메뉴 건너뛰기




Volumn 13, Issue 2, 2014, Pages 777-785

Accurate identification of deamidated peptides in global proteomics using a quadrupole orbitrap mass spectrometer

Author keywords

deamidation; post translational modification; quadrupole orbitrap mass spectrometry

Indexed keywords

AMIDES; CHROMATOGRAPHY, LIQUID; PEPTIDES; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84893821087     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400848n     Document Type: Article
Times cited : (32)

References (31)
  • 1
    • 37249014081 scopus 로고    scopus 로고
    • The biological impact of mass-spectrometry-based proteomics
    • Cravatt, B. F.; Simon, G. M.; Yates, J. R., III. The biological impact of mass-spectrometry-based proteomics Nature 2007, 450 (7172) 991-1000
    • (2007) Nature , vol.450 , Issue.7172 , pp. 991-1000
    • Cravatt, B.F.1    Simon, G.M.2    Yates III, J.R.3
  • 2
    • 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.; Yates, J. R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5 (11) 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , Issue.11 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 3
    • 0029644596 scopus 로고
    • Method to correlate tandem mass-spectra of modified peptides to amino-acid-sequences in the protein database
    • Yates, J. R.; Eng, J. K.; Mccormack, A. L.; Schieltz, D. Method to correlate tandem mass-spectra of modified peptides to amino-acid-sequences in the protein database Anal. Chem. 1995, 67 (8) 1426-1436
    • (1995) Anal. Chem. , vol.67 , Issue.8 , pp. 1426-1436
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 4
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-3567
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 5
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R.; Beavis, R. C. TANDEM: Matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-1467
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 7
    • 84861800006 scopus 로고    scopus 로고
    • Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer
    • Kelstrup, C. D.; Young, C.; Lavallee, R.; Nielsen, M. L.; Olsen, J. V. Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer J. Proteome Res. 2012, 11 (6) 3487-3497
    • (2012) J. Proteome Res. , vol.11 , Issue.6 , pp. 3487-3497
    • Kelstrup, C.D.1    Young, C.2    Lavallee, R.3    Nielsen, M.L.4    Olsen, J.V.5
  • 9
    • 76149132007 scopus 로고    scopus 로고
    • Comparison of database search strategies for high precursor mass accuracy MS/MS data
    • Hsieh, E. J.; Hoopmann, M. R.; MacLean, B.; MacCoss, M. J. Comparison of database search strategies for high precursor mass accuracy MS/MS data J. Proteome Res. 2010, 9 (2) 1138-1143
    • (2010) J. Proteome Res. , vol.9 , Issue.2 , pp. 1138-1143
    • Hsieh, E.J.1    Hoopmann, M.R.2    MacLean, B.3    MacCoss, M.J.4
  • 10
    • 80054030914 scopus 로고    scopus 로고
    • Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation
    • 009381
    • Hao, P.; Ren, Y.; Alpert, A. J.; Sze, S. K. Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation Mol. Cell. Proteomics 2011, 10 (10) O111 009381
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.10 , pp. 111
    • Hao, P.1    Ren, Y.2    Alpert, A.J.3    Sze, S.K.4
  • 11
    • 84861831985 scopus 로고    scopus 로고
    • Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry
    • Shuford, C. M.; Li, Q. Z.; Sun, Y. H.; Chen, H. C.; Wang, J.; Shi, R.; Sederoff, R. R.; Chiang, V. L.; Muddiman, D. C. Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry J. Proteome Res. 2012, 11 (6) 3390-3404
    • (2012) J. Proteome Res. , vol.11 , Issue.6 , pp. 3390-3404
    • Shuford, C.M.1    Li, Q.Z.2    Sun, Y.H.3    Chen, H.C.4    Wang, J.5    Shi, R.6    Sederoff, R.R.7    Chiang, V.L.8    Muddiman, D.C.9
  • 13
    • 0035584865 scopus 로고    scopus 로고
    • The metal-catalyzed oxidation of methionine in peptides by Fenton systems involves two consecutive one-electron oxidation processes
    • Hong, J.; Schoneich, C. The metal-catalyzed oxidation of methionine in peptides by Fenton systems involves two consecutive one-electron oxidation processes Free Radical Biol. Med. 2001, 31 (11) 1432-1441
    • (2001) Free Radical Biol. Med. , vol.31 , Issue.11 , pp. 1432-1441
    • Hong, J.1    Schoneich, C.2
  • 14
    • 0027647713 scopus 로고
    • Oxidation of peptides during electrospray ionization
    • Morand, K.; Talbo, G.; Mann, M. Oxidation of peptides during electrospray ionization Rapid Commun. Mass Spectrom. 1993, 7 (8) 738-743
    • (1993) Rapid Commun. Mass Spectrom. , vol.7 , Issue.8 , pp. 738-743
    • Morand, K.1    Talbo, G.2    Mann, M.3
  • 16
    • 1842525883 scopus 로고    scopus 로고
    • Amide molecular clocks in drosophila proteins: Potential regulators of aging and other processes
    • Robinson, N. E.; Robinson, A. B. Amide molecular clocks in drosophila proteins: Potential regulators of aging and other processes Mech. Ageing Dev. 2004, 125 (4) 259-267
