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Volumn 753, Issue , 2011, Pages 1-27

Mass spectrometry-driven proteomics: An introduction

Author keywords

Gel free proteomics; Mass spectrometry; Peptide centric proteomics; Protein modifications; Proteomics bioinformatics

Indexed keywords

ION; PEPTIDE; PROTEIN;

EID: 84891698406     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-148-2_1     Document Type: Article
Times cited : (8)

References (133)
  • 1
    • 34047262671 scopus 로고    scopus 로고
    • Transcriptional regulation by chromatin disassembly and reassembly
    • Williams, S.K. & Tyler, J.K. (2007) Transcriptional regulation by chromatin disassembly and reassembly. Curr Opin Genet Dev 17, 88-93.
    • (2007) Curr Opin Genet Dev , vol.17 , pp. 88-93
    • Williams, S.K.1    Tyler, J.K.2
  • 3
    • 0347281686 scopus 로고    scopus 로고
    • Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E
    • Gross, J.D. et al. (2003) Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell 115, 739-750.
    • (2003) Cell , vol.115 , pp. 739-750
    • Gross, J.D.1
  • 4
    • 0001433809 scopus 로고
    • Method for determination of the amino acid sequence in peptides
    • Edman, P. (1950) Method for determination of the amino acid sequence in peptides. Acta Chem Scand 4, 283-293.
    • (1950) Acta Chem Scand , vol.4 , pp. 283-293
    • Edman, P.1
  • 5
    • 0015776538 scopus 로고
    • Automated Edman degradation: The protein sequenator
    • Niall, H. (1973) Automated Edman degradation: the protein sequenator. Methods Enzymol 27, 942-1010.
    • (1973) Methods Enzymol , vol.27 , pp. 942-1010
    • Niall, H.1
  • 6
    • 33745591083 scopus 로고    scopus 로고
    • Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
    • de Godoy, L.M.F. et al. (2006) Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol 7, R50.
    • (2006) Genome Biol , vol.7
    • De Godoy, L.M.F.1
  • 7
    • 0000583317 scopus 로고
    • Isoelectric fractionation, analysis, and characterization of ampholytes in natural pH gradients
    • Svensson, H. (1961) Isoelectric fractionation, analysis, and characterization of ampholytes in natural pH gradients. Acta Chem Scand 15, 325.
    • (1961) Acta Chem Scand , vol.15 , pp. 325
    • Svensson, H.1
  • 8
    • 0014949207 scopus 로고
    • Cleavage of structural proteins during the assembly of the head of bacteriophage T4
    • Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685.
    • (1970) Nature , vol.227 , pp. 680-685
    • Laemmli, U.K.1
  • 9
    • 0016711037 scopus 로고
    • High resolution two-dimensional electrophoresis of proteins
    • O'Farrell, P.H. (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250, 4007-4021.
    • (1975) J Biol Chem , vol.250 , pp. 4007-4021
    • O'Farrell, P.H.1
  • 10
    • 0016637146 scopus 로고
    • Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues
    • Klose, J. (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. Hum Genet 26, 231-243.
    • (1975) Hum Genet , vol.26 , pp. 231-243
    • Klose, J.1
  • 11
    • 0035047761 scopus 로고    scopus 로고
    • Mass spectrometry compatibility of two-dimensional gel protein stains
    • Lauber, W.M. et al. (2001) Mass spectrometry compatibility of two-dimensional gel protein stains. Electrophoresis 22, 906-918.
    • (2001) Electrophoresis , vol.22 , pp. 906-918
    • Lauber, W.M.1
  • 12
    • 0022243081 scopus 로고
    • Protein-blotting on Polybrene-coated glassfiber sheets. A basis for acid hydrolysis and gas-phase sequencing of picomole quantities of protein previously separated on sodium dodecyl sulfate/polyacrylamide gel
    • Vandekerckhove, J., Bauw, G., Puype, M., Van Damme, J. & Van Montagu, M. (1985) Protein-blotting on Polybrene-coated glassfiber sheets. A basis for acid hydrolysis and gas-phase sequencing of picomole quantities of protein previously separated on sodium dodecyl sulfate/polyacrylamide gel. Eur J Biochem 152, 9-19.
    • (1985) Eur J Biochem , vol.152 , pp. 9-19
    • Vandekerckhove, J.1    Bauw, G.2    Puype, M.3    Van Damme, J.4    Van Montagu, M.5
  • 13
    • 12944269065 scopus 로고
    • Rapid identification of proteins by peptide-mass fingerprinting
    • Pappin, D.J., Hojrup, P. & Bleasby, A.J. (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3, 327-332.
    • (1993) Curr Biol , vol.3 , pp. 327-332
    • Pappin, D.J.1    Hojrup, P.2    Bleasby, A.J.3
  • 14
    • 39749191319 scopus 로고    scopus 로고
    • Molecular dynamic theories in chromatography
    • Felinger, A. (2008) Molecular dynamic theories in chromatography. J Chromatogr A 1184, 20-41.
