메뉴 건너뛰기




Volumn 14, Issue 4-5, 2014, Pages 547-565

Quantitative proteomics in the field of microbiology

Author keywords

Absolute quantitation; Gel based; Gel free; Isotopic labeling; Mass spectrometry; Microbial proteomics

Indexed keywords

NITROGEN 15; STABLE ISOTOPE; PROTEOME;

EID: 84896777061     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300403     Document Type: Review
Times cited : (65)

References (188)
  • 1
    • 77949517375 scopus 로고    scopus 로고
    • A proteomic view of an important human pathogen-towards the quantification of the entire Staphylococcus aureus proteome
    • Becher, D., Hempel, K., Sievers, S., Zühlke, D. et al., A proteomic view of an important human pathogen-towards the quantification of the entire Staphylococcus aureus proteome. PLoS One 2009, 4, e8176.
    • (2009) PLoS One , vol.4
    • Becher, D.1    Hempel, K.2    Sievers, S.3    Zühlke, D.4
  • 2
    • 79251551042 scopus 로고    scopus 로고
    • Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis
    • Otto, A., Bernhardt, J., Meyer, H., Schaffer, M. et al., Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis. Nat. Commun. 2010, 1, 137.
    • (2010) Nat. Commun. , vol.1 , pp. 137
    • Otto, A.1    Bernhardt, J.2    Meyer, H.3    Schaffer, M.4
  • 3
    • 84855549488 scopus 로고    scopus 로고
    • System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap
    • doi:10.1074/mcp.M111.013722.
    • Nagaraj, N., Kulak, N. A., Cox, J., Neuhauser, N. et al., System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol. Cell. Proteomics 2012, 11, doi:10.1074/mcp.M111.013722.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Nagaraj, N.1    Kulak, N.A.2    Cox, J.3    Neuhauser, N.4
  • 4
    • 68449102172 scopus 로고    scopus 로고
    • Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
    • Malmström, J., Beck, M., Schmidt, A., Lange, V. et al., Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 2009, 460, 762-765.
    • (2009) Nature , vol.460 , pp. 762-765
    • Malmström, J.1    Beck, M.2    Schmidt, A.3    Lange, V.4
  • 5
    • 80855128254 scopus 로고    scopus 로고
    • Deep proteome and transcriptome mapping of a human cancer cell line
    • Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J. et al., Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 2011, 7, 548.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 548
    • Nagaraj, N.1    Wisniewski, J.R.2    Geiger, T.3    Cox, J.4
  • 6
    • 42649132889 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins
    • Graumann, J., Hubner, N. C., Kim, J. B., Ko, K. et al., Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5, 111 proteins. Mol. Cell. Proteomics 2008, 7, 672-683.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 672-683
    • Graumann, J.1    Hubner, N.C.2    Kim, J.B.3    Ko, K.4
  • 7
    • 77955119702 scopus 로고    scopus 로고
    • Time-resolved quantitative proteome profiling of host-pathogen interactions: the response of Staphylococcus aureus RN1HG to internalisation by human airway epithelial cells
    • Schmidt, F., Scharf, S. S., Hildebrandt, P., Burian, M. et al., Time-resolved quantitative proteome profiling of host-pathogen interactions: the response of Staphylococcus aureus RN1HG to internalisation by human airway epithelial cells. Proteomics 2010, 10, 2801-2811.
    • (2010) Proteomics , vol.10 , pp. 2801-2811
    • Schmidt, F.1    Scharf, S.S.2    Hildebrandt, P.3    Burian, M.4
  • 8
    • 84859573112 scopus 로고    scopus 로고
    • Exploring mixed microbial community functioning: recent advances in metaproteomics
    • Siggins, A., Gunnigle, E., Abram, F., Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol. Ecol. 2012, 80, 265-280.
    • (2012) FEMS Microbiol. Ecol. , vol.80 , pp. 265-280
    • Siggins, A.1    Gunnigle, E.2    Abram, F.3
  • 9
    • 84864035417 scopus 로고    scopus 로고
    • Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
    • Hettich, R. L., Sharma, R., Chourey, K., Giannone, R. J., Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr. Opin. Microbiol. 2012, 15, 373-380.
    • (2012) Curr. Opin. Microbiol. , vol.15 , pp. 373-380
    • Hettich, R.L.1    Sharma, R.2    Chourey, K.3    Giannone, R.J.4
  • 10
    • 79960416662 scopus 로고    scopus 로고
    • A proteomic view of the host-pathogen interaction: the host perspective
    • Hartlova, A., Krocova, Z., Cerveny, L., Stulik, J., A proteomic view of the host-pathogen interaction: the host perspective. Proteomics 2011, 11, 3212-3220.
    • (2011) Proteomics , vol.11 , pp. 3212-3220
    • Hartlova, A.1    Krocova, Z.2    Cerveny, L.3    Stulik, J.4
  • 11
    • 79959424627 scopus 로고    scopus 로고
    • Quantitative, high-resolution proteomics for data-driven systems biology
    • Cox, J., Mann, M., Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 2011, 80, 273-299.
    • (2011) Annu. Rev. Biochem. , vol.80 , pp. 273-299
    • Cox, J.1    Mann, M.2
  • 12
    • 84872650023 scopus 로고    scopus 로고
    • Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast
    • Schmidt, S. A., Jacob, S. S., Ahn, S. B., Rupasinghe, T. et al., Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast. Metabolomics 2013, 9, 173-188.
    • (2013) Metabolomics , vol.9 , pp. 173-188
    • Schmidt, S.A.1    Jacob, S.S.2    Ahn, S.B.3    Rupasinghe, T.4
  • 13
    • 0016637146 scopus 로고
    • Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals
    • Klose, J., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 1975, 26, 231-243.
    • (1975) Humangenetik , vol.26 , pp. 231-243
    • Klose, J.1
  • 14
    • 0016711037 scopus 로고
    • High resolution two-dimensional electrophoresis of proteins
    • O'Farrell, P. H., High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250, 4007-4021.
    • (1975) J. Biol. Chem. , vol.250 , pp. 4007-4021
    • O'Farrell, P.H.1
  • 16
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M. P., Wolters, D., Yates, J. R., 3rd, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 17
    • 0142215475 scopus 로고    scopus 로고
    • Global analysis of protein expression in yeast
    • Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W. et al., Global analysis of protein expression in yeast. Nature 2003, 425, 737-741.
    • (2003) Nature , vol.425 , pp. 737-741
    • Ghaemmaghami, S.1    Huh, W.K.2    Bower, K.3    Howson, R.W.4
  • 18
    • 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. et al., Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 2006, 7, R50.
    • (2006) Genome Biol. , vol.7
    • de Godoy, L.M.1    Olsen, J.V.2    de Souza, G.A.3    Li, G.4
  • 19
    • 0042386240 scopus 로고    scopus 로고
    • Protein identification: the origins of peptide mass fingerprinting
    • Henzel, W. J., Watanabe, C., Stults, J. T., Protein identification: the origins of peptide mass fingerprinting. J. Am. Soc. Mass Spectrom. 2003, 14, 931-942.
    • (2003) J. Am. Soc. Mass Spectrom. , vol.14 , pp. 931-942
    • Henzel, W.J.1    Watanabe, C.2    Stults, J.T.3
  • 20
    • 77957220211 scopus 로고    scopus 로고
    • Two-dimensional gel electrophoresis in proteomics: past, present and future
    • Rabilloud, T., Chevallet, M., Luche, S., Lelong, C., Two-dimensional gel electrophoresis in proteomics: past, present and future. J. Proteomics 2010, 73, 2064-2077.
    • (2010) J. Proteomics , vol.73 , pp. 2064-2077
    • Rabilloud, T.1    Chevallet, M.2    Luche, S.3    Lelong, C.4
  • 21
    • 57649218829 scopus 로고    scopus 로고
    • Gel-based proteomics of Gram-positive bacteria: a powerful tool to address physiological questions
    • Hecker, M., Antelmann, H., Büttner, K., Bernhardt, J., Gel-based proteomics of Gram-positive bacteria: a powerful tool to address physiological questions. Proteomics 2008, 8, 4958-4975.
    • (2008) Proteomics , vol.8 , pp. 4958-4975
    • Hecker, M.1    Antelmann, H.2    Büttner, K.3    Bernhardt, J.4
  • 22
    • 77955591792 scopus 로고    scopus 로고
    • Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL
    • Fuchs, S., Mehlan, H., Kusch, H., Teumer, A. et al., Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics 2010, 10, 2982-3000.
    • (2010) Proteomics , vol.10 , pp. 2982-3000
    • Fuchs, S.1    Mehlan, H.2    Kusch, H.3    Teumer, A.4
  • 23
    • 33645467362 scopus 로고    scopus 로고
    • Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling
    • Resch, A., Leicht, S., Saric, M., Pasztor, L. et al., Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling. Proteomics 2006, 6, 1867-1877.
