메뉴 건너뛰기




Volumn 4, Issue 4, 2009, Pages 484-494

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

Author keywords

[No Author keywords available]

Indexed keywords

RADIOISOTOPE;

EID: 64749108158     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2009.21     Document Type: Article
Times cited : (1166)

References (42)
  • 2
    • 33644524918 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics turns quantitative
    • Ong, S.E. & Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262 (2005).
    • (2005) Nat. Chem. Biol , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 3
    • 20444508181 scopus 로고    scopus 로고
    • Heck, A.J.R. & Krijgsveld, J. Mass spectrometry-based quantitative proteomics. Expert Rev. Proteomics 1, 317-326 (2004).
    • Heck, A.J.R. & Krijgsveld, J. Mass spectrometry-based quantitative proteomics. Expert Rev. Proteomics 1, 317-326 (2004).
  • 4
    • 34247396011 scopus 로고    scopus 로고
    • A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
    • Ong, S.E. & Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 1, 2650-2660 (2006).
    • (2006) Nat. Protoc , vol.1 , pp. 2650-2660
    • Ong, S.E.1    Mann, M.2
  • 5
    • 34548178909 scopus 로고    scopus 로고
    • In-gel digestion for mass spectrometric characterization of proteins and proteomes
    • Shevchenko, A., Tomas, H., Havlis, J., Olsen, J.V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856-2860 (2006).
    • (2006) Nat. Protoc , vol.1 , pp. 2856-2860
    • Shevchenko, A.1    Tomas, H.2    Havlis, J.3    Olsen, J.V.4    Mann, M.5
  • 6
    • 34250657012 scopus 로고    scopus 로고
    • Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry
    • Shiio, Y. & Aebersold, R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat. Protoc. 1, 139-145 (2006).
    • (2006) Nat. Protoc , vol.1 , pp. 139-145
    • Shiio, Y.1    Aebersold, R.2
  • 7
    • 0034282457 scopus 로고    scopus 로고
    • Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety
    • Munchbach, M., Quadroni, M., Miotto, G. & James, P. Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal. Chem. 72, 4047-4057 (2000).
    • (2000) Anal. Chem , vol.72 , pp. 4047-4057
    • Munchbach, M.1    Quadroni, M.2    Miotto, G.3    James, P.4
  • 8
    • 42049084149 scopus 로고    scopus 로고
    • Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
    • Staes, A. et al. Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 8, 1362-1370 (2008).
    • (2008) Proteomics , vol.8 , pp. 1362-1370
    • Staes, A.1
  • 9
    • 4444371652 scopus 로고    scopus 로고
    • Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics
    • Blagoev, B., Ong, S.E., Kratchmarova, I. & Mann, M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotech. 22, 1139-1145 (2004).
    • (2004) Nat. Biotech , vol.22 , pp. 1139-1145
    • Blagoev, B.1    Ong, S.E.2    Kratchmarova, I.3    Mann, M.4
  • 10
    • 40649095957 scopus 로고    scopus 로고
    • Quantitative proteomics using stable isotope labeling with amino acids in cell culture
    • Harsha, H.C., Molina, H. & Pandey, A. Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat. Protoc. 3, 505-516 (2008).
    • (2008) Nat. Protoc , vol.3 , pp. 505-516
    • Harsha, H.C.1    Molina, H.2    Pandey, A.3
  • 11
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P.L. et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3, 1154-1169 (2004).
    • (2004) Mol. Cell Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1
  • 12
    • 43849113605 scopus 로고    scopus 로고
    • Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases
    • Pierce, A. et al. Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Mol. Cell Proteomics 7, 853-863 (2008).
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 853-863
    • Pierce, A.1