    • (2008) J Chromatogr a , vol.1184 , pp. 20-41
    • Felinger, A.1
  • 15
    • 0020569578 scopus 로고
    • Peptide separation by reversed-phase high-performance liquid chromatography
    • Imoto, T. & Yamada, H. (1983) Peptide separation by reversed-phase high-performance liquid chromatography. Mol Cell Biochem 51, 111-121.
    • (1983) Mol Cell Biochem , vol.51 , pp. 111-121
    • Imoto, T.1    Yamada, H.2
  • 16
    • 84984042980 scopus 로고
    • Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry
    • Tanaka, K., Waki, H., Ido, Y., Akita, S. & Yoshida, Y. (1988) Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2, 151-153.
    • (1988) Rapid Commun Mass Spectrom , vol.2 , pp. 151-153
    • Tanaka, K.1    Waki, H.2    Ido, Y.3    Akita, S.4    Yoshida, Y.5
  • 17
    • 0024289037 scopus 로고
    • Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons
    • Karas, M. & Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60, 2299-2301.
    • (1988) Anal Chem , vol.60 , pp. 2299-2301
    • Karas, M.1    Hillenkamp, F.2
  • 18
    • 11544375741 scopus 로고    scopus 로고
    • Ion formation in MALDI mass spectrometry
    • Zenobi, R. & Knochenmuss, R. (1998) Ion formation in MALDI mass spectrometry. Mass Spectrom Rev 17, 337-366.
    • (1998) Mass Spectrom Rev , vol.17 , pp. 337-366
    • Zenobi, R.1    Knochenmuss, R.2
  • 19
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F. & Whitehouse, C.M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71.
    • (1989) Science , vol.246 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 20
    • 0001191099 scopus 로고
    • Disintegration of water drops in an electric field
    • Taylor, G. (1964) Disintegration of water drops in an electric field. Proc R Soc Lond A 280, 383-397.
    • (1964) Proc R Soc Lond a , vol.280 , pp. 383-397
    • Taylor, G.1
  • 21
    • 0001605719 scopus 로고
    • Further observations upon liquid jets
    • Rayleigh, L. (1882) Further observations upon liquid jets. Proc R Soc Lond 34, 130-145.
    • (1882) Proc R Soc Lond , vol.34 , pp. 130-145
    • Rayleigh, L.1
  • 22
    • 70449354921 scopus 로고    scopus 로고
    • The benefit of combining nLC-MALDI-Orbitrap MS data with nLC-MALDI-TOF/TOF data for proteomic analyses employing elastase
    • Rietschel, B. et al. (2009) The benefit of combining nLC-MALDI-Orbitrap MS data with nLC-MALDI-TOF/TOF data for proteomic analyses employing elastase. J Proteome Res 8, 5317-5324.
    • (2009) J Proteome Res , vol.8 , pp. 5317-5324
    • Rietschel, B.1
  • 24
    • 70449094032 scopus 로고    scopus 로고
    • Quadrupole ion traps
    • March, R. (2009) Quadrupole ion traps. Mass Spectrom Rev 28, 961-989.
    • (2009) Mass Spectrom Rev , vol.28 , pp. 961-989
    • March, R.1
  • 25
    • 33645654439 scopus 로고    scopus 로고
    • Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer
    • Makarov, A. et al. (2006) Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem 78, 2113-2120.
    • (2006) Anal Chem , vol.78 , pp. 2113-2120
    • Makarov, A.1
  • 26
    • 0041408938 scopus 로고    scopus 로고
    • Electrostatic axially harmonic orbital trapping: A high-performance technique of mass analysis
    • Makarov, A. (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72, 1156-1162.
    • (2000) Anal Chem , vol.72 , pp. 1156-1162
    • Makarov, A.1
  • 27
    • 0000323481 scopus 로고
    • High-resolution tandem FT mass spectrometry above 10 kDa
    • Mclafferty, F.W. (1994) High-resolution tandem FT mass spectrometry above 10 kDa. Acc Chem Res 27, 379-386.
    • (1994) Acc Chem Res , vol.27 , pp. 379-386
    • Mclafferty, F.W.1
  • 28
    • 33845512477 scopus 로고    scopus 로고
    • Glycomics using mass spectrometry
    • Kameyama, A. (2006) Glycomics using mass spectrometry. Trends Glycosci Glycotechnol 18, 323-341.
    • (2006) Trends Glycosci Glycotechnol , vol.18 , pp. 323-341
    • Kameyama, A.1
  • 29
    • 55849122284 scopus 로고    scopus 로고
    • Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis
    • Villén, J., Beausoleil, S.A. & Gygi, S.P. (2008) Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics 8, 4444.