    • (2006) Proteomics , vol.6 , pp. 1867-1877
    • Resch, A.1    Leicht, S.2    Saric, M.3    Pasztor, L.4
  • 24
  • 25
    • 80051814606 scopus 로고    scopus 로고
    • Characterization of the global impact of low temperature gas plasma on vegetative microorganisms
    • Winter, T., Winter, J., Polak, M., Kusch, K. et al., Characterization of the global impact of low temperature gas plasma on vegetative microorganisms. Proteomics 2011, 11, 3518-3530.
    • (2011) Proteomics , vol.11 , pp. 3518-3530
    • Winter, T.1    Winter, J.2    Polak, M.3    Kusch, K.4
  • 26
    • 79960399946 scopus 로고    scopus 로고
    • Proteomic signatures in antibiotic research
    • Wenzel, M., Bandow, J. E., Proteomic signatures in antibiotic research. Proteomics 2011, 11, 3256-3268.
    • (2011) Proteomics , vol.11 , pp. 3256-3268
    • Wenzel, M.1    Bandow, J.E.2
  • 27
    • 0344329881 scopus 로고    scopus 로고
    • Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis
    • Bernhardt, J., Büttner, K., Scharf, C., Hecker, M., Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis. Electrophoresis 1999, 20, 2225-2240.
    • (1999) Electrophoresis , vol.20 , pp. 2225-2240
    • Bernhardt, J.1    Büttner, K.2    Scharf, C.3    Hecker, M.4
  • 28
    • 37549068524 scopus 로고    scopus 로고
    • Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis
    • Gerth, U., Kock, H., Küsters, I., Michalik, S. et al., Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J. Bacteriol. 2008, 190, 321-331.
    • (2008) J. Bacteriol. , vol.190 , pp. 321-331
    • Gerth, U.1    Kock, H.2    Küsters, I.3    Michalik, S.4
  • 29
    • 70350238657 scopus 로고    scopus 로고
    • Proteolysis during long-term glucose starvation in Staphylococcus aureus COL
    • Michalik, S., Liebeke, M., Zühlke, D., Lalk, M. et al., Proteolysis during long-term glucose starvation in Staphylococcus aureus COL. Proteomics 2009, 9, 4468-4477.
    • (2009) Proteomics , vol.9 , pp. 4468-4477
    • Michalik, S.1    Liebeke, M.2    Zühlke, D.3    Lalk, M.4
  • 30
    • 76449115656 scopus 로고    scopus 로고
    • Integrating multiple 'omics' analysis for microbial biology: application and methodologies
    • Zhang, W., Li, F., Nie, L., Integrating multiple 'omics' analysis for microbial biology: application and methodologies. Microbiology 2010, 156, 287-301.
    • (2010) Microbiology , vol.156 , pp. 287-301
    • Zhang, W.1    Li, F.2    Nie, L.3
  • 31
    • 84865705987 scopus 로고    scopus 로고
    • Life and death of proteins: a case study of glucose-starved Staphylococcus aureus
    • Michalik, S., Bernhardt, J., Otto, A., Moche, M. et al., Life and death of proteins: a case study of glucose-starved Staphylococcus aureus. Mol. Cell. Proteomics 2012, 11, 558-570.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 558-570
    • Michalik, S.1    Bernhardt, J.2    Otto, A.3    Moche, M.4
  • 32
    • 84867641516 scopus 로고    scopus 로고
    • Dynamic 13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains
    • Hong, K. K., Hou, J., Shoaie, S., Nielsen, J., Bordel, S., Dynamic 13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains. FEMS Yeast Res. 2012, 12, 741-747.
    • (2012) FEMS Yeast Res. , vol.12 , pp. 741-747
    • Hong, K.K.1    Hou, J.2    Shoaie, S.3    Nielsen, J.4    Bordel, S.5
  • 34
    • 73649114530 scopus 로고    scopus 로고
    • A proteomic view of cell physiology and virulence of Staphylococcus aureus
    • Hecker, M., Becher, D., Fuchs, S., Engelmann, S., A proteomic view of cell physiology and virulence of Staphylococcus aureus. Int. J. Med. Microbiol. 2010, 300, 76-87.
    • (2010) Int. J. Med. Microbiol. , vol.300 , pp. 76-87
    • Hecker, M.1    Becher, D.2    Fuchs, S.3    Engelmann, S.4
  • 35
    • 62349101329 scopus 로고    scopus 로고
    • Classical proteomics: two-dimensional electrophoresis/MALDI mass spectrometry
    • Zimny-Arndt, U., Schmid, M., Ackermann, R., Jungblut, P. R., Classical proteomics: two-dimensional electrophoresis/MALDI mass spectrometry. Methods Mol. Biol. 2009, 492, 65-91.
    • (2009) Methods Mol. Biol. , vol.492 , pp. 65-91
    • Zimny-Arndt, U.1    Schmid, M.2    Ackermann, R.3    Jungblut, P.R.4
  • 36
    • 34648857991 scopus 로고    scopus 로고
    • Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis
    • Eymann, C., Becher, D., Bernhardt, J., Gronau, K. et al., Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 2007, 7, 3509-3526.
    • (2007) Proteomics , vol.7 , pp. 3509-3526
    • Eymann, C.1    Becher, D.2    Bernhardt, J.3    Gronau, K.4
  • 37
    • 84855901086 scopus 로고    scopus 로고
    • Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG
    • Koponen, J., Laakso, K., Koskenniemi, K., Kankainen, M. et al., Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG. J. Proteomics 2012, 75, 1357-1374.
    • (2012) J. Proteomics , vol.75 , pp. 1357-1374
    • Koponen, J.1    Laakso, K.2    Koskenniemi, K.3    Kankainen, M.4
  • 38
    • 67650360389 scopus 로고    scopus 로고
    • Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes
    • Soung, G. Y., Miller, J. L., Koc, H., Koc, E. C., Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes. J. Proteome Res. 2009, 8, 3390-3402.
    • (2009) J. Proteome Res. , vol.8 , pp. 3390-3402
    • Soung, G.Y.1    Miller, J.L.2    Koc, H.3    Koc, E.C.4
  • 39
  • 40
    • 84892900045 scopus 로고    scopus 로고
    • Analysis of protein species differentiation among mycobacterial low-Mr-secreted proteins by narrow pH range immobiline gel 2-DE-MALDI-MS
    • doi:10.1016/j.jprot.2013.06.036.
    • Lange, S., Rosenkrands, I., Stein, R., Andersen, P. et al., Analysis of protein species differentiation among mycobacterial low-Mr-secreted proteins by narrow pH range immobiline gel 2-DE-MALDI-MS. J. Proteomics 2013, doi:10.1016/j.jprot.2013.06.036.
    • (2013) J. Proteomics
    • Lange, S.1    Rosenkrands, I.2    Stein, R.3    Andersen, P.4
  • 42
    • 34648834050 scopus 로고    scopus 로고
    • The state of the art in the analysis of two-dimensional gel electrophoresis images
    • Berth, M., Moser, F. M., Kolbe, M., Bernhardt, J., The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl. Microbiol. Biotechnol. 2007, 76, 1223-1243.
    • (2007) Appl. Microbiol. Biotechnol. , vol.76 , pp. 1223-1243
    • Berth, M.1    Moser, F.M.2    Kolbe, M.3    Bernhardt, J.4
  • 43
    • 84878666768 scopus 로고    scopus 로고
    • The new horizon in 2D electrophoresis: new technology to increase resolution and sensitivity
    • Moche, M., Albrecht, D., Maass, S., Hecker, M. et al., The new horizon in 2D electrophoresis: new technology to increase resolution and sensitivity. Electrophoresis 2013, 34, 1510-1518.
    • (2013) Electrophoresis , vol.34 , pp. 1510-1518
    • Moche, M.1    Albrecht, D.2    Maass, S.3    Hecker, M.4
  • 44
    • 44049091137 scopus 로고    scopus 로고
    • Difference gel electrophoresis based on lys/cys tagging
    • Westermeier, R., Scheibe, B., Difference gel electrophoresis based on lys/cys tagging. Methods Mol. Biol. 2008, 424, 73-85.
    • (2008) Methods Mol. Biol. , vol.424 , pp. 73-85
    • Westermeier, R.1    Scheibe, B.2
  • 45
    • 0042386237 scopus 로고    scopus 로고
    • Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis
    • Schmidt, F., Schmid, M., Jungblut, P. R., Mattow, J. et al., Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J. Am. Soc. Mass Spectrom. 2003, 14, 943-956.
    • (2003) J. Am. Soc. Mass Spectrom. , vol.14 , pp. 943-956
    • Schmidt, F.1    Schmid, M.2    Jungblut, P.R.3    Mattow, J.4
  • 46
    • 69249222678 scopus 로고    scopus 로고
    • Membrane proteins and proteomics: love is possible, but so difficult
    • Rabilloud, T., Membrane proteins and proteomics: love is possible, but so difficult. Electrophoresis 2009, 30(Suppl 1), S174-S180.
