메뉴 건너뛰기




Volumn 12, Issue 4, 2013, Pages 1996-2004

Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current

Author keywords

label free; metabolic acidosis; MS MS TIC; quantitative proteomics; spectral counting; spectral TIC; total ion current

Indexed keywords

ION;

EID: 84875915737     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400100k     Document Type: Article
Times cited : (16)

References (36)
  • 1
    • 80054732682 scopus 로고    scopus 로고
    • Quantitative proteomics of complex mixtures
    • Coombs, K. M. Quantitative proteomics of complex mixtures Expert Rev. Proteomics 2011, 8 (5) 659-77
    • (2011) Expert Rev. Proteomics , vol.8 , Issue.5 , pp. 659-677
    • Coombs, K.M.1
  • 2
    • 79251535011 scopus 로고    scopus 로고
    • Quantitative proteomics for investigating psychiatric disorders
    • Filiou, M. D.; Turck, C. W.; Martins-de-Souza, D. Quantitative proteomics for investigating psychiatric disorders Proteomics. Clin. Appl. 2011, 5 (1-2) 38-49
    • (2011) Proteomics. Clin. Appl. , vol.5 , Issue.12 , pp. 38-49
    • Filiou, M.D.1    Turck, C.W.2    Martins-De-Souza, D.3
  • 4
    • 79951518985 scopus 로고    scopus 로고
    • Mining the plasma proteome for disease applications across seven logs of protein abundance
    • Zhang, Q.; Faca, V.; Hanash, S. Mining the plasma proteome for disease applications across seven logs of protein abundance J. Proteome Res. 2011, 10 (1) 46-50
    • (2011) J. Proteome Res. , vol.10 , Issue.1 , pp. 46-50
    • Zhang, Q.1    Faca, V.2    Hanash, S.3
  • 5
    • 37249014081 scopus 로고    scopus 로고
    • The biological impact of mass-spectrometry-based proteomics
    • Cravatt, B. F.; Simon, G. M.; Yates Iii, J. R. The biological impact of mass-spectrometry-based proteomics Nature 2007, 450 (7172) 991-1000
    • (2007) Nature , vol.450 , Issue.7172 , pp. 991-1000
    • Cravatt, B.F.1    Simon, G.M.2    Yates Iii, J.R.3
  • 6
    • 79960396255 scopus 로고    scopus 로고
    • Liquid chromatography-mass spectrometry-based quantitative proteomics
    • Xie, F.; Liu, T.; Qian, W. J.; Petyuk, V. A.; Smith, R. D. Liquid chromatography-mass spectrometry-based quantitative proteomics J.. Biol. Chem. 2011, 286 (29) 25443-9
    • (2011) J. Biol. Chem. , vol.286 , Issue.29 , pp. 25443-25449
    • Xie, F.1    Liu, T.2    Qian, W.J.3    Petyuk, V.A.4    Smith, R.D.5
  • 7
    • 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.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 1999, 17 (10) 994-9
    • (1999) Nat. Biotechnol. , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 8
    • 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.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 2002, 1 (5) 376-86
    • (2002) Mol. Cell. Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 9
    • 12444345515 scopus 로고    scopus 로고
    • Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
    • Thompson, A.; Schäfer, J.; Kuhn, K.; Kienle, S.; Schwarz, J.; Schmidt, G.; Neumann, T.; Hamon, C. Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Anal. Chem. 2003, 75 (8) 1895-1904
    • (2003) Anal. Chem. , vol.75 , Issue.8 , pp. 1895-1904
    • Thompson, A.1    Schäfer, J.2    Kuhn, K.3    Kienle, S.4    Schwarz, J.5    Schmidt, G.6    Neumann, T.7    Hamon, C.8
  • 11
    • 44049105535 scopus 로고    scopus 로고
    • Experimental and computational approaches to quantitative proteomics: Status quo and outlook
    • Panchaud, A.; Affolter, M.; Moreillon, P.; Kussmann, M. Experimental and computational approaches to quantitative proteomics: status quo and outlook J. Proteomics 2008, 71 (1) 19-33
    • (2008) J. Proteomics , vol.71 , Issue.1 , pp. 19-33
    • Panchaud, A.1    Affolter, M.2    Moreillon, P.3    Kussmann, M.4
  • 12
    • 84864134293 scopus 로고    scopus 로고
    • Quantitative mass spectrometry-based proteomics: An overview
    • Nikolov, M.; Schmidt, C.; Urlaub, H. Quantitative mass spectrometry-based proteomics: An overview Methods Mol. Biol. 2012, 893, 85-100
    • (2012) Methods Mol. Biol. , vol.893 , pp. 85-100
    • Nikolov, M.1    Schmidt, C.2    Urlaub, H.3
  • 14
    • 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., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76 (14) 4193-201
    • (2004) Anal. Chem. , vol.76 , Issue.14 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates III, J.R.3
  • 16
