
    • Zelter, A.1    Hoopmann, M.R.2    Vernon, R.3    Baker, D.4    MacCoss, M.J.5    Davis, T.N.6
  • 41
  • 42
    • 57949096717 scopus 로고    scopus 로고
    • Envelope: Interactive software for modeling and fitting complex isotope distributions
    • Sykes, M. T. and Williamson, J. R. (2008) Envelope: interactive software for modeling and fitting complex isotope distributions BMC Bioinformatics 9, 446
    • (2008) BMC Bioinformatics , vol.9 , pp. 446
    • Sykes, M.T.1    Williamson, J.R.2
  • 43
    • 34547727671 scopus 로고    scopus 로고
    • High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry
    • DOI 10.1021/ac0700833
    • Hoopmann, M. R., Finney, G. L., and MacCoss, M. J. (2007) High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry Anal. Chem. 79, 5620-5632 (Pubitemid 47229808)
    • (2007) Analytical Chemistry , vol.79 , Issue.15 , pp. 5620-5632
    • Hoopmann, M.R.1    Finney, G.L.2    MacCoss, M.J.3
  • 44
    • 58149209843 scopus 로고
    • Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions
    • Senko, M. W., Beu, S. C., and McLafferty, F. W. (1995) Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions J. Am. Soc. Mass. Spectrom. 6, 229-233
    • (1995) J. Am. Soc. Mass. Spectrom. , vol.6 , pp. 229-233
    • Senko, M.W.1    Beu, S.C.2    McLafferty, F.W.3
  • 45
    • 38649091017 scopus 로고    scopus 로고
    • Improving mass spectrometry peak detection using multiple peak alignment results
    • DOI 10.1021/pr070370n
    • Yu, W., He, Z., Liu, J., and Zhao, H. (2008) Improving mass spectrometry peak detection using multiple peak alignment results J. Proteome Res. 7, 123-129 (Pubitemid 351171123)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 123-129
    • Yu, W.1    He, Z.2    Liu, J.3    Zhao, H.4
  • 46
    • 23944500826 scopus 로고    scopus 로고
    • Extended Range Proteomic Analysis (ERPA): A new and sensitive LC-MS platform for high sequence coverage of complex proteins with extensive post-translational modifications-comprehensive analysis of beta-casein and Epidermal Growth Factor Receptor (EGFR)
    • DOI 10.1021/pr050113n
    • Wu, S. L., Kim, J., Hancock, W. S., and Karger, B. (2005) Extended Range Proteomic Analysis (ERPA): a new and sensitive LC-MS platform for high sequence coverage of complex proteins with extensive post-translational modifications-comprehensive analysis of beta-casein and epidermal growth factor receptor (EGFR) J. Proteome Res. 4, 1155-1170 (Pubitemid 41208674)
    • (2005) Journal of Proteome Research , vol.4 , Issue.4 , pp. 1155-1170
    • Wu, S.-L.1    Kim, J.2    Hancock, W.S.3    Karger, B.4
  • 47
    • 3442888009 scopus 로고    scopus 로고
    • New chemical crosslinking methods for the identification of transient protein-protein interactions with multiprotein complexes
    • DOI 10.2174/1389203043379701
    • Melcher, K. (2004) New chemical crosslinking methods for the identification of transient protein-protein interactions with multiprotein complexes Curr. Protein Pept. Sci. 5, 287-296 (Pubitemid 39004422)
    • (2004) Current Protein and Peptide Science , vol.5 , Issue.4 , pp. 287-296
    • Melcher, K.1


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