    • (2009) Electrophoresis , vol.30 , Issue.SUPPL. 1
    • Rabilloud, T.1
  • 47
    • 0034066471 scopus 로고    scopus 로고
    • Membrane proteins and proteomics: un amour impossible
    • Santoni, V., Molloy, M., Rabilloud, T., Membrane proteins and proteomics: un amour impossible? Electrophoresis 2000, 21, 1054-1070.
    • (2000) Electrophoresis , vol.21 , pp. 1054-1070
    • Santoni, V.1    Molloy, M.2    Rabilloud, T.3
  • 48
    • 35448967750 scopus 로고    scopus 로고
    • Top-down quantitation and characterization of SILAC-labeled proteins
    • Waanders, L. F., Hanke, S., Mann, M., Top-down quantitation and characterization of SILAC-labeled proteins. J. Am. Soc. Mass Spectrom. 2007, 18, 2058-2064.
    • (2007) J. Am. Soc. Mass Spectrom. , vol.18 , pp. 2058-2064
    • Waanders, L.F.1    Hanke, S.2    Mann, M.3
  • 49
    • 79952012529 scopus 로고    scopus 로고
    • The emerging process of top down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput
    • Kellie, J. F., Tran, J. C., Lee, J. E., Ahlf, D. R. et al., The emerging process of top down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. Mol. Biosyst. 2010, 6, 1532-1539.
    • (2010) Mol. Biosyst. , vol.6 , pp. 1532-1539
    • Kellie, J.F.1    Tran, J.C.2    Lee, J.E.3    Ahlf, D.R.4
  • 50
    • 46849122859 scopus 로고    scopus 로고
    • Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer
    • Collier, T. S., Hawkridge, A. M., Georgianna, D. R., Payne, G. A., Muddiman, D. C., Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal. Chem. 2008, 80, 4994-5001.
    • (2008) Anal. Chem. , vol.80 , pp. 4994-5001
    • Collier, T.S.1    Hawkridge, A.M.2    Georgianna, D.R.3    Payne, G.A.4    Muddiman, D.C.5
  • 51
    • 77954513767 scopus 로고    scopus 로고
    • The pros and cons of peptide-centric proteomics
    • Duncan, M. W., Aebersold, R., Caprioli, R. M., The pros and cons of peptide-centric proteomics. Nat. Biotechnol. 2010, 28, 659-664.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 659-664
    • Duncan, M.W.1    Aebersold, R.2    Caprioli, R.M.3
  • 52
    • 84864805910 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics for systems biology
    • Sabido, E., Selevsek, N., Aebersold, R., Mass spectrometry-based proteomics for systems biology. Curr. Opin. Biotechnol. 2012, 23, 591-597.
    • (2012) Curr. Opin. Biotechnol. , vol.23 , pp. 591-597
    • Sabido, E.1    Selevsek, N.2    Aebersold, R.3
  • 53
    • 37249014081 scopus 로고    scopus 로고
    • The biological impact of mass-spectrometry-based proteomics
    • Cravatt, B. F., Simon, G. M., Yates, J. R., 3rd, The biological impact of mass-spectrometry-based proteomics. Nature 2007, 450, 991-1000.
    • (2007) Nature , vol.450 , pp. 991-1000
    • Cravatt, B.F.1    Simon, G.M.2    Yates III, J.R.3
  • 54
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 55
    • 0015456112 scopus 로고
    • High accuracy determination of calcium in blood serum by isotope dilution mass spectrometry
    • Moore, L. J., Machlan, L. A., High accuracy determination of calcium in blood serum by isotope dilution mass spectrometry. Anal. Chem. 1972, 44, 2291-2296.
    • (1972) Anal. Chem. , vol.44 , pp. 2291-2296
    • Moore, L.J.1    Machlan, L.A.2
  • 57
    • 64749108158 scopus 로고    scopus 로고
    • Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
    • Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., Heck, A. J., Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 2009, 4, 484-494.
    • (2009) Nat. Protoc. , vol.4 , pp. 484-494
    • Boersema, P.J.1    Raijmakers, R.2    Lemeer, S.3    Mohammed, S.4    Heck, A.J.5
  • 58
    • 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. 2005, 1, 252-262.
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 59
    • 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. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4
  • 60
    • 0036428393 scopus 로고    scopus 로고
    • Amino acid residue specific stable isotope labeling for quantitative proteomics
    • Zhu, H., Pan, S., Gu, S., Bradbury, E. M., Chen, X., Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 2002, 16, 2115-2123.
    • (2002) Rapid Commun. Mass Spectrom. , vol.16 , pp. 2115-2123
    • Zhu, H.1    Pan, S.2    Gu, S.3    Bradbury, E.M.4    Chen, X.5
  • 61
    • 44649164495 scopus 로고    scopus 로고
    • Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques
    • Dreisbach, A., Otto, A., Becher, D., Hammer, E. et al., Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques. Proteomics 2008, 8, 2062-2076.
    • (2008) Proteomics , vol.8 , pp. 2062-2076
    • Dreisbach, A.1    Otto, A.2    Becher, D.3    Hammer, E.4
  • 62
    • 76649083593 scopus 로고    scopus 로고
    • Quantitative proteomics by metabolic labeling of model organisms
    • Gouw, J. W., Krijgsveld, J., Heck, A. J., Quantitative proteomics by metabolic labeling of model organisms. Mol. Cell. Proteomics 2010, 9, 11-24.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 11-24
    • Gouw, J.W.1    Krijgsveld, J.2    Heck, A.J.3
  • 63
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L. et al., Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1254.
    • (2008) Nature , vol.455 , pp. 1251-1254
    • de Godoy, L.M.1    Olsen, J.V.2    Cox, J.3    Nielsen, M.L.4
  • 64
    • 0036164157 scopus 로고    scopus 로고
    • Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level
    • Martinović, S., Veenstra, T. D., Anderson, G. A., Paša-Tolić, L., Smith, R. D., Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J. Mass Spectrom. 2002, 37, 99-107.
    • (2002) J. Mass Spectrom. , vol.37 , pp. 99-107
    • Martinović, S.1    Veenstra, T.D.2    Anderson, G.A.3    Paša-Tolić, L.4    Smith, R.D.5
  • 65
    • 0042432365 scopus 로고    scopus 로고
    • High throughput proteome-wide precision measurements of protein expression using mass spectrometry
    • Pasa-Tolic, L., Jensen, P. K., Anderson, G. A., Lipton, M. S. et al., High throughput proteome-wide precision measurements of protein expression using mass spectrometry. J. Am. Chem. Soc. 1999, 121, 7949-7950.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 7949-7950
    • Pasa-Tolic, L.1    Jensen, P.K.2    Anderson, G.A.3    Lipton, M.S.4
  • 66
    • 0037112472 scopus 로고    scopus 로고
    • Use of deuterium-labeled lysine for efficient protein identification and peptide de novo sequencing
    • Gu, S., Pan, S., Bradbury, E. M., Chen, X., Use of deuterium-labeled lysine for efficient protein identification and peptide de novo sequencing. Anal. Chem. 2002, 74, 5774-5785.
    • (2002) Anal. Chem. , vol.74 , pp. 5774-5785
    • Gu, S.1    Pan, S.2    Bradbury, E.M.3    Chen, X.4
  • 67
    • 0036534547 scopus 로고    scopus 로고
    • Using stable-isotope-labeled proteins for hydrogen exchange studies in complex mixtures
    • Engen, J. R., Bradbury, E. M., Chen, X., Using stable-isotope-labeled proteins for hydrogen exchange studies in complex mixtures. Anal. Chem. 2002, 74, 1680-1686.
    • (2002) Anal. Chem. , vol.74 , pp. 1680-1686
    • Engen, J.R.1    Bradbury, E.M.2    Chen, X.3
  • 69
    • 0036164157 scopus 로고    scopus 로고
    • Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level
    • Martinovic, S., Veenstra, T. D., Anderson, G. A., Pasa-Tolic, L., Smith, R. D., Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J. Mass Spectrom. 2002, 37, 99-107.
    • (2002) J. Mass Spectrom. , vol.37 , pp. 99-107
    • Martinovic, S.1    Veenstra, T.D.2    Anderson, G.A.3    Pasa-Tolic, L.4    Smith, R.D.5
  • 70
    • 0034654593 scopus 로고    scopus 로고
    • Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification
    • Chen, X., Smith, L. M., Bradbury, E. M., Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Anal. Chem. 2000, 72, 1134-1143.
    • (2000) Anal. Chem. , vol.72 , pp. 1134-1143
    • Chen, X.1    Smith, L.M.2    Bradbury, E.M.3
  • 71
    • 77954371891 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis
    • Soufi, B., Kumar, C., Gnad, F., Mann, M. et al., Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis. J. Proteome Res. 2010, 9, 3638-3646.