    • (2008) Proteomics , vol.8 , pp. 4444
    • Villén, J.1    Beausoleil, S.A.2    Gygi, S.P.3
  • 30
    • 75149144996 scopus 로고    scopus 로고
    • A dual pressure linear ion trap - Orbitrap instrument with very high sequencing speed
    • Olsen, J. et al. (2009) A dual pressure linear ion trap - Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics 8, 2759-2769.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2759-2769
    • Olsen, J.1
  • 31
    • 0018478296 scopus 로고
    • Microchannel plate detectors
    • Wiza, J. (1979) Microchannel plate detectors. Nucl Instrum Methods 162, 587-601.
    • (1979) Nucl Instrum Methods , vol.162 , pp. 587-601
    • Wiza, J.1
  • 32
    • 52249085686 scopus 로고
    • Electron multiplier
    • US Patent 1,969,399
    • Farnsworth, P. (1934) Electron multiplier. US Patent 1,969,399.
    • (1934)
    • Farnsworth, P.1
  • 34
    • 30144438909 scopus 로고    scopus 로고
    • Collision-induced dissociation (CID) of peptides and proteins
    • Wells, J. & McLuckey, S. (2005) Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol 402, 148-185.
    • (2005) Methods Enzymol , vol.402 , pp. 148-185
    • Wells, J.1    McLuckey, S.2
  • 35
    • 0000183664 scopus 로고
    • Lowmass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry
    • Falick, A., Hines, W., Medzihradszky, K., Baldwin, M. & Gibson, B. (1993) Lowmass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry. J Am Soc Mass Spectrom 4, 882-893.
    • (1993) J Am Soc Mass Spectrom , vol.4 , pp. 882-893
    • Falick, A.1    Hines, W.2    Medzihradszky, K.3    Baldwin, M.4    Gibson, B.5
  • 36
    • 38649129381 scopus 로고    scopus 로고
    • A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns
    • Huang, Y. et al. (2008) A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns. J Proteome Res 7, 70-79.
    • (2008) J Proteome Res , vol.7 , pp. 70-79
    • Huang, Y.1
  • 37
    • 0032237775 scopus 로고    scopus 로고
    • Fragmentation of phosphopeptides in an ion trap mass spectrometer
    • DeGnore, J. & Qin, J. (1998) Fragmentation of phosphopeptides in an ion trap mass spectrometer. J Am Soc Mass Spectrom 9, 1175-1188.
    • (1998) J Am Soc Mass Spectrom , vol.9 , pp. 1175-1188
    • DeGnore, J.1    Qin, J.2
  • 38
    • 3042789073 scopus 로고    scopus 로고
    • Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
    • Syka, J., Coon, J. & Schroeder, M. (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci 101, 9528-9533.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 9528-9533
    • Syka, J.1    Coon, J.2    Schroeder, M.3
  • 39
    • 0000944563 scopus 로고    scopus 로고
    • Electron capture dissociation of multiply charged protein cations. A nonergodic process
    • Zubarev, R., Kelleher, N. & McLafferty, F. (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. J Am Chem Soc 120, 3265-3266.
    • (1998) J Am Chem Soc , vol.120 , pp. 3265-3266
    • Zubarev, R.1    Kelleher, N.2    McLafferty, F.3
  • 40
    • 33847782587 scopus 로고    scopus 로고
    • Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry
    • Molina, H., Horn, D.M., Tang, N., Mathivanan, S. & Pandey, A. (2007) Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci USA 104, 2199-2204.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 2199-2204
    • Molina, H.1    Horn, D.M.2    Tang, N.3    Mathivanan, S.4    Pandey, A.5
  • 41
    • 33847778786 scopus 로고    scopus 로고
    • Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry
    • Chi, A. et al. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA 104, 2193-2198.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 2193-2198
    • Chi, A.1
  • 42
    • 0001331640 scopus 로고
    • Multiple reaction monitoring in mass spectrometry/mass spectrometry for direct analysis of complex mixtures
    • Kondrat, R.W., Mcclusky, G.A. & Cooks, R.G. (1978) Multiple reaction monitoring in mass spectrometry/mass spectrometry for direct analysis of complex mixtures. Anal Chem 50, 2017-2021.
    • (1978) Anal Chem , vol.50 , pp. 2017-2021
    • Kondrat, R.W.1    Mcclusky, G.A.2    Cooks, R.G.3
  • 43
    • 35348863892 scopus 로고    scopus 로고
    • High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites
    • Stahl-Zeng, J. et al. (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 6, 1809-1817.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1809-1817
    • Stahl-Zeng, J.1
  • 44
    • 68749094119 scopus 로고    scopus 로고
    • Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
    • Picotti, P., Bodenmiller, B., Mueller, L.N., Domon, B. & Aebersold, R. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806.
    • (2009) Cell , vol.138 , pp. 795-806
    • Picotti, P.1    Bodenmiller, B.2    Mueller, L.N.3    Domon, B.4    Aebersold, R.5
  • 45
    • 54049090766 scopus 로고    scopus 로고
    • Selected reaction monitoring for quantitative proteomics: A tutorial
    • Lange, V., Picotti, P., Domon, B. & Aebersold, R. (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4, 222.
