메뉴 건너뛰기




Volumn 11, Issue 8, 2012, Pages 4044-4051

Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS

Author keywords

decision tree learning; iTRAQ; MALDI TOF TOF; peptide fragmentation

Indexed keywords

PEPTIDE FRAGMENT;

EID: 84864607727     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300083x     Document Type: Article
Times cited : (2)

References (29)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • DOI 10.1038/nature01511
    • Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422, 198-207 (Pubitemid 36362757)
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 3
    • 35648942133 scopus 로고    scopus 로고
    • 8-Plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease
    • DOI 10.1002/pmic.200700316
    • Choe, L.; D'Ascenzo, M.; Relkin, N. R.; Pappin, D.; Ross, P.; Williamson, B.; Guertin, S.; Pribil, P.; Lee, K. H. 8-Plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease Proteomics 2007, 7, 3651-3660 (Pubitemid 350022271)
    • (2007) Proteomics , vol.7 , Issue.20 , pp. 3651-3660
    • Choe, L.1    D'Ascenzo, M.2    Relkin, N.R.3    Pappin, D.4    Ross, P.5    Williamson, B.6    Guertin, S.7    Pribil, P.8    Lee, K.H.9
  • 5
    • 33745591083 scopus 로고    scopus 로고
    • Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
    • de Godoy, L. M.; Olsen, J. V.; de Souza, G. A.; Li, G.; Mortensen, P.; Mann, M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system GenomeBiology 2006, 7, R50
    • (2006) GenomeBiology , vol.7 , pp. 50
    • De Godoy, L.M.1    Olsen, J.V.2    De Souza, G.A.3    Li, G.4    Mortensen, P.5    Mann, M.6
  • 7
    • 77954693858 scopus 로고    scopus 로고
    • Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets
    • Ning, K.; Fermin, D.; Nesvizhskii, A. I. Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets Proteomics 2010, 10, 2712-2718
    • (2010) Proteomics , vol.10 , pp. 2712-2718
    • Ning, K.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 8
    • 77955159809 scopus 로고    scopus 로고
    • Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap
    • Pichler, P.; Köcher, T.; Holzmann, J.; Mazanek, M.; Taus, T.; Ammerer, G.; Mechtler, K. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap Anal. Chem. 2010, 82, 6549-6558
    • (2010) Anal. Chem. , vol.82 , pp. 6549-6558
    • Pichler, P.1    Köcher, T.2    Holzmann, J.3    Mazanek, M.4    Taus, T.5    Ammerer, G.6    Mechtler, K.7
  • 9
    • 23944451618 scopus 로고    scopus 로고
    • An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis
    • DOI 10.1002/pmic.200500126
    • Kapp, E. A.; Schütz, F.; Connolly, L. M.; Chakel, J. A.; Meza, J. E.; Miller, C. A.; Fenyo, D.; Eng, J. K.; Adkins, J. N.; Omenn, G. S.; Simpson, R. J. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis Proteomics 2005, 5, 3475-3490 (Pubitemid 41192052)
    • (2005) Proteomics , vol.5 , Issue.13 , pp. 3475-3490
    • Kapp, E.A.1    Schutz, F.2    Connolly, L.M.3    Chakel, J.A.4    Meza, J.E.5    Miller, C.A.6    Fenyo, D.7    Eng, J.K.8    Adkins, J.N.9    Omenn, G.S.10    Simpson, R.J.11
  • 10
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • DOI 10.1038/nmeth785
    • Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations Nat. Methods 2005, 2, 667-675 (Pubitemid 41223093)
    • (2005) Nature Methods , vol.2 , Issue.9 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4
  • 12
    • 0242653718 scopus 로고    scopus 로고
    • Mining a Tandem Mass Spectrometry Database to Determine the Trends and Global Factors Influencing Peptide Fragmentation