    • (2010) J. Proteome Res. , vol.9 , pp. 3638-3646
    • Soufi, B.1    Kumar, C.2    Gnad, F.3    Mann, M.4
  • 72
    • 84885648123 scopus 로고    scopus 로고
    • Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics
    • Tzouros, M., Golling, S., Avila, D., Lamerz, J. et al., Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics. Mol. Cell. Proteomics 2013, 12, 3339-3349.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3339-3349
    • Tzouros, M.1    Golling, S.2    Avila, D.3    Lamerz, J.4
  • 73
    • 33845329203 scopus 로고    scopus 로고
    • Functional and quantitative proteomics using SILAC
    • Mann, M., Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 2006, 7, 952-958.
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 952-958
    • Mann, M.1
  • 74
    • 52649125713 scopus 로고    scopus 로고
    • The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins
    • Soufi, B., Gnad, F., Jensen, P. R., Petranovic, D. et al., The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins. Proteomics 2008, 8, 3486-3493.
    • (2008) Proteomics , vol.8 , pp. 3486-3493
    • Soufi, B.1    Gnad, F.2    Jensen, P.R.3    Petranovic, D.4
  • 75
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4
  • 76
    • 0012351964 scopus 로고    scopus 로고
    • 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC)
    • 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2003, 2, 173-181.
    • (2003) J. Proteome Res. , vol.2 , pp. 173-181
    • Ong, S.E.1    Kratchmarova, I.2    Mann, M.3
  • 77
    • 79958227262 scopus 로고    scopus 로고
    • Analyses of soluble and membrane proteomes of Ralstonia eutropha H16 reveal major changes in the protein complement in adaptation to lithoautotrophy
    • Kohlmann, Y., Pohlmann, A., Otto, A., Becher, D. et al., Analyses of soluble and membrane proteomes of Ralstonia eutropha H16 reveal major changes in the protein complement in adaptation to lithoautotrophy. J. Proteome Res. 2011, 10, 2767-2776.
    • (2011) J. Proteome Res. , vol.10 , pp. 2767-2776
    • Kohlmann, Y.1    Pohlmann, A.2    Otto, A.3    Becher, D.4
  • 78
    • 77956555964 scopus 로고    scopus 로고
    • Differential effect of YidC depletion on the membrane proteome of Escherichia coli under aerobic and anaerobic growth conditions
    • Price, C. E., Otto, A., Fusetti, F., Becher, D. et al., Differential effect of YidC depletion on the membrane proteome of Escherichia coli under aerobic and anaerobic growth conditions. Proteomics 2010, 10, 3235-3247.
    • (2010) Proteomics , vol.10 , pp. 3235-3247
    • Price, C.E.1    Otto, A.2    Fusetti, F.3    Becher, D.4
  • 79
    • 0346122950 scopus 로고    scopus 로고
    • A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
    • MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., Yates, J. R., 3rd, A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 2003, 75, 6912-6921.
    • (2003) Anal. Chem. , vol.75 , pp. 6912-6921
    • MacCoss, M.J.1    Wu, C.C.2    Liu, H.3    Sadygov, R.4    Yates III, J.R.5
  • 80
    • 84868117448 scopus 로고    scopus 로고
    • The 15N isotope effect in Escherichia coli: a neutron can make the difference
    • Filiou, M. D., Varadarajulu, J., Teplytska, L., Reckow, S. et al., The 15N isotope effect in Escherichia coli: a neutron can make the difference. Proteomics 2012, 12, 3121-3128.
    • (2012) Proteomics , vol.12 , pp. 3121-3128
    • Filiou, M.D.1    Varadarajulu, J.2    Teplytska, L.3    Reckow, S.4
  • 81
    • 0029365773 scopus 로고
    • Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis
    • Kigawa, T., Muto, Y., Yokoyama, S., Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis. J. Biomol. NMR 1995, 6, 129-134.
    • (1995) J. Biomol. NMR , vol.6 , pp. 129-134
    • Kigawa, T.1    Muto, Y.2    Yokoyama, S.3
  • 82
    • 20844442252 scopus 로고    scopus 로고
    • Quantitation of de novo localized (15)N-labeled lipoproteins and membrane proteins having one and two transmembrane segments in a Bacillus subtilis secA temperature-sensitive mutant using 2D-PAGE and MALDI-TOF MS
    • Bunai, K., Nozaki, M., Kakeshita, H., Nemoto, T., Yamane, K., Quantitation of de novo localized (15)N-labeled lipoproteins and membrane proteins having one and two transmembrane segments in a Bacillus subtilis secA temperature-sensitive mutant using 2D-PAGE and MALDI-TOF MS. J. Proteome Res. 2005, 4, 826-836.
    • (2005) J. Proteome Res. , vol.4 , pp. 826-836
    • Bunai, K.1    Nozaki, M.2    Kakeshita, H.3    Nemoto, T.4    Yamane, K.5
  • 83
    • 84885466975 scopus 로고    scopus 로고
    • Comparative proteome analysis of spontaneous outer membrane vesicles and purified outer membranes of Neisseria meningitidis
    • Lappann, M., Otto, A., Becher, D., Vogel, U., Comparative proteome analysis of spontaneous outer membrane vesicles and purified outer membranes of Neisseria meningitidis. J. Bacteriol. 2013, 195, 4425-4435.
    • (2013) J. Bacteriol. , vol.195 , pp. 4425-4435
    • Lappann, M.1    Otto, A.2    Becher, D.3    Vogel, U.4
  • 84
    • 79952248038 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: comparison of growing- and energy-starved cells
    • Pellitteri-Hahn, M. C., Halligan, B. D., Scalf, M., Smith, L., Hickey, W. J., Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: comparison of growing- and energy-starved cells. J. Proteomics 2011, 74, 411-419.
    • (2011) J. Proteomics , vol.74 , pp. 411-419
    • Pellitteri-Hahn, M.C.1    Halligan, B.D.2    Scalf, M.3    Smith, L.4    Hickey, W.J.5
  • 86
    • 84860426985 scopus 로고    scopus 로고
    • Global proteome survey of protocatechuate-and glucose-grown Corynebacterium glutamicum reveals multiple physiological differences
    • Haußmann, U., Poetsch, A., Global proteome survey of protocatechuate-and glucose-grown Corynebacterium glutamicum reveals multiple physiological differences. J. Proteomics 2012, 75, 2649-2659.
    • (2012) J. Proteomics , vol.75 , pp. 2649-2659
    • Haußmann, U.1    Poetsch, A.2
  • 87
    • 50249172221 scopus 로고    scopus 로고
    • Complementary analysis of the vegetative membrane proteome of the human pathogen Staphylococcus aureus
    • Wolff, S., Hahne, H., Hecker, M., Becher, D., Complementary analysis of the vegetative membrane proteome of the human pathogen Staphylococcus aureus. Mol. Cell. Proteomics 2008, 7, 1460-1468.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1460-1468
    • Wolff, S.1    Hahne, H.2    Hecker, M.3    Becher, D.4
  • 88
    • 84856070845 scopus 로고    scopus 로고
    • 15N metabolically labeled bacteriophage amplification coupled with a multiple reaction monitoring proteomic workflow
    • doi:10.1074/mcp.M111.012849.
    • 15N metabolically labeled bacteriophage amplification coupled with a multiple reaction monitoring proteomic workflow. Mol. Cell. Proteomics 2012, 11, doi:10.1074/mcp.M111.012849.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Pierce, C.L.1    Rees, J.C.2    Fernández, F.M.3    Barr, J.R.4
  • 89
    • 84884671955 scopus 로고    scopus 로고
    • Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology
    • von Bergen, M., Jehmlich, N., Taubert, M., Vogt, C. et al., Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J. 2013, 10, 1877-1885.
    • (2013) ISME J. , vol.10 , pp. 1877-1885
    • von Bergen, M.1    Jehmlich, N.2    Taubert, M.3    Vogt, C.4
  • 90
    • 84867574489 scopus 로고    scopus 로고
    • Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
    • Seifert, J., Taubert, M., Jehmlich, N., Schmidt, F. et al., Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom. Rev. 2012, 31, 683-697.
    • (2012) Mass Spectrom. Rev. , vol.31 , pp. 683-697
    • Seifert, J.1    Taubert, M.2    Jehmlich, N.3    Schmidt, F.4
  • 91
    • 60749119754 scopus 로고    scopus 로고
    • Systems biology functional analysis of natural microbial consortia using community proteomics
    • VerBerkmoes, N. C., Denef, V. J., Hettich, R. L., Banfield, J. F., Systems biology functional analysis of natural microbial consortia using community proteomics. Nat. Rev. Microbiol. 2009, 7, 196-205.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 196-205
    • VerBerkmoes, N.C.1    Denef, V.J.2    Hettich, R.L.3    Banfield, J.F.4
  • 92
    • 19144372182 scopus 로고    scopus 로고
    • Stable isotope probing-linking microbial identity to function
    • Dumont, M. G., Murrell, J. C., Stable isotope probing-linking microbial identity to function. Nat. Rev. Microbiol. 2005, 3, 499-504.
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 499-504
    • Dumont, M.G.1    Murrell, J.C.2
  • 94
    • 29144431588 scopus 로고    scopus 로고
    • Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics
    • Snijders, A. P., de Koning, B., Wright, P. C., Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics. J. Proteome Res. 2005, 4, 2185-2191.