    • (2008) Mol Syst Biol , vol.4 , pp. 222
    • Lange, V.1    Picotti, P.2    Domon, B.3    Aebersold, R.4
  • 46
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu, H., Sadygov, R.G. & Yates, J.R. (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76, 4193-4201.
    • (2004) Anal Chem , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates, J.R.3
  • 47
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M., Wolters, D. & Yates, J. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19, 242-247.
    • (2001) Nat Biotechnol , vol.19 , pp. 242-247
    • Washburn, M.1    Wolters, D.2    Yates, J.3
  • 48
    • 0033051101 scopus 로고    scopus 로고
    • Direct analysis of protein complexes using mass spectrometry
    • Link, A. et al. (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17, 676-682.
    • (1999) Nat Biotechnol , vol.17 , pp. 676-682
    • Link, A.1
  • 49
    • 0037277179 scopus 로고    scopus 로고
    • Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome
    • Peng, J., Elias, J., Thoreen, C., Licklider, L. & Gygi, S. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2, 43-50.
    • (2003) J Proteome Res , vol.2 , pp. 43-50
    • Peng, J.1    Elias, J.2    Thoreen, C.3    Licklider, L.4    Gygi, S.5
  • 50
    • 49549113643 scopus 로고    scopus 로고
    • Global mapping of the topography and magnitude of proteolytic events in apoptosis
    • Dix, M.M., Simon, G.M. & Cravatt, B.F. (2008) Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 134, 679-691.
    • (2008) Cell , vol.134 , pp. 679-691
    • Dix, M.M.1    Simon, G.M.2    Cravatt, B.F.3
  • 51
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy, L.M.F. et al. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254.
    • (2008) Nature , vol.455 , pp. 1251-1254
    • De Godoy, L.M.F.1
  • 52
    • 0142215475 scopus 로고    scopus 로고
    • Global analysis of protein expression in yeast
    • Ghaemmaghami, S. et al. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741.
    • (2003) Nature , vol.425 , pp. 737-741
    • Ghaemmaghami, S.1
  • 53
    • 0142184341 scopus 로고    scopus 로고
    • Global analysis of protein localization in budding yeast
    • Huh, W.-K. et al. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686-691.
    • (2003) Nature , vol.425 , pp. 686-691
    • Huh, W.-K.1
  • 54
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • Nesvizhskii, A.I. & Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 4, 1419-1440.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 55
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotopecoded affinity tags
    • Gygi, S.P. et al. (1999) Quantitative analysis of complex protein mixtures using isotopecoded affinity tags. Nat Biotechnol 17, 994-999.
    • (1999) Nat Biotechnol , vol.17 , pp. 994-999
    • Gygi, S.P.1
  • 56
    • 0038271634 scopus 로고    scopus 로고
    • Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: Identification of more than 800 Escherichia coli proteins
    • Gevaert, K. et al. (2002) Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol Cell Proteomics 1, 896-903.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 896-903
    • Gevaert, K.1
  • 57
    • 34548400394 scopus 로고    scopus 로고
    • A la carte proteomics with an emphasis on gel-free techniques
    • Gevaert, K. et al. (2007) A la carte proteomics with an emphasis on gel-free techniques. Proteomics 7, 2698-2718.
    • (2007) Proteomics , vol.7 , pp. 2698-2718
    • Gevaert, K.1
  • 58
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • Gevaert, K. et al. (2003) Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 21, 566-569.
    • (2003) Nat Biotechnol , vol.21 , pp. 566-569
    • Gevaert, K.1
  • 59
    • 42049084149 scopus 로고    scopus 로고
    • Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
    • Staes, A. et al. (2008) Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 8, 1362-1370.
    • (2008) Proteomics , vol.8 , pp. 1362-1370
    • Staes, A.1
  • 60
    • 33745800293 scopus 로고    scopus 로고
    • Interpreting the protein language using proteomics
    • Jensen, O. (2006) Interpreting the protein language using proteomics. Nat Rev Mol Cell Biol 7, 391-403.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 391-403
    • Jensen, O.1
  • 61
    • 34547191179 scopus 로고    scopus 로고
    • Identification of proteolytic cleavage sites by quantitative proteomics
    • Enoksson, M. et al. (2007) Identification of proteolytic cleavage sites by quantitative proteomics. J Proteome Res 6, 2850-2858.
    • (2007) J Proteome Res , vol.6 , pp. 2850-2858
    • Enoksson, M.1
  • 62
    • 35148891761 scopus 로고    scopus 로고
    • Profiling constitutive proteolytic events in vivo
    • Timmer, J.C. et al. (2007) Profiling constitutive proteolytic events in vivo. Biochem J 407, 41-48.
    • (2007) Biochem J , vol.407 , pp. 41-48
    • Timmer, J.C.1
  • 63
    • 52949151513 scopus 로고    scopus 로고
    • Protease proteomics: Revealing protease in vivo functions using systems biology approaches
    • Doucet, A. & Overall, C.M. (2008) Protease proteomics: revealing protease in vivo functions using systems biology approaches. Mol Aspects Med 29, 339-358.