  • 13
    • 0348014635 scopus 로고    scopus 로고
    • Stable-isotope dimethyl labeling for quantitative proteomics
    • Hsu, J.L., Huang, S.Y., Chow, N.H. & Chen, S.H. Stable-isotope dimethyl labeling for quantitative proteomics. Anal. Chem. 75, 6843-6852 (2003).
    • (2003) Anal. Chem , vol.75 , pp. 6843-6852
    • Hsu, J.L.1    Huang, S.Y.2    Chow, N.H.3    Chen, S.H.4
  • 14
    • 55849093586 scopus 로고    scopus 로고
    • Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates
    • Boersema, P.J., Aye, T.T., Van Veen, T.A.B., Heck, A.J.R. & Mohammed, S. Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Proteomics 8, 4624-4632 (2008).
    • (2008) Proteomics , vol.8 , pp. 4624-4632
    • Boersema, P.J.1    Aye, T.T.2    Van Veen, T.A.B.3    Heck, A.J.R.4    Mohammed, S.5
  • 15
    • 52649181646 scopus 로고    scopus 로고
    • Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue-specific diversity
    • Raijmakers, R. et al. Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue-specific diversity. Mol. Cell Proteomics 7, 1755-1762 (2008).
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 1755-1762
    • Raijmakers, R.1
  • 16
    • 14844331822 scopus 로고    scopus 로고
    • Beyond quantitative proteomics: Signal enhancement of the a(1) ion as a mass tag for peptide sequencing using dimethyl labeling
    • Hsu, J.L., Huang, S.Y., Shiea, J.T., Huang, W.Y. & Chen, S.H. Beyond quantitative proteomics: Signal enhancement of the a(1) ion as a mass tag for peptide sequencing using dimethyl labeling. J. Proteome Res. 4, 101-108 (2005).
    • (2005) J. Proteome Res , vol.4 , pp. 101-108
    • Hsu, J.L.1    Huang, S.Y.2    Shiea, J.T.3    Huang, W.Y.4    Chen, S.H.5
  • 17
    • 33749474110 scopus 로고    scopus 로고
    • Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics
    • Hsu, J.L., Huang, S.Y. & Chen, S.H. Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics. Electrophoresis 27, 3652-3660 (2006).
    • (2006) Electrophoresis , vol.27 , pp. 3652-3660
    • Hsu, J.L.1    Huang, S.Y.2    Chen, S.H.3
  • 18
    • 34250854662 scopus 로고    scopus 로고
    • Enhanced a(1) fragmentation for dimethylated proteins and its applications for N-terminal identification and comparative protein quantitation
    • Hsu, J.L., Chen, S.H., Li, D.T. & Shi, F.K. Enhanced a(1) fragmentation for dimethylated proteins and its applications for N-terminal identification and comparative protein quantitation. J. Proteome Res. 6, 2376-2383 (2007).
    • (2007) J. Proteome Res , vol.6 , pp. 2376-2383
    • Hsu, J.L.1    Chen, S.H.2    Li, D.T.3    Shi, F.K.4
  • 19
    • 37249092935 scopus 로고    scopus 로고
    • Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS
    • Shen, P.T., Hsu, J.L. & Chen, S.H. Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS. Anal. Chem. 79, 9520-9530 (2007).
    • (2007) Anal. Chem , vol.79 , pp. 9520-9530
    • Shen, P.T.1    Hsu, J.L.2    Chen, S.H.3
  • 20
    • 49949087278 scopus 로고    scopus 로고
    • Comparative phosphoproteomics of zebrafish Fyn/ Yesmorpholino knockdown embryos
    • Lemeer, S. et al. Comparative phosphoproteomics of zebrafish Fyn/ Yesmorpholino knockdown embryos. Mol. Cell Proteomics 7, 2176-2187 (2008).
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 2176-2187
    • Lemeer, S.1
  • 21
    • 46749110073 scopus 로고    scopus 로고
    • Proteomics of photoreceptor outer segments identifies a subset of SNARE and Rab proteins implicated in membrane vesicle trafficking and fusion
    • Kwok, M.C.M., Holopainen, J.M., Molday, L.L., Foster, L.J. & Molday, R.S. Proteomics of photoreceptor outer segments identifies a subset of SNARE and Rab proteins implicated in membrane vesicle trafficking and fusion. Mol. Cell Proteomics 7, 1053-1066 (2008).