    • (2005) J. Proteome Res. , vol.4 , pp. 2185-2191
    • Snijders, A.P.1    de Koning, B.2    Wright, P.C.3
  • 95
    • 79959576957 scopus 로고    scopus 로고
    • Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions
    • Belnap, C. P., Pan, C., Denef, V. J., Samatova, N. F. et al., Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J. 2011, 5, 1152-1161.
    • (2011) ISME J. , vol.5 , pp. 1152-1161
    • Belnap, C.P.1    Pan, C.2    Denef, V.J.3    Samatova, N.F.4
  • 96
    • 79953305843 scopus 로고    scopus 로고
    • Quantitative tracking of isotope flows in proteomes of microbial communities
    • Pan, C., Fischer, C. R., Hyatt, D., Bowen, B. P. et al., Quantitative tracking of isotope flows in proteomes of microbial communities. Mol. Cell. Proteomics 2011, 10, M110 006049.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Pan, C.1    Fischer, C.R.2    Hyatt, D.3    Bowen, B.P.4
  • 97
    • 55549089274 scopus 로고    scopus 로고
    • Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures
    • Jehmlich, N., Schmidt, F., von Bergen, M., Richnow, H. H., Vogt, C., Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2008, 2, 1122-1133.
    • (2008) ISME J. , vol.2 , pp. 1122-1133
    • Jehmlich, N.1    Schmidt, F.2    von Bergen, M.3    Richnow, H.H.4    Vogt, C.5
  • 98
    • 84855451689 scopus 로고    scopus 로고
    • Sulfur-36S stable isotope labeling of amino acids for quantification (SULAQ)
    • Jehmlich, N., Kopinke, F. D., Lenhard, S., Vogt, C. et al., Sulfur-36S stable isotope labeling of amino acids for quantification (SULAQ). Proteomics 2012, 12, 37-42.
    • (2012) Proteomics , vol.12 , pp. 37-42
    • Jehmlich, N.1    Kopinke, F.D.2    Lenhard, S.3    Vogt, C.4
  • 99
    • 84881102933 scopus 로고    scopus 로고
    • Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation
    • Herbst, F. A., Taubert, M., Jehmlich, N., Behr, T. et al., Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation. Mol. Cell. Proteomics 2013, 8, 2060-2069.
    • (2013) Mol. Cell. Proteomics , vol.8 , pp. 2060-2069
    • Herbst, F.A.1    Taubert, M.2    Jehmlich, N.3    Behr, T.4
  • 100
    • 84865576726 scopus 로고    scopus 로고
    • Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
    • Bantscheff, M., Lemeer, S., Savitski, M. M., Küster, B., Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 2012, 404, 939-965.
    • (2012) Anal. Bioanal. Chem. , vol.404 , pp. 939-965
    • Bantscheff, M.1    Lemeer, S.2    Savitski, M.M.3    Küster, B.4
  • 101
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
    • (1999) Nat. Biotechnol. , vol.17 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4
  • 102
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • Gygi, S. P., Rochon, Y., Franza, B. R., Aebersold, R., Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19, 1720-1730.
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 103
    • 33847174067 scopus 로고    scopus 로고
    • Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research
    • Wiese, S., Reidegeld, K. A., Meyer, H. E., Warscheid, B., Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 2007, 7, 340-350.
    • (2007) Proteomics , vol.7 , pp. 340-350
    • Wiese, S.1    Reidegeld, K.A.2    Meyer, H.E.3    Warscheid, B.4
  • 104
    • 0038371369 scopus 로고    scopus 로고
    • Quantitative chemical proteomics for identifying candidate drug targets
    • Oda, Y., Owa, T., Sato, T., Boucher, B. et al., Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 2003, 75, 2159-2165.
    • (2003) Anal. Chem. , vol.75 , pp. 2159-2165
    • Oda, Y.1    Owa, T.2    Sato, T.3    Boucher, B.4
  • 106
    • 1042284932 scopus 로고    scopus 로고
    • Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response
    • Li, J., Steen, H., Gygi, S. P., Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol. Cell. Proteomics 2003, 2, 1198-1204.
    • (2003) Mol. Cell. Proteomics , vol.2 , pp. 1198-1204
    • Li, J.1    Steen, H.2    Gygi, S.P.3
  • 107
    • 2542574741 scopus 로고    scopus 로고
    • Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology
    • Schmidt, F., Donahoe, S., Hagens, K., Mattow, J. et al., Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol. Cell. Proteomics 2004, 3, 24-42.
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 24-42
    • Schmidt, F.1    Donahoe, S.2    Hagens, K.3    Mattow, J.4
  • 108
    • 33750080170 scopus 로고    scopus 로고
    • ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis
    • Cho, S. H., Goodlett, D., Franzblau, S., ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis. Tuberculosis 2006, 86, 445-460.
    • (2006) Tuberculosis , vol.86 , pp. 445-460
    • Cho, S.H.1    Goodlett, D.2    Franzblau, S.3
  • 109
    • 0037069421 scopus 로고    scopus 로고
    • Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach
    • Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C. et al., Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. USA 2002, 99, 14913-14918.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14913-14918
    • Baliga, N.S.1    Pan, M.2    Goo, Y.A.3    Yi, E.C.4
  • 110
    • 10044245551 scopus 로고    scopus 로고
    • Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry
    • Goodchild, A., Raftery, M., Saunders, N. F., Guilhaus, M., Cavicchioli, R., Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2004, 3, 1164-1176.
    • (2004) J. Proteome Res. , vol.3 , pp. 1164-1176
    • Goodchild, A.1    Raftery, M.2    Saunders, N.F.3    Guilhaus, M.4    Cavicchioli, R.5
  • 111
    • 0037418318 scopus 로고    scopus 로고
    • Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways
    • Guina, T., Purvine, S. O., Yi, E. C., Eng, J. et al., Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proc. Natl. Acad. Sci. USA 2003, 100, 2771-2776.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 2771-2776
    • Guina, T.1    Purvine, S.O.2    Yi, E.C.3    Eng, J.4
  • 112
    • 17044432706 scopus 로고    scopus 로고
    • Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling
    • Molloy, M. P., Donohoe, S., Brzezinski, E. E., Kilby, G. W. et al., Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics 2005, 5, 1204-1208.
    • (2005) Proteomics , vol.5 , pp. 1204-1208
    • Molloy, M.P.1    Donohoe, S.2    Brzezinski, E.E.3    Kilby, G.W.4
  • 113
    • 46149125288 scopus 로고    scopus 로고
    • Quantifying changes in the thiol redox proteome upon oxidative stress in vivo
    • Leichert, L. I., Gehrke, F., Gudiseva, H. V., Blackwell, T. et al., Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc. Natl. Acad. Sci. USA 2008, 105, 8197-8202.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 8197-8202
    • Leichert, L.I.1    Gehrke, F.2    Gudiseva, H.V.3    Blackwell, T.4
  • 114
    • 82355181555 scopus 로고    scopus 로고
    • Using quantitative redox proteomics to dissect the yeast redoxome
    • Brandes, N., Reichmann, D., Tienson, H., Leichert, L. I., Jakob, U., Using quantitative redox proteomics to dissect the yeast redoxome. J. Biol. Chem. 2011, 286, 41893-41903.
    • (2011) J. Biol. Chem. , vol.286 , pp. 41893-41903
    • Brandes, N.1    Reichmann, D.2    Tienson, H.3    Leichert, L.I.4    Jakob, U.5
  • 116
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L., Huang, Y. L. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.L.N.2    Marchese, J.N.3    Williamson, B.4
  • 117
    • 12444345515 scopus 로고    scopus 로고
    • Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
    • Thompson, A., Schafer, J., Kuhn, K., Kienle, S. et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895-1904.
    • (2003) Anal. Chem. , vol.75 , pp. 1895-1904
    • Thompson, A.1    Schafer, J.2    Kuhn, K.3    Kienle, S.4
  • 118
    • 84865454296 scopus 로고    scopus 로고
    • High-resolution enabled TMT 8-plexing
    • Werner, T., Becher, I., Sweetman, G., Doce, C. et al., High-resolution enabled TMT 8-plexing. Anal. Chem. 2012, 84, 7188-7194.
    • (2012) Anal. Chem. , vol.84 , pp. 7188-7194
    • Werner, T.1    Becher, I.2    Sweetman, G.3    Doce, C.4
  • 119
    • 33746295997 scopus 로고    scopus 로고
    • Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study
    • Wolff, S., Otto, A., Albrecht, D., Zeng, J. S. et al., Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study. Mol. Cell. Proteomics 2006, 5, 1183-1192.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 1183-1192
    • Wolff, S.1    Otto, A.2    Albrecht, D.3    Zeng, J.S.4
  • 120
    • 84876700652 scopus 로고    scopus 로고
    • Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome
    • Adav, S. S., Chao, L. T., Sze, S. K., Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome. J. Proteomics 2013, 83, 180-196.