    • (2004) Mech. Ageing Dev. , vol.125 , Issue.4 , pp. 259-267
    • Robinson, N.E.1    Robinson, A.B.2
  • 17
    • 34948889296 scopus 로고    scopus 로고
    • Reliable detection of deamidated peptides from lens Crystallin proteins using changes in reversed-phase elution times and parent ion masses
    • Dasari, S.; Wilmarth, P. A.; Rustvold, D. L.; Riviere, M. A.; Nagalla, S. R.; David, L. L. Reliable detection of deamidated peptides from lens Crystallin proteins using changes in reversed-phase elution times and parent ion masses J. Proteome Res. 2007, 6 (9) 3819-3826
    • (2007) J. Proteome Res. , vol.6 , Issue.9 , pp. 3819-3826
    • Dasari, S.1    Wilmarth, P.A.2    Rustvold, D.L.3    Riviere, M.A.4    Nagalla, S.R.5    David, L.L.6
  • 20
    • 33748788003 scopus 로고    scopus 로고
    • Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: Consequences for MALDI and HPLC-MALDI analysis
    • 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) 6645-6650
    • (2006) Anal. Chem. , 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
  • 21
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis Nat. Methods 2009, 6 (5) 359-362
    • (2009) Nat. Methods , vol.6 , Issue.5 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 22
    • 84870862194 scopus 로고    scopus 로고
    • In-depth analysis of the Magnaporthe oryzae conidial proteome
    • Gokce, E.; Franck, W. L.; Oh, Y.; Dean, R. A.; Muddiman, D. C. In-depth analysis of the Magnaporthe oryzae conidial proteome J. Proteome Res. 2012, 11 (12) 5827-5835
    • (2012) J. Proteome Res. , vol.11 , Issue.12 , pp. 5827-5835
    • Gokce, E.1    Franck, W.L.2    Oh, Y.3    Dean, R.A.4    Muddiman, D.C.5
  • 23
    • 62249095261 scopus 로고    scopus 로고
    • Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides
    • Andrews, G. L.; Shuford, C. M.; Burnett, J. C., Jr.; Hawkridge, A. M.; Muddiman, D. C. Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides J. Chromatogr. B: Anal. Technol. Biomed. Life Sci 2009, 877 (10) 948-954
    • (2009) J. Chromatogr. B: Anal. Technol. Biomed. Life Sci , vol.877 , Issue.10 , pp. 948-954
    • Andrews, G.L.1    Shuford, C.M.2    Burnett, Jr.J.C.3    Hawkridge, A.M.4    Muddiman, D.C.5
  • 24
    • 84884583449 scopus 로고    scopus 로고
    • Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole orbitrap mass spectrometer
    • Randall, S.; Cardasis, H.; Muddiman, D. Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole orbitrap mass spectrometer J. Am. Soc. Mass Spectrom. 2013, 1-12
    • (2013) J. Am. Soc. Mass Spectrom. , pp. 1-12
    • Randall, S.1    Cardasis, H.2    Muddiman, D.3
  • 25
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74 (20) 5383-5392
    • (2002) Anal. Chem. , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 26
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003, 75 (17) 4646-4658
    • (2003) Anal. Chem. , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 27
    • 21044459357 scopus 로고    scopus 로고
    • A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results
    • Weatherly, D. B.; Atwood, J. A.; Minning, T. A.; Cavola, C.; Tarleton, R. L.; Orlando, R. A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results Mol. Cell. Proteomics 2005, 4 (6) 762-772
    • (2005) Mol. Cell. Proteomics , vol.4 , Issue.6 , pp. 762-772
    • Weatherly, D.B.1    Atwood, J.A.2    Minning, T.A.3    Cavola, C.4    Tarleton, R.L.5    Orlando, R.6
  • 28
    • 33645235084 scopus 로고    scopus 로고
    • Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra
    • Venable, J. D.; Xu, T.; Cociorva, D.; Yates, J. R., III. Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra Anal. Chem. 2006, 78 (6) 1921-1929
    • (2006) Anal. Chem. , vol.78 , Issue.6 , pp. 1921-1929
    • Venable, J.D.1    Xu, T.2    Cociorva, D.3    Yates III, J.R.4
  • 29
    • 33748515682 scopus 로고    scopus 로고
    • Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS
    • Krokhin, O. V.; Ying, S.; Cortens, J. P.; Ghosh, D.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A. Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS Anal. Chem. 2006, 78 (17) 6265-6269
    • (2006) Anal. Chem. , vol.78 , Issue.17 , pp. 6265-6269
    • Krokhin, O.V.1    Ying, S.2    Cortens, J.P.3    Ghosh, D.4    Spicer, V.5    Ens, W.6    Standing, K.G.7    Beavis, R.C.8    Wilkins, J.A.9
  • 30
    • 6044226889 scopus 로고    scopus 로고
    • Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures
    • Wiener, M. C.; Sachs, J. R.; Deyanova, E. G.; Yates, N. A. Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures Anal. Chem. 2004, 76 (20) 6085-6096
    • (2004) Anal. Chem. , vol.76 , Issue.20 , pp. 6085-6096
    • Wiener, M.C.1    Sachs, J.R.2    Deyanova, E.G.3    Yates, N.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.