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 1053-1066
    • Kwok, M.C.M.1    Holopainen, J.M.2    Molday, L.L.3    Foster, L.J.4    Molday, R.S.5
  • 22
    • 23944500823 scopus 로고    scopus 로고
    • Identification and quantification of differentially expressed proteins in E-Cadherin deficient SCC9 cells and SCC9 transfectants expressing E-Cadherin by dimethyl isotope labeling, LC-MALDI MS and MS/MS
    • Ji, C., Li, L., Gebre, M., Pasdar, M. & Li, L. Identification and quantification of differentially expressed proteins in E-Cadherin deficient SCC9 cells and SCC9 transfectants expressing E-Cadherin by dimethyl isotope labeling, LC-MALDI MS and MS/MS. J. Proteome Res. 4, 1419-1426 (2005).
    • (2005) J. Proteome Res , vol.4 , pp. 1419-1426
    • Ji, C.1    Li, L.2    Gebre, M.3    Pasdar, M.4    Li, L.5
  • 23
    • 58149344947 scopus 로고    scopus 로고
    • Comparative multiplexed mass spectrometric analyses of the endogenously expressed yeast nuclear and cytoplasmic exosome
    • Synowsky, S.A., van Wijk, M., Raijmakers, R. & Heck, A.J.R. Comparative multiplexed mass spectrometric analyses of the endogenously expressed yeast nuclear and cytoplasmic exosome. J. Mol. Biol. 385, 1300-1313 (2009).
    • (2009) J. Mol. Biol , vol.385 , pp. 1300-1313
    • Synowsky, S.A.1    van Wijk, M.2    Raijmakers, R.3    Heck, A.J.R.4
  • 24
    • 34548356772 scopus 로고    scopus 로고
    • An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics
    • Van Hoof, D. et al. An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nat. Methods 4, 677-678 (2007).
    • (2007) Nat. Methods , vol.4 , pp. 677-678
    • Van Hoof, D.1
  • 25
    • 33644856320 scopus 로고    scopus 로고
    • Effects of modified digestion schemes on the identification of proteins from complex mixtures
    • Klammer, A.A. & MacCoss, M.J. Effects of modified digestion schemes on the identification of proteins from complex mixtures. J. Proteome Res. 5, 695-700 (2006).
    • (2006) J. Proteome Res , vol.5 , pp. 695-700
    • Klammer, A.A.1    MacCoss, M.J.2
  • 26
    • 3242688830 scopus 로고    scopus 로고
    • Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns
    • Pinkse, M.W.H., Uitto, P.M., Hilhorst, M.J., Ooms, B. & Heck, A.J.R. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 76, 3935-3943 (2004).
    • (2004) Anal. Chem , vol.76 , pp. 3935-3943
    • Pinkse, M.W.H.1    Uitto, P.M.2    Hilhorst, M.J.3    Ooms, B.4    Heck, A.J.R.5
  • 27
    • 33645468211 scopus 로고    scopus 로고
    • Quantitation of protein phosphorylation in pregnant rat uteri using stable isotope dimethyl labeling coupled with IMAC
    • Huang, S.Y. et al. Quantitation of protein phosphorylation in pregnant rat uteri using stable isotope dimethyl labeling coupled with IMAC. Proteomics 6, 1722-1734 (2006).
    • (2006) Proteomics , vol.6 , pp. 1722-1734
    • Huang, S.Y.1
  • 28
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectromeitry data
    • Perkins, D.N., Pappin, D.J.C., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectromeitry data. Electrophoresis 20, 3551-3567 (1999).
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 29
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass-spectral data of peptide with amino-acid-sequence in a protein database
    • Eng, J.K., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass-spectral data of peptide with amino-acid-sequence in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994).
    • (1994) J. Am. Soc. Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 30
    • 0041358793 scopus 로고    scopus 로고
    • Colinge, J., Masselot, A., Giron, M., Dessingy, T. & Magnin, J. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463 (2003).
    • Colinge, J., Masselot, A., Giron, M., Dessingy, T. & Magnin, J. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463 (2003).