    • (2013) J. Proteomics , vol.83 , pp. 180-196
    • Adav, S.S.1    Chao, L.T.2    Sze, S.K.3
  • 121
    • 77955445449 scopus 로고    scopus 로고
    • Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes
    • Adav, S. S., Li, A. A., Manavalan, A., Punt, P., Sze, S. K., Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes. J. Proteome Res. 2010, 9, 3932-3940.
    • (2010) J. Proteome Res. , vol.9 , pp. 3932-3940
    • Adav, S.S.1    Li, A.A.2    Manavalan, A.3    Punt, P.4    Sze, S.K.5
  • 123
    • 76149128021 scopus 로고    scopus 로고
    • Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part II: the effect of different methylated growth substrates
    • Williams, T. J., Burg, D. W., Ertan, H., Raftery, M. J. et al., Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part II: the effect of different methylated growth substrates. J. Proteome Res. 2010, 9, 653-663.
    • (2010) J. Proteome Res. , vol.9 , pp. 653-663
    • Williams, T.J.1    Burg, D.W.2    Ertan, H.3    Raftery, M.J.4
  • 124
    • 76149124222 scopus 로고    scopus 로고
    • Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part I: the effect of growth temperature
    • Williams, T. J., Burg, D. W., Raftery, M. J., Poljak, A. et al., Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part I: the effect of growth temperature. J. Proteome Res. 2010, 9, 640-652.
    • (2010) J. Proteome Res. , vol.9 , pp. 640-652
    • Williams, T.J.1    Burg, D.W.2    Raftery, M.J.3    Poljak, A.4
  • 125
    • 17444384908 scopus 로고    scopus 로고
    • Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT
    • Goodchild, A., Raftery, M., Saunders, N. F., Guilhaus, M., Cavicchioli, R., Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT. J. Proteome Res. 2005, 4, 473-480.
    • (2005) J. Proteome Res. , vol.4 , pp. 473-480
    • Goodchild, A.1    Raftery, M.2    Saunders, N.F.3    Guilhaus, M.4    Cavicchioli, R.5
  • 126
    • 65349188082 scopus 로고    scopus 로고
    • Identification of proteins of Neisseria meningitidis induced under iron-limiting conditions using the isobaric tandem mass tag (TMT) labeling approach
    • van Ulsen, P., Kuhn, K., Prinz, T., Legner, H. et al., Identification of proteins of Neisseria meningitidis induced under iron-limiting conditions using the isobaric tandem mass tag (TMT) labeling approach. Proteomics 2009, 9, 1771-1781.
    • (2009) Proteomics , vol.9 , pp. 1771-1781
    • van Ulsen, P.1    Kuhn, K.2    Prinz, T.3    Legner, H.4
  • 127
    • 38049042725 scopus 로고    scopus 로고
    • Comparative proteomics analyses reveal a potential biomarker for the detection of vancomycin-intermediate Staphylococcus aureus strains
    • Drummelsmith, J., Winstall, E., Bergeron, M. G., Poirier, G. G., Ouellette, M., Comparative proteomics analyses reveal a potential biomarker for the detection of vancomycin-intermediate Staphylococcus aureus strains. J. Proteome Res. 2007, 6, 4690-4702.
    • (2007) J. Proteome Res. , vol.6 , pp. 4690-4702
    • Drummelsmith, J.1    Winstall, E.2    Bergeron, M.G.3    Poirier, G.G.4    Ouellette, M.5
  • 128
    • 84855978197 scopus 로고    scopus 로고
    • The impact of CodY on virulence determinant production in community-associated methicillin-resistant Staphylococcus aureus
    • Rivera, F. E., Miller, H. K., Kolar, S. L., Stevens, S. M., Jr., Shaw, L. N., The impact of CodY on virulence determinant production in community-associated methicillin-resistant Staphylococcus aureus. Proteomics 2012, 12, 263-268.
    • (2012) Proteomics , vol.12 , pp. 263-268
    • Rivera, F.E.1    Miller, H.K.2    Kolar, S.L.3    Stevens Jr, S.M.4    Shaw, L.N.5
  • 129
    • 52649098504 scopus 로고    scopus 로고
    • Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer
    • Bantscheff, M., Boesche, M., Eberhard, D., Matthieson, T. et al., Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol. Cell. Proteomics 2008, 7, 1702-1713.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1702-1713
    • Bantscheff, M.1    Boesche, M.2    Eberhard, D.3    Matthieson, T.4
  • 130
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4
  • 131
    • 33748319353 scopus 로고    scopus 로고
    • Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
    • Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K. et al., Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 2006, 5, 2339-2347.
    • (2006) J. Proteome Res. , vol.5 , pp. 2339-2347
    • Zybailov, B.1    Mosley, A.L.2    Sardiu, M.E.3    Coleman, M.K.4
  • 132
    • 0036674269 scopus 로고    scopus 로고
    • Large-scale proteomic analysis of the human spliceosome
    • Rappsilber, J., Ryder, U., Lamond, A. I., Mann, M., Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002, 12, 1231-1245.
    • (2002) Genome Res. , vol.12 , pp. 1231-1245
    • Rappsilber, J.1    Ryder, U.2    Lamond, A.I.3    Mann, M.4
  • 133
    • 60649101258 scopus 로고    scopus 로고
    • The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results
    • Braisted, J. C., Kuntumalla, S., Vogel, C., Marcotte, E. M. et al., The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 2008, 9, 529.
    • (2008) BMC Bioinformatics , vol.9 , pp. 529
    • Braisted, J.C.1    Kuntumalla, S.2    Vogel, C.3    Marcotte, E.M.4
  • 134
    • 77958056802 scopus 로고    scopus 로고
    • Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics
    • Collier, T. S., Sarkar, P., Franck, W. L., Rao, B. M. et al., Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics. Anal. Chem. 2010, 82, 8696-8702.
    • (2010) Anal. Chem. , vol.82 , pp. 8696-8702
    • Collier, T.S.1    Sarkar, P.2    Franck, W.L.3    Rao, B.M.4
  • 135
    • 58149299336 scopus 로고    scopus 로고
    • Significance analysis of spectral count data in label-free shotgun proteomics
    • Choi, H., Fermin, D., Nesvizhskii, A. I., Significance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell. Proteomics 2008, 7, 2373-2385.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 2373-2385
    • Choi, H.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 137
    • 77349126360 scopus 로고    scopus 로고
    • Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
    • Denef, V. J., Kalnejais, L. H., Mueller, R. S., Wilmes, P. et al., Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. USA 2010, 107, 2383-2390.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 2383-2390
    • Denef, V.J.1    Kalnejais, L.H.2    Mueller, R.S.3    Wilmes, P.4
  • 138
    • 84877338299 scopus 로고    scopus 로고
    • Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities
    • Hettich, R. L., Pan, C., Chourey, K., Giannone, R. J., Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal. Chem. 2013, 85, 4203-4214.
    • (2013) Anal. Chem. , vol.85 , pp. 4203-4214
    • Hettich, R.L.1    Pan, C.2    Chourey, K.3    Giannone, R.J.4
  • 139
    • 84869476850 scopus 로고    scopus 로고
    • Effects of stoichiometry and temperature perturbations on beech leaf litter decomposition, enzyme activities and protein expression
    • Keiblinger, K. M., Schneider, T., Roschitzki, B., Schmid, E. et al., Effects of stoichiometry and temperature perturbations on beech leaf litter decomposition, enzyme activities and protein expression. Biogeosciences 2012, 9, 4537-4551.
    • (2012) Biogeosciences , vol.9 , pp. 4537-4551
    • Keiblinger, K.M.1    Schneider, T.2    Roschitzki, B.3    Schmid, E.4
  • 140
    • 84865341467 scopus 로고    scopus 로고
    • Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions
    • Schneider, T., Keiblinger, K. M., Schmid, E., Sterflinger-Gleixner, K. et al., Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. ISME J. 2012, 6, 1749-1762.
    • (2012) ISME J. , vol.6 , pp. 1749-1762
    • Schneider, T.1    Keiblinger, K.M.2    Schmid, E.3    Sterflinger-Gleixner, K.4
  • 141
    • 84860488672 scopus 로고    scopus 로고
    • Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom
    • Teeling, H., Fuchs, B. M., Becher, D., Klockow, C. et al., Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 2012, 336, 608-611.
    • (2012) Science , vol.336 , pp. 608-611
    • Teeling, H.1    Fuchs, B.M.2    Becher, D.3    Klockow, C.4
  • 143
    • 79961096901 scopus 로고    scopus 로고
    • Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship
    • Giannone, R. J., Huber, H., Karpinets, T., Heimerl, T. et al., Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship. PLoS One 2011, 6, e22942.
    • (2011) PLoS One , vol.6
    • Giannone, R.J.1    Huber, H.2    Karpinets, T.3    Heimerl, T.4
  • 144
    • 84883295723 scopus 로고    scopus 로고
    • Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome
    • Tanca, A., Biosa, G., Pagnozzi, D., Addis, M. F., Uzzau, S., Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome. Proteomics 2013, 17, 2597-2607.