    • (2008) Mol Aspects Med , vol.29 , pp. 339-358
    • Doucet, A.1    Overall, C.M.2
  • 64
    • 52649141086 scopus 로고    scopus 로고
    • Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
    • Mahrus, S. et al. (2008) Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 134, 866-876.
    • (2008) Cell , vol.134 , pp. 866-876
    • Mahrus, S.1
  • 65
    • 0022541790 scopus 로고
    • Isolation of phosphoproteins by immobilized metal (Fe-3+) affinity chromatography
    • Andersson, L. & Porath, J. (1986) Isolation of phosphoproteins by immobilized metal (Fe-3+) affinity chromatography. Anal Biochem 154, 250-254.
    • (1986) Anal Biochem , vol.154 , pp. 250-254
    • Andersson, L.1    Porath, J.2
  • 66
    • 0037417791 scopus 로고    scopus 로고
    • Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry
    • Bonenfant, D. et al. (2003) Quantitation of changes in protein phosphorylation: a simple method based on stable isotope labeling and mass spectrometry. Proc Natl Acad Sci USA 100, 880-885.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 880-885
    • Bonenfant, D.1
  • 67
    • 3242688830 scopus 로고    scopus 로고
    • Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESIMS/ MS and titanium oxide precolumns
    • Pinkse, M., Uitto, P., Hilhorst, M., Ooms, B. & Heck, A. (2004) Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESIMS/ MS and titanium oxide precolumns. Anal Chem 76, 3935-3943.
    • (2004) Anal Chem , vol.76 , pp. 3935-3943
    • Pinkse, M.1    Uitto, P.2    Hilhorst, M.3    Ooms, B.4    Heck, A.5
  • 68
    • 43849091451 scopus 로고    scopus 로고
    • Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection
    • Mcnulty, D. & Annan, R. (2008) Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol Cell Proteomics 7, 971.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 971
    • Mcnulty, D.1    Annan, R.2
  • 69
    • 4344574540 scopus 로고    scopus 로고
    • Large-scale characterization of HeLa cell nuclear phosphoproteins
    • Beausoleil, S. et al. (2004) Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci USA 101, 12130-12135.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 12130-12135
    • Beausoleil, S.1
  • 70
    • 0035836061 scopus 로고    scopus 로고
    • Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests
    • Geng, M., Zhang, X., Bina, M. & Regnier, F. (2001) Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests. J Chromatogr B 752, 293-306.
    • (2001) J Chromatogr B , vol.752 , pp. 293-306
    • Geng, M.1    Zhang, X.2    Bina, M.3    Regnier, F.4
  • 71
    • 1042275609 scopus 로고    scopus 로고
    • Chemical probes and tandem mass spectrometry: A strategy for the quantitative analysis of proteomes and subproteomes
    • Zhang, H., Yan, W. & Aebersold, R. (2004) Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr Opin Chem Biol 8, 66-75.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 66-75
    • Zhang, H.1    Yan, W.2    Aebersold, R.3
  • 72
    • 34249032767 scopus 로고    scopus 로고
    • Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics
    • Khidekel, N. et al. (2007) Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nat Chem Biol 3, 339-348.
    • (2007) Nat Chem Biol , vol.3 , pp. 339-348
    • Khidekel, N.1
  • 73
    • 68949212379 scopus 로고    scopus 로고
    • Lysine acetylation targets protein complexes and co-regulates major cellular functions
    • Choudhary, C. et al. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840.
    • (2009) Science , vol.325 , pp. 834-840
    • Choudhary, C.1
  • 74
    • 0041706156 scopus 로고    scopus 로고
    • A proteomics approach to understanding protein ubiquitination
    • Peng, J. et al. (2003) A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 21, 921-926.
    • (2003) Nat Biotechnol , vol.21 , pp. 921-926
    • Peng, J.1
  • 75
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R. & Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 76
    • 0033918391 scopus 로고    scopus 로고
    • Mass spectrometry: A tool for the identification of proteins separated by gels
    • Lahm, H. & Langen, H. (2000) Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis 21, 2105-2114.
    • (2000) Electrophoresis , vol.21 , pp. 2105-2114
    • Lahm, H.1    Langen, H.2
  • 77
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. et al. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1, 376-386.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 376-386
    • Ong, S.1
  • 78
    • 33845329203 scopus 로고    scopus 로고
    • Functional and quantitative proteomics using SILAC
    • Mann, M. (2006) Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7, 952-958.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 952-958
    • Mann, M.1
  • 79
    • 47549099572 scopus 로고    scopus 로고
    • SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function
    • Krueger, M. et al. (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134, 353-364.
    • (2008) Cell , vol.134 , pp. 353-364
    • Krueger, M.1
  • 80
    • 0041706161 scopus 로고    scopus 로고
    • Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics
    • Krijgsveld, J. et al. (2003) Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 21, 927-931.