  • 31
    • 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 20, 1466-1467 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 32
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254 (1976).
    • (1976) Anal. Biochem , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 33
    • 17244383269 scopus 로고    scopus 로고
    • Nagele, E., Vollmer, M., Horth, P. & Vad, C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev. Proteomics 1, 37-46 (2004).
    • Nagele, E., Vollmer, M., Horth, P. & Vad, C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev. Proteomics 1, 37-46 (2004).
  • 34
    • 39749186759 scopus 로고    scopus 로고
    • 2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster
    • 2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J. Proteome Res. 7 687-697 (2008).
    • (2008) J. Proteome Res , vol.7 , pp. 687-697
    • Pinkse, M.W.H.1
  • 35
    • 20844458723 scopus 로고    scopus 로고
    • Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS
    • Ji, C. & Li, L. Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS. J. Proteome Res. 4, 734-742 (2005).
    • (2005) J. Proteome Res , vol.4 , pp. 734-742
    • Ji, C.1    Li, L.2
  • 36
    • 33750112261 scopus 로고    scopus 로고
    • Effect of 2MEGA labeling on membrane proteome analysis using LC-ESI QTOF MS
    • Ji, C., Lo, A., Marcus, S. & Li, L. Effect of 2MEGA labeling on membrane proteome analysis using LC-ESI QTOF MS. J. Proteome Res. 5, 2567-2576 (2006).
    • (2006) J. Proteome Res , vol.5 , pp. 2567-2576
    • Ji, C.1    Lo, A.2    Marcus, S.3    Li, L.4
  • 37
    • 29144504045 scopus 로고    scopus 로고
    • Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis
    • Ji, C., Guo, N. & Li, L. Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis. J. Proteome Res. 4, 2099-2108 (2005).
    • (2005) J. Proteome Res , vol.4 , pp. 2099-2108
    • Ji, C.1    Guo, N.2    Li, L.3
  • 38
    • 34249032767 scopus 로고    scopus 로고
    • Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics
    • Khidekel, N. et al. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nat. Chem. Biol. 3 339-348 (2007).
    • (2007) Nat. Chem. Biol , vol.3 , pp. 339-348
    • Khidekel, N.1
  • 39
    • 36448966459 scopus 로고    scopus 로고
    • Stable-isotope dimethylation labeling combined with LC-ESI MS for quantification of amine-containing metabolites in biological samples
    • Guo, K., Ji, C. & Li, L. Stable-isotope dimethylation labeling combined with LC-ESI MS for quantification of amine-containing metabolites in biological samples. Anal. Chem. 79, 8631-8638 (2007).
    • (2007) Anal. Chem , vol.79 , pp. 8631-8638
    • Guo, K.1    Ji, C.2    Li, L.3
  • 40
    • 36749031760 scopus 로고    scopus 로고
    • The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum
    • Rogers, L.D. & Foster, L.J. The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 104, 18520-18525 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 18520-18525
    • Rogers, L.D.1    Foster, L.J.2
  • 41
    • 64749111032 scopus 로고    scopus 로고
    • Selectivity in enrichment of PKA RI and RII isoforms and their interactors using modified cAMP affinity resins
    • in press
    • Aye, T.T. et al. Selectivity in enrichment of PKA RI and RII isoforms and their interactors using modified cAMP affinity resins. Mol. Cell. Proteomics (in press).
    • Mol. Cell. Proteomics
    • Aye, T.T.1
  • 42
    • 34548183872 scopus 로고    scopus 로고
    • Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
    • Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896-1906 (2007).
    • (2007) Nat. Protoc , vol.2 , pp. 1896-1906
    • Rappsilber, J.1    Mann, M.2    Ishihama, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.