    • DOI 10.1021/ac034616t
    • Kapp, E. A.; Schütz, F.; Reid, G. E.; Eddes, J. S.; Moritz, R. L.; O'Hair, R. A.; Speed, T. P.; Simpson, R. J. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation Anal. Chem. 2003, 75, 6251-6264 (Pubitemid 37420620)
    • (2003) Analytical Chemistry , vol.75 , Issue.22 , pp. 6251-6264
    • Kapp, E.A.1    Schutz, F.2    Reid, G.E.3    Eddes, J.S.4    Moritz, R.L.5    O'Hair, R.A.J.6    Speed, T.P.7    Simpson, R.J.8
  • 13
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    • DOI 10.1038/nbt930
    • Elias, J. E.; Gibbons, F. D.; King, O. D.; Roth, F. P.; Gygi, S. P. Intensity-based protein identification by machine learning from a library of tandem mass spectra Nat. Biotechnol. 2004, 22, 214-219 (Pubitemid 38160538)
    • (2004) Nature Biotechnology , vol.22 , Issue.2 , pp. 214-219
    • Elias, J.E.1    Gibbons, F.D.2    King, O.D.3    Roth, F.P.4    Gygi, S.P.5
  • 14
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • DOI 10.1021/ac049951b
    • Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides Anal. Chem. 2004, 76, 3908-3922 (Pubitemid 38943659)
    • (2004) Analytical Chemistry , vol.76 , Issue.14 , pp. 3908-3922
    • Zhang, Z.1
  • 15
    • 20444459841 scopus 로고    scopus 로고
    • Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns
    • DOI 10.1021/ac0480949
    • Huang, Y.; Triscari, J. M.; Tseng, G. C.; Pasa-Tolic, L.; Lipton, M. S.; Smith, R. D.; Wysocki, V. H. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns Anal. Chem. 2005, 77, 5800-5813 (Pubitemid 41324278)
    • (2005) Analytical Chemistry , vol.77 , Issue.18 , pp. 5800-5813
    • Huang, Y.1    Triscari, J.M.2    Tseng, G.C.3    Pasa-Tolic, L.4    Lipton, M.S.5    Smith, R.D.6    Wysocki, V.H.7
  • 16
    • 34247354641 scopus 로고    scopus 로고
    • Fragmentation characteristics of collision-induced dissociation in MALDI TOF/TOF mass spectrometry
    • DOI 10.1021/ac061455v
    • Khatun, J.; Ramkissoon, K.; Giddings, M. C. Fragmentation characteristics of collision-induced dissociation in MALDI TOF/TOF mass spectrometry Anal. Chem. 2007, 79, 3032-3040 (Pubitemid 46640524)
    • (2007) Analytical Chemistry , vol.79 , Issue.8 , pp. 3032-3040
    • Khatun, J.1    Ramkissoon, K.2    Giddings, M.C.3
  • 17
    • 34547732831 scopus 로고    scopus 로고
    • Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS
    • DOI 10.1021/ac0700272
    • Barton, S. J.; Richardson, S.; Perkins, D. N.; Bellahn, I.; Bryant, T. N.; Whittaker, J. C. Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS Anal. Chem. 2007, 79, 5601-5607 (Pubitemid 47229805)
    • (2007) Analytical Chemistry , vol.79 , Issue.15 , pp. 5601-5607
    • Barton, S.J.1    Richardson, S.2    Perkins, D.N.3    Bellahn, I.4    Bryant, T.N.5    Whittaker, J.C.6
  • 18
    • 66749169317 scopus 로고    scopus 로고
    • Predicting intensity ranks of peptide fragment ions
    • Frank, A. M. Predicting intensity ranks of peptide fragment ions J. Proteome Res. 2009, 8, 2226-2240
    • (2009) J. Proteome Res. , vol.8 , pp. 2226-2240
    • Frank, A.M.1
  • 19
    • 0029810698 scopus 로고    scopus 로고
    • Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: Evidence for the mobile proton model
    • DOI 10.1021/ja9542193
    • Dongre, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model J. Am. Chem. Soc. 1996, 118, 8365-8374 (Pubitemid 26305258)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.35 , pp. 8365-8374
    • Dongre, A.R.1    Jones, J.L.2    Somogyi, A.3    Wysocki, V.H.4
  • 21