    • (2013) Proteomics , vol.17 , pp. 2597-2607
    • Tanca, A.1    Biosa, G.2    Pagnozzi, D.3    Addis, M.F.4    Uzzau, S.5
  • 145
    • 79959701373 scopus 로고    scopus 로고
    • Surface shaving as a versatile tool to profile global interactions between human serum proteins and the Staphylococcus aureus cell surface
    • Dreisbach, A., van der Kooi-Pol, M. M., Otto, A., Gronau, K. et al., Surface shaving as a versatile tool to profile global interactions between human serum proteins and the Staphylococcus aureus cell surface. Proteomics 2011, 11, 2921-2930.
    • (2011) Proteomics , vol.11 , pp. 2921-2930
    • Dreisbach, A.1    van der Kooi-Pol, M.M.2    Otto, A.3    Gronau, K.4
  • 146
    • 84863230118 scopus 로고    scopus 로고
    • Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos
    • Li, Z., Adams, R. M., Chourey, K., Hurst, G. B. et al., Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J. Proteome Res. 2012, 11, 1582-1590.
    • (2012) J. Proteome Res. , vol.11 , pp. 1582-1590
    • Li, Z.1    Adams, R.M.2    Chourey, K.3    Hurst, G.B.4
  • 147
    • 74049132731 scopus 로고    scopus 로고
    • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
    • Griffin, N. M., Yu, J., Long, F., Oh, P. et al., Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat. Biotechnol. 2010, 28, 83-89.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 83-89
    • Griffin, N.M.1    Yu, J.2    Long, F.3    Oh, P.4
  • 148
    • 79551500036 scopus 로고    scopus 로고
    • Less label, more free: approaches in label-free quantitative mass spectrometry
    • Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
    • (2011) Proteomics , vol.11 , pp. 535-553
    • Neilson, K.A.1    Ali, N.A.2    Muralidharan, S.3    Mirzaei, M.4
  • 149
    • 84867045160 scopus 로고    scopus 로고
    • Current challenges in software solutions for mass spectrometry-based quantitative proteomics
    • Cappadona, S., Baker, P. R., Cutillas, P. R., Heck, A. J., van Breukelen, B., Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012, 43, 1087-1108.
    • (2012) Amino Acids , vol.43 , pp. 1087-1108
    • Cappadona, S.1    Baker, P.R.2    Cutillas, P.R.3    Heck, A.J.4    van Breukelen, B.5
  • 150
    • 38649095599 scopus 로고    scopus 로고
    • An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
    • Mueller, L. N., Brusniak, M. Y., Mani, D. R., Aebersold, R., An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7, 51-61.
    • (2008) J. Proteome Res. , vol.7 , pp. 51-61
    • Mueller, L.N.1    Brusniak, M.Y.2    Mani, D.R.3    Aebersold, R.4
  • 151
    • 67650351489 scopus 로고    scopus 로고
    • A comparison of labeling and label-free mass spectrometry-based proteomics approaches
    • Patel, V. J., Thalassinos, K., Slade, S. E., Connolly, J. B. et al., A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J. Proteome Res. 2009, 8, 3752-3759.
    • (2009) J. Proteome Res. , vol.8 , pp. 3752-3759
    • Patel, V.J.1    Thalassinos, K.2    Slade, S.E.3    Connolly, J.B.4
  • 152
    • 84875928072 scopus 로고    scopus 로고
    • An automated pipeline for high-throughput label-free quantitative proteomics
    • Weisser, H., Nahnsen, S., Grossmann, J., Nilse, L. et al., An automated pipeline for high-throughput label-free quantitative proteomics. J. Proteome Res. 2013, 12, 1628-1644.
    • (2013) J. Proteome Res. , vol.12 , pp. 1628-1644
    • Weisser, H.1    Nahnsen, S.2    Grossmann, J.3    Nilse, L.4
  • 153
    • 84861860481 scopus 로고    scopus 로고
    • Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis
    • Gillet, L. C., Navarro, P., Tate, S., Rost, H. et al., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 2012, 11, O111 016717.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Rost, H.4
  • 154
    • 79960578471 scopus 로고    scopus 로고
    • Quantification of mRNA and protein and integration with protein turnover in a bacterium
    • Maier, T., Schmidt, A., Guell, M., Kuhner, S. et al., Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol. Syst. Biol. 2011, 7, 511.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 511
    • Maier, T.1    Schmidt, A.2    Guell, M.3    Kuhner, S.4
  • 155
    • 84873338251 scopus 로고    scopus 로고
    • Label-free quantitative proteomics reveals differentially regulated proteins in experimental gingivitis
    • Bostanci, N., Ramberg, P., Wahlander, A., Grossman, J. et al., Label-free quantitative proteomics reveals differentially regulated proteins in experimental gingivitis. J. Proteome Res. 2013, 12, 657-678.
    • (2013) J. Proteome Res. , vol.12 , pp. 657-678
    • Bostanci, N.1    Ramberg, P.2    Wahlander, A.3    Grossman, J.4
  • 156
    • 84878619680 scopus 로고    scopus 로고
    • Photobacterium profundum under pressure: a MS-based label-free quantitative proteomics study
    • Le Bihan, T., Rayner, J., Roy, M. M., Spagnolo, L., Photobacterium profundum under pressure: a MS-based label-free quantitative proteomics study. PLoS One 2013, 8, e60897.
    • (2013) PLoS One , vol.8
    • Le Bihan, T.1    Rayner, J.2    Roy, M.M.3    Spagnolo, L.4
  • 157
    • 82155175628 scopus 로고    scopus 로고
    • Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms
    • Saka, H. A., Thompson, J. W., Chen, Y. S., Kumar, Y. et al., Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms. Mol. Microbiol. 2011, 82, 1185-1203.
    • (2011) Mol. Microbiol. , vol.82 , pp. 1185-1203
    • Saka, H.A.1    Thompson, J.W.2    Chen, Y.S.3    Kumar, Y.4
  • 158
    • 77957730037 scopus 로고    scopus 로고
    • Survival defects of Cryptococcus neoformans mutants exposed to human cerebrospinal fluid result in attenuated virulence in an experimental model of meningitis
    • Lee, A., Toffaletti, D. L., Tenor, J., Soderblom, E. J. et al., Survival defects of Cryptococcus neoformans mutants exposed to human cerebrospinal fluid result in attenuated virulence in an experimental model of meningitis. Infect. Immun. 2010, 78, 4213-4225.
    • (2010) Infect. Immun. , vol.78 , pp. 4213-4225
    • Lee, A.1    Toffaletti, D.L.2    Tenor, J.3    Soderblom, E.J.4
  • 159
    • 79953314476 scopus 로고    scopus 로고
    • Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440
    • Frank, S., Schmidt, F., Klockgether, J., Davenport, C. F. et al., Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440. FEMS Microbiol. Lett. 2011, 318, 47-54.
    • (2011) FEMS Microbiol. Lett. , vol.318 , pp. 47-54
    • Frank, S.1    Schmidt, F.2    Klockgether, J.3    Davenport, C.F.4
  • 160
    • 84857088697 scopus 로고    scopus 로고
    • An exclusion list based label-free proteome quantification approach using an LTQ Orbitrap
    • Muntel, J., Hecker, M., Becher, D., An exclusion list based label-free proteome quantification approach using an LTQ Orbitrap. Rapid Commun. Mass Spectrom. 2012, 26, 701-709.
    • (2012) Rapid Commun. Mass Spectrom. , vol.26 , pp. 701-709
    • Muntel, J.1    Hecker, M.2    Becher, D.3
  • 161
    • 76949097340 scopus 로고    scopus 로고
    • Quantitative proteomics reveals subset-specific viral recognition in dendritic cells
    • Luber, C. A., Cox, J., Lauterbach, H., Fancke, B. et al., Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010, 32, 279-289.
    • (2010) Immunity , vol.32 , pp. 279-289
    • Luber, C.A.1    Cox, J.2    Lauterbach, H.3    Fancke, B.4
  • 162
    • 78751645686 scopus 로고    scopus 로고
    • Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains
    • Målen, H., De Souza, G. A., Pathak, S., Søfteland, T., Wiker, H. G., Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiol. 2011, 11, 18.
    • (2011) BMC Microbiol. , vol.11 , pp. 18
    • Målen, H.1    De Souza, G.A.2    Pathak, S.3    Søfteland, T.4    Wiker, H.G.5
  • 163
    • 84883619568 scopus 로고    scopus 로고
    • Proteomic identification of novel secreted anti-bacterial toxins of the Serratia marcescens type VI secretion system
    • Fritsch, M. J., Trunk, K., Alcoforado Diniz, J., Guo, M. et al., Proteomic identification of novel secreted anti-bacterial toxins of the Serratia marcescens type VI secretion system. Mol. Cell. Proteomics 2013, 10, 2735-2749.