    • (2003) Nat Biotechnol , vol.21 , pp. 927-931
    • Krijgsveld, J.1
  • 81
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
    • Han, D.K., Eng, J., Zhou, H. & Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 19, 946-951.
    • (2001) Nat Biotechnol , vol.19 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 82
    • 4444271864 scopus 로고    scopus 로고
    • Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18
    • Staes, A. et al. (2004) Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res 3, 786-791.
    • (2004) J Proteome Res , vol.3 , pp. 786-791
    • Staes, A.1
  • 83
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. et al. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3, 1154-1169.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.1
  • 84
    • 0037795741 scopus 로고    scopus 로고
    • Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
    • Gerber, S., Rush, J., Stemman, O., Kirschner, M. & Gygi, S. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100, 6940-6945.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 6940-6945
    • Gerber, S.1    Rush, J.2    Stemman, O.3    Kirschner, M.4    Gygi, S.5
  • 85
    • 68449102172 scopus 로고    scopus 로고
    • Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
    • Malmström, J. et al. (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460, 762-765.
    • (2009) Nature , vol.460 , pp. 762-765
    • Malmström, J.1
  • 86
    • 58149299336 scopus 로고    scopus 로고
    • Significance analysis of spectral count data in label-free shotgun proteomics
    • Choi, H., Fermin, D. & Nesvizhskii, A. (2008) Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics 7, 2373.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 2373
    • Choi, H.1    Fermin, D.2    Nesvizhskii, A.3
  • 87
    • 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., Sachs, J., Deyanova, E. & Yates, N. (2004) Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem 76, 6085-6096.
    • (2004) Anal Chem , vol.76 , pp. 6085-6096
    • Wiener, M.1    Sachs, J.2    Deyanova, E.3    Yates, N.4
  • 88
    • 42249108173 scopus 로고    scopus 로고
    • OpenMS-An opensource software framework for mass spectrometry
    • Sturm, M. et al. (2008) OpenMS-An opensource software framework for mass spectrometry. BMC Bioinformatics 9, 163.
    • (2008) BMC Bioinformatics , vol.9 , pp. 163
    • Sturm, M.1
  • 89
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J. & Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367-1372.
    • (2008) Nat Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 90
    • 34347405493 scopus 로고    scopus 로고
    • Data processing for mass spectrometry-based metabolomics
    • Katajamaa, M. & Oresic, M. (2007) Data processing for mass spectrometry-based metabolomics. J Chromatogr A 1158, 318-328.
    • (2007) J Chromatogr a , vol.1158 , pp. 318-328
    • Katajamaa, M.1    Oresic, M.2
  • 91
    • 0028575316 scopus 로고
    • Errortolerant identification of peptides in sequence databases by peptide sequence tags
    • Mann, M. & Wilm, M. (1994) Errortolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66, 4390-4399.
    • (1994) Anal Chem , vol.66 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 92
    • 70349160394 scopus 로고    scopus 로고
    • Database on Demand - An online tool for the custom generation of FASTA-formatted sequence databases
    • Reisinger, F. & Martens, L. (2009) Database on Demand - An online tool for the custom generation of FASTA-formatted sequence databases. Proteomics 9, 4421-4424.
    • (2009) Proteomics , vol.9 , pp. 4421-4424
    • Reisinger, F.1    Martens, L.2
  • 93
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A.I., Vitek, O. & Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4, 787-797.
    • (2007) Nat Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 94
    • 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. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem 67, 1426-1436.
    • (1995) Anal Chem , vol.67 , pp. 1426-1436
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 95
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D., Pappin, D., Creasy, D. & Cottrell, J. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.1    Pappin, D.2    Creasy, D.3    Cottrell, J.4
  • 96
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • Fenyo, D. & Beavis, R. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 75, 768-774.
    • (2003) Anal Chem , vol.75 , pp. 768-774
    • Fenyo, D.1    Beavis, R.2
  • 97
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: Towards high-throughput tandem mass spectrometry data identification
    • Colinge, J., Masselot, A., Giron, M., Dessingy, T. & Magnin, J. (2003) OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463.
    • (2003) Proteomics , vol.3 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 98
    • 7044246160 scopus 로고    scopus 로고
    • Open mass spectrometry search algorithm
    • Geer, L. et al. (2004) Open mass spectrometry search algorithm. J Proteome Res 3, 958-964.
    • (2004) J Proteome Res , vol.3 , pp. 958-964
    • Geer, L.1
  • 99
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: De novo peptide sequencing via probabilistic network modeling
    • Frank, A. & Pevzner, P. (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem 77, 964-973.
    • (2005) Anal Chem , vol.77 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 100
    • 0036828610 scopus 로고    scopus 로고
    • Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry
    • Johnson, R. & Taylor, J. (2002) Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol Biotechnol 22, 301-315.