    • 0032828711 scopus 로고    scopus 로고
    • Fragmentation of protonated oligopeptides XLDVLQ (X=L, H, K or R) by surface induced dissociation: additional evidence for the 'mobile proton' model
    • DOI 10.1016/S0003-2670(99)00409-2, PII S0003267099004092
    • Gu, C.; Somogyi, A.; Wysocki, V. H.; Medzihradszky, K. F. Fragmentation of protonated oligopeptides XLDVLQ (X = L, H, K or R) by surface-induced dissociation: additional evidence for the ″mobile proton″ model Anal. Chim. Acta 1999, 397, 247-256 (Pubitemid 29443941)
    • (1999) Analytica Chimica Acta , vol.397 , Issue.1-3 , pp. 247-256
    • Gu, C.1    Somogyi, A.2    Wysocki, V.H.3    Medzihradszky, K.F.4
  • 22
    • 0034501099 scopus 로고    scopus 로고
    • Mobile and localized protons: A framework for understanding peptide dissociation
    • DOI 10.1002/1096-9888(200012)35:12<1399::AID-JMS86>3.0.CO;2-R
    • Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and localized protons: a framework for understanding peptide dissociation J. Mass Spectrom. 2000, 35, 1399-1406 (Pubitemid 32063646)
    • (2000) Journal of Mass Spectrometry , vol.35 , Issue.12 , pp. 1399-1406
    • Wysocki, V.H.1    Tsaprailis, G.2    Smith, L.L.3    Breci, L.A.4
  • 24
    • 0037353846 scopus 로고    scopus 로고
    • Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides
    • DOI 10.1021/ac026122m
    • Tabb, D. L.; Smith, L. L.; Breci, L. A.; Wysocki, V. H.; Lin, D.; Yates, J. R. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides Anal. Chem. 2003, 75, 1155-1163 (Pubitemid 36402645)
    • (2003) Analytical Chemistry , vol.75 , Issue.5 , pp. 1155-1163
    • Tabb, D.L.1    Smith, L.L.2    Breci, L.A.3    Wysocki, V.H.4    Lin, D.5    Yates III, J.R.6
  • 25
    • 0037592846 scopus 로고    scopus 로고
    • Analysis of high mass peptides using a novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight mass spectrometer
    • DOI 10.1002/rcm.1044
    • Martin, R. L.; Brancia, F. L. Analysis of high mass peptides using a novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight mass spectrometer Rapid Commun. Mass Spectrom. 2003, 17, 1358-1365 (Pubitemid 36750021)
    • (2003) Rapid Communications in Mass Spectrometry , vol.17 , Issue.12 , pp. 1358-1365
    • Martin, R.L.1    Brancia, F.L.2
  • 26
    • 1442324456 scopus 로고    scopus 로고
    • Influence of Basic Residue Content on Fragment Ion Peak Intensities in Low-Energy Collision-Induced Dissociation Spectra of Peptides
    • DOI 10.1021/ac0351163
    • Tabb, D. L.; Huang, Y.; Wysocki, V. H.; Yates, J. R. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides Anal. Chem. 2004, 76, 1243-1248 (Pubitemid 38280470)
    • (2004) Analytical Chemistry , vol.76 , Issue.5 , pp. 1243-1248
    • Tabb, D.L.1    Huang, Y.2    Wysocki, V.H.3    Yates III, J.R.4
  • 27
    • 78149365542 scopus 로고    scopus 로고
    • Apex peptide elution chain selection: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples
    • Gandhi, T.; Fusetti, F.; Wiederhold, E.; Breitling, R.; Poolman, B.; Permentier, H. P. Apex peptide elution chain selection: a new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples J. Proteome Res. 2010, 9, 5922-5928
    • (2010) J. Proteome Res. , vol.9 , pp. 5922-5928
    • Gandhi, T.1    Fusetti, F.2    Wiederhold, E.3    Breitling, R.4    Poolman, B.5    Permentier, H.P.6
  • 28
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-3567 (Pubitemid 30007252)
    • (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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.