    • (2013) Mol. Cell. Proteomics , vol.10 , pp. 2735-2749
    • Fritsch, M.J.1    Trunk, K.2    Alcoforado Diniz, J.3    Guo, M.4
  • 164
    • 20144388265 scopus 로고    scopus 로고
    • Quantitative proteomic analysis by accurate mass retention time pairs
    • Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
    • (2005) Anal. Chem. , vol.77 , pp. 2187-2200
    • Silva, J.C.1    Denny, R.2    Dorschel, C.A.3    Gorenstein, M.4
  • 166
    • 33645725976 scopus 로고    scopus 로고
    • Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale
    • Silva, J. C., Denny, R., Dorschel, C., Gorenstein, M. V. et al., Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol. Cell. Proteomics 2006, 5, 589-607.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 589-607
    • Silva, J.C.1    Denny, R.2    Dorschel, C.3    Gorenstein, M.V.4
  • 167
    • 84892843325 scopus 로고    scopus 로고
    • Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains
    • doi:10.1016/j.jprot.2013.06.022.
    • Gonzalez-Fernandez, R., Aloria, K., Valero-Galvan, J., Redondo, I. et al., Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains. J. Proteomics 2013, doi:10.1016/j.jprot.2013.06.022.
    • (2013) J. Proteomics
    • Gonzalez-Fernandez, R.1    Aloria, K.2    Valero-Galvan, J.3    Redondo, I.4
  • 168
    • 78651404635 scopus 로고    scopus 로고
    • A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis
    • Pacheco, L. G., Slade, S. E., Seyffert, N., Santos, A. R. et al., A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis. BMC Microbiol. 2011, 11, 12.
    • (2011) BMC Microbiol. , vol.11 , pp. 12
    • Pacheco, L.G.1    Slade, S.E.2    Seyffert, N.3    Santos, A.R.4
  • 170
    • 84873334559 scopus 로고    scopus 로고
    • Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes
    • Fan, Y., Thompson, J. W., Dubois, L. G., Moseley, M. A., Wernegreen, J. J., Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes. J. Proteome Res. 2013, 12, 704-718.
    • (2013) J. Proteome Res. , vol.12 , pp. 704-718
    • Fan, Y.1    Thompson, J.W.2    Dubois, L.G.3    Moseley, M.A.4    Wernegreen, J.J.5
  • 171
    • 84887864604 scopus 로고    scopus 로고
    • Label-free quantitation and mapping of the ErbB2 tumor receptor by multiple protease digestion with data-dependent (MS1) and data-independent (MS2) acquisitions
    • Held, J. M., Schilling, B., D'Souza, A. K., Srinivasan, T. et al., Label-free quantitation and mapping of the ErbB2 tumor receptor by multiple protease digestion with data-dependent (MS1) and data-independent (MS2) acquisitions. Int. J. Proteomics 2013, 2013, 791985.
    • (2013) Int. J. Proteomics , vol.2013 , pp. 791985
    • Held, J.M.1    Schilling, B.2    D'Souza, A.K.3    Srinivasan, T.4
  • 172
    • 68049114653 scopus 로고    scopus 로고
    • Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean
    • Panchaud, A., Scherl, A., Shaffer, S. A., von Haller, P. D. et al., Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal. Chem. 2009, 81, 6481-6488.
    • (2009) Anal. Chem. , vol.81 , pp. 6481-6488
    • Panchaud, A.1    Scherl, A.2    Shaffer, S.A.3    von Haller, P.D.4
  • 173
    • 77957220208 scopus 로고    scopus 로고
    • Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
    • Vizcaino, J. A., Foster, J. M., Martens, L., Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J. Proteomics 2010, 73, 2136-2146.
    • (2010) J. Proteomics , vol.73 , pp. 2136-2146
    • Vizcaino, J.A.1    Foster, J.M.2    Martens, L.3
  • 174
    • 84883169428 scopus 로고    scopus 로고
    • Proteomics data exchange and storage: the need for common standards and public repositories
    • Jimenez, R. C., Vizcaino, J. A., Proteomics data exchange and storage: the need for common standards and public repositories. Methods Mol. Biol. 2013, 1007, 317-333.
    • (2013) Methods Mol. Biol. , vol.1007 , pp. 317-333
    • Jimenez, R.C.1    Vizcaino, J.A.2
  • 175
    • 0142184341 scopus 로고    scopus 로고
    • Global analysis of protein localization in budding yeast
    • Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S. et al., Global analysis of protein localization in budding yeast. Nature 2003, 425, 686-691.
    • (2003) Nature , vol.425 , pp. 686-691
    • Huh, W.K.1    Falvo, J.V.2    Gerke, L.C.3    Carroll, A.S.4
  • 176
    • 38349037650 scopus 로고    scopus 로고
    • Isotope-labeled protein standards: toward absolute quantitative proteomics
    • Brun, V., Dupuis, A., Adrait, A., Marcellin, M. et al., Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell. Proteomics 2007, 6, 2139-2149.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 2139-2149
    • Brun, V.1    Dupuis, A.2    Adrait, A.3    Marcellin, M.4
  • 177
    • 0037795741 scopus 로고    scopus 로고
    • Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
    • Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., Gygi, S. P., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 2003, 100, 6940-6945.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 6940-6945
    • Gerber, S.A.1    Rush, J.2    Stemman, O.3    Kirschner, M.W.4    Gygi, S.P.5
  • 178
    • 16344389629 scopus 로고    scopus 로고
    • Metabolic labeling of proteins for proteomics
    • Beynon, R. J., Pratt, J. M., Metabolic labeling of proteins for proteomics. Mol. Cell. Proteomics 2005, 4, 857-872.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 857-872
    • Beynon, R.J.1    Pratt, J.M.2
  • 179
    • 33847179916 scopus 로고    scopus 로고
    • Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes
    • Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J. et al., Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 2006, 1, 1029-1043.
    • (2006) Nat. Protoc. , vol.1 , pp. 1029-1043
    • Pratt, J.M.1    Simpson, D.M.2    Doherty, M.K.3    Rivers, J.4
  • 180
    • 84883275474 scopus 로고    scopus 로고
    • Critical assessment of proteome-wide label-free absolute abundance estimation strategies
    • Ahrné, E., Molzahn, L., Glatter, T., Schmidt, A., Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 2013, 17, 2567-2578.
    • (2013) Proteomics , vol.17 , pp. 2567-2578
    • Ahrné, E.1    Molzahn, L.2    Glatter, T.3    Schmidt, A.4
  • 181
    • 79953271667 scopus 로고    scopus 로고
    • Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics
    • Maass, S., Sievers, S., Zühlke, D., Kuzinski, J. et al., Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics. Anal. Chem. 2011, 83, 2677-2684.
    • (2011) Anal. Chem. , vol.83 , pp. 2677-2684
    • Maass, S.1    Sievers, S.2    Zühlke, D.3    Kuzinski, J.4
  • 182
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhausser, B., Busse, D., Li, N., Dittmar, G. et al., Global quantification of mammalian gene expression control. Nature 2011, 473, 337-342.
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhausser, B.1    Busse, D.2    Li, N.3    Dittmar, G.4
  • 183
    • 77954660028 scopus 로고    scopus 로고
    • Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods
    • Grossmann, J., Roschitzki, B., Panse, C., Fortes, C. et al., Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods. J. Proteomics 2010, 73, 1740-1746.
    • (2010) J. Proteomics , vol.73 , pp. 1740-1746
    • Grossmann, J.1    Roschitzki, B.2    Panse, C.3    Fortes, C.4
  • 184
    • 84866270468 scopus 로고    scopus 로고
    • A software toolkit and interface for performing stable isotope labeling and Top3 quantification using progenesis LC-MS
    • Qi, D., Brownridge, P., Xia, D., Mackay, K. et al., A software toolkit and interface for performing stable isotope labeling and Top3 quantification using progenesis LC-MS. OMICS 2012, 16, 489-495.
    • (2012) OMICS , vol.16 , pp. 489-495
    • Qi, D.1    Brownridge, P.2    Xia, D.3    Mackay, K.4
  • 185
    • 84866296979 scopus 로고    scopus 로고
    • A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis
    • Gonzalez-Galarza, F. F., Lawless, C., Hubbard, S. J., Fan, J. et al., A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS 2012, 16, 431-442.
    • (2012) OMICS , vol.16 , pp. 431-442
    • Gonzalez-Galarza, F.F.1    Lawless, C.2    Hubbard, S.J.3    Fan, J.4
  • 186
    • 77957990113 scopus 로고    scopus 로고
    • Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
    • Geiger, T., Cox, J., Mann, M., Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell. Proteomics 2010, 9, 2252-2261.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 2252-2261
    • Geiger, T.1    Cox, J.2    Mann, M.3
  • 187
    • 77954464041 scopus 로고    scopus 로고
    • Proteomics: a pragmatic perspective
    • Mallick, P., Küster, B., Proteomics: a pragmatic perspective. Nat. Biotechnol. 2010, 28, 695-709.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 695-709
    • Mallick, P.1    Küster, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.