    • (2002) Mol Biotechnol , vol.22 , pp. 301-315
    • Johnson, R.1    Taylor, J.2
  • 101
    • 33847630405 scopus 로고    scopus 로고
    • Targetdecoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J.E. & Gygi, S.P. (2007) Targetdecoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4, 207-214.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 102
    • 33645708138 scopus 로고    scopus 로고
    • Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data - Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    • Nesvizhskii, A. et al. (2006) Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data - Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 5, 652-670.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.1
  • 103
    • 33645653958 scopus 로고    scopus 로고
    • Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
    • Flikka, K., Martens, L., Vandekerckhoe, J., Gevaert, K. & Eidhammer, I. (2006) Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 6, 2086-2094.
    • (2006) Proteomics , vol.6 , pp. 2086-2094
    • Flikka, K.1    Martens, L.2    Vandekerckhoe, J.3    Gevaert, K.4    Eidhammer, I.5
  • 104
    • 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., Kolker, E. & Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74, 5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.2    Kolker, E.3    Aebersold, R.4
  • 105
    • 35748972060 scopus 로고    scopus 로고
    • Semisupervised learning for peptide identification from shotgun proteomics datasets
    • Kall, L., Canterbury, J.D., Weston, J., Noble, W.S. & MacCoss, M.J. (2007) Semisupervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4, 923-925.
    • (2007) Nat Methods , vol.4 , pp. 923-925
    • Kall, L.1    Canterbury, J.D.2    Weston, J.3    Noble, W.S.4    MacCoss, M.J.5
  • 106
    • 30744444934 scopus 로고    scopus 로고
    • PepHMM: A hidden Markov model based scoring function for mass spectrometry database search
    • Wan, Y., Yang, A. & Chen, T. (2006) PepHMM: a hidden Markov model based scoring function for mass spectrometry database search. Anal Chem 78, 432-437.
    • (2006) Anal Chem , vol.78 , pp. 432-437
    • Wan, Y.1    Yang, A.2    Chen, T.3
  • 107
    • 58149289353 scopus 로고    scopus 로고
    • Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results
    • Helsens, K., Timmerman, E., Vandekerckhove, J., Gevaert, K. & Martens, L. (2008) Peptizer: a tool for assessing false positive peptide identifications and manually validating selected results. Mol Cell Proteomics 7, 2363-2372.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 2363-2372
    • Helsens, K.1    Timmerman, E.2    Vandekerckhove, J.3    Gevaert, K.4    Martens, L.5
  • 108
    • 34547176285 scopus 로고    scopus 로고
    • Proteomics data validation: Why all must provide data
    • Martens, L. & Hermjakob, H. (2007) Proteomics data validation: why all must provide data. Mol Biosyst 3, 518-522.
    • (2007) Mol Biosyst , vol.3 , pp. 518-522
    • Martens, L.1    Hermjakob, H.2
  • 109
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A., Keller, A., Kolker, E. & Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75, 4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 110
    • 33846847440 scopus 로고    scopus 로고
    • Annotating the human proteome: Beyond establishing a parts list
    • Mueller, M., Martens, L. & Apweiler, R. (2007) Annotating the human proteome: beyond establishing a parts list. Biochim Biophys Acta 1774, 175-191.
    • (2007) Biochim Biophys Acta , vol.1774 , pp. 175-191
    • Mueller, M.1    Martens, L.2    Apweiler, R.3
  • 111
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 112
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere, S., Heymans, K. & Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 113
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for annotation, visualization, and integrated discovery
    • Dennis, G. et al. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4, R60.
    • (2003) Genome Biol , vol.4
    • Dennis, G.1
  • 114
    • 0141974922 scopus 로고    scopus 로고
    • PANDORA: Keyword-based analysis of protein sets by integration of annotation sources
    • Kaplan, N., Vaaknin, A. & Linial, M. (2003) PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res 31, 5617-5626.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5617-5626
    • Kaplan, N.1    Vaaknin, A.2    Linial, M.3
  • 115
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider, T.D. & Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18, 6097-6100.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 117
    • 29144535689 scopus 로고    scopus 로고
    • VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins
    • Matthiesen, R., Trelle, M., Hojrup, P., Bunkenborg, J. & Jensen, O. (2005) VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J Proteome Res 4, 2338-2347.
    • (2005) J Proteome Res , vol.4 , pp. 2338-2347
    • Matthiesen, R.1    Trelle, M.2    Hojrup, P.3    Bunkenborg, J.4    Jensen, O.5
  • 118
    • 30744438115 scopus 로고    scopus 로고
    • Computational Proteomics Analysis System (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments
    • Rauch, A. et al. (2006) Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res 5, 112-121.
    • (2006) J Proteome Res , vol.5 , pp. 112-121
    • Rauch, A.1
  • 119
    • 67049100049 scopus 로고    scopus 로고
    • The proteios software environment: An extensible multiuser platform for management and analysis of proteomics data
    • Hakkinen, J., Vincic, G., Mansson, O., Warell, K. & Levander, F. (2009) The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. J Proteome Res 8, 3037-3043.
    • (2009) J Proteome Res , vol.8 , pp. 3037-3043
    • Hakkinen, J.1    Vincic, G.2    Mansson, O.3    Warell, K.4    Levander, F.5
  • 120
    • 34447260760 scopus 로고    scopus 로고
    • MASPECTRAS: A platform for management and analysis of proteomics LC-MS/MS data
    • Hartler, J. et al. (2007) MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. BMC Bioinformatics 8, 197.
    • (2007) BMC Bioinformatics , vol.8 , pp. 197
    • Hartler, J.1
  • 121
    • 77954787122 scopus 로고    scopus 로고
    • ms-lims, a simple yet powerful open source LIMS for mass spectrometry-driven proteomics
    • Helsens, K. et al. (2010) ms-lims, a simple yet powerful open source LIMS for mass spectrometry-driven proteomics. Proteomics 10, 2560.
    • (2010) Proteomics , vol.10 , pp. 2560
    • Helsens, K.1
  • 122
    • 23944526367 scopus 로고    scopus 로고
    • PRIDE: The proteomics identifications database
    • Martens, L. et al. (2005) PRIDE: the proteomics identifications database. Proteomics 5, 3537-3545.
    • (2005) Proteomics , vol.5 , pp. 3537-3545
    • Martens, L.1
  • 123
    • 67650479361 scopus 로고    scopus 로고
    • NCBI Peptidome: A new public repository for mass spectrometry peptide identifications
    • Slotta, D.J., Barrett, T. & Edgar, R. (2009) NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. Nat Biotechnol 27, 600-601.
    • (2009) Nat Biotechnol , vol.27 , pp. 600-601
    • Slotta, D.J.1    Barrett, T.2    Edgar, R.3
  • 124
    • 33644876912 scopus 로고    scopus 로고
    • The PeptideAtlas project
    • Desiere, F. et al. (2006) The PeptideAtlas project. Nucleic Acids Res 34, D655-D658.
    • (2006) Nucleic Acids Res , vol.34
    • Desiere, F.1
  • 125
    • 11144320641 scopus 로고    scopus 로고
    • Open source system for analyzing, validating, and storing protein identification data
    • Craig, R., Cortens, J.P. & Beavis, R.C. (2004) Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 3, 1234-1242.
    • (2004) J Proteome Res , vol.3 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 126
    • 38649129380 scopus 로고    scopus 로고
    • Analyzing largescale proteomics projects with latent semantic indexing
    • Klie, S. et al. (2008) Analyzing largescale proteomics projects with latent semantic indexing. J Proteome Res 7, 182-191.
    • (2008) J Proteome Res , vol.7 , pp. 182-191
    • Klie, S.1
  • 127
    • 41549097236 scopus 로고    scopus 로고
    • Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
    • Mueller, M. et al. (2008) Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics 8, 1138-1148.
    • (2008) Proteomics , vol.8 , pp. 1138-1148
    • Mueller, M.1
  • 128
    • 1842423659 scopus 로고    scopus 로고
    • Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies
    • Gevaert K, Ghesquière B, et al (2004) Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies. Proteomics 4, 897-908.
    • (2004) Proteomics , vol.4 , pp. 897-908
    • Gevaert, K.1    Ghesquière, B.2
  • 129
    • 25844524834 scopus 로고    scopus 로고
    • Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC
    • Gevaert K, Staes A, et al (2005) Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC. Proteomics 5, 3589-3599.
    • (2005) Proteomics , vol.5 , pp. 3589-3599
    • Gevaert, K.1    Staes, A.2
  • 130
    • 33748295546 scopus 로고    scopus 로고
    • Proteome-wide characterization of N-glycosylation events by diagonal chromatography
    • Ghesquière B, Van Damme J, et al (2006) Proteome-wide characterization of N-glycosylation events by diagonal chromatography. J Proteome Res 5, 2438-2447.
    • (2006) J Proteome Res , vol.5 , pp. 2438-2447
    • Ghesquière, B.1    Van Damme, J.2
  • 131
    • 33845425069 scopus 로고    scopus 로고
    • A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes
    • Hanoulle X, Van Damme J, et al (2006) A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes. J Proteome Res 5, 3438-3445.
    • (2006) J Proteome Res , vol.5 , pp. 3438-3445
    • Hanoulle, X.1    Van Damme, J.2
  • 132
    • 36348974133 scopus 로고    scopus 로고
    • A new approach for mapping sialylated N-glycosites in serum proteomes
    • Ghesquière B, Buyl L, et al (2007) A new approach for mapping sialylated N-glycosites in serum proteomes. J Proteome Res 6, 4304-4312.
    • (2007) J Proteome Res , vol.6 , pp. 4304-4312
    • Ghesquière, B.1    Buyl, L.2
  • 133
    • 75149167439 scopus 로고    scopus 로고
    • In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography
    • Ghesquière B, Colaert N, et al (2009) In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography. Mol Cell Proteomics 8, 2642-2652.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2642-2652
    • Ghesquière, B.1    Colaert, N.2


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