    • 74049115774 scopus 로고    scopus 로고
    • Mass spectrometry-based label-free quantitative proteomics
    • Zhu, W.; Smith, J. W.; Huang, C. M. Mass spectrometry-based label-free quantitative proteomics J. Biomed. Biotechnol. 2010, 2010, 840518
    • (2010) J. Biomed. Biotechnol. , vol.2010 , pp. 840518
    • Zhu, W.1    Smith, J.W.2    Huang, C.M.3
  • 17
    • 34250722602 scopus 로고    scopus 로고
    • Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
    • Wolf-Yadlin, A.; Hautaniemi, S.; Lauffenburger, D. A.; White, F. M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (14) 5860-5
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , Issue.14 , pp. 5860-5865
    • Wolf-Yadlin, A.1    Hautaniemi, S.2    Lauffenburger, D.A.3    White, F.M.4
  • 18
    • 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.; Shore, S.; Li, Y.; Koziol, J. A.; Schnitzer, J. E. Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis Nat. Biotechnol. 2010, 28 (1) 83-89
    • (2010) Nat. Biotechnol. , vol.28 , Issue.1 , pp. 83-89
    • Griffin, N.M.1    Yu, J.2    Long, F.3    Oh, P.4    Shore, S.5    Li, Y.6    Koziol, J.A.7    Schnitzer, J.E.8
  • 19
    • 41149127192 scopus 로고    scopus 로고
    • A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen
    • Asara, J. M.; Christofk, H. R.; Freimark, L. M.; Cantley, L. C. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen Proteomics 2008, 8 (5) 994-9
    • (2008) Proteomics , vol.8 , Issue.5 , pp. 994-999
    • Asara, J.M.1    Christofk, H.R.2    Freimark, L.M.3    Cantley, L.C.4
  • 20
    • 84862202249 scopus 로고    scopus 로고
    • NSI and NSMT: Usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification
    • Wu, Q.; Zhao, Q.; Liang, Z.; Qu, Y.; Zhang, L.; Zhang, Y. NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification The Analyst 2012, 137 (13) 3146-53
    • (2012) The Analyst , vol.137 , Issue.13 , pp. 3146-3153
    • Wu, Q.1    Zhao, Q.2    Liang, Z.3    Qu, Y.4    Zhang, L.5    Zhang, Y.6
  • 21
    • 84872420006 scopus 로고    scopus 로고
    • Response of the mitochondrial proteome of rat renal proximal convoluted tubules to chronic metabolic acidosis
    • Freund, D. M.; Prenni, J. E.; Curthoys, N. P. Response of the mitochondrial proteome of rat renal proximal convoluted tubules to chronic metabolic acidosis Am. J. Physiol.: Renal Physiol. 2013, 304 (2) F145-55
    • (2013) Am. J. Physiol.: Renal Physiol. , vol.304 , Issue.2 , pp. 145-155
    • Freund, D.M.1    Prenni, J.E.2    Curthoys, N.P.3
  • 22
    • 0027639332 scopus 로고
    • Metabolic aspects of metabolic acidosis
    • Halperin, M. L. Metabolic aspects of metabolic acidosis Clin. Invest. Med. 1993, 16 (4) 294-305
    • (1993) Clin. Invest. Med. , vol.16 , Issue.4 , pp. 294-305
    • Halperin, M.L.1
  • 23
    • 0015918917 scopus 로고
    • The distribution of glutaminase isoenzymes in the various structures of the nephron in normal, acidotic, and alkalotic rat kidney
    • Curthoys, N. P.; Lowry, O. H. The distribution of glutaminase isoenzymes in the various structures of the nephron in normal, acidotic, and alkalotic rat kidney J. Biol. Chem. 1973, 248 (1) 162-8
    • (1973) J. Biol. Chem. , vol.248 , Issue.1 , pp. 162-168
    • Curthoys, N.P.1    Lowry, O.H.2
  • 24
    • 0025650951 scopus 로고
    • Phosphate-dependent glutaminase activity in rat renal cortical and medullary tubule segments
    • Wright, P. A.; Knepper, M. A. Phosphate-dependent glutaminase activity in rat renal cortical and medullary tubule segments Am. J. Physiol. 1990, 259 (6 Pt 2) F961-70
    • (1990) Am. J. Physiol. , vol.259 , Issue.6 PART 2 , pp. 961-970
    • Wright, P.A.1    Knepper, M.A.2
  • 25
    • 0025003679 scopus 로고
    • Glutamate dehydrogenase activities in microdissected rat nephron segments: Effects of acid-base loading
    • Wright, P. A.; Knepper, M. A. Glutamate dehydrogenase activities in microdissected rat nephron segments: effects of acid-base loading Am. J. Physiol. 1990, 259 (1 Pt 2) F53-9
    • (1990) Am. J. Physiol. , vol.259 , Issue.1 PART 2 , pp. 53-59
    • Wright, P.A.1    Knepper, M.A.2
  • 26
    • 33846248808 scopus 로고    scopus 로고
    • Proteomic analysis of the adaptive response of rat renal proximal tubules to metabolic acidosis
    • Curthoys, N. P.; Taylor, L.; Hoffert, J. D.; Knepper, M. A. Proteomic analysis of the adaptive response of rat renal proximal tubules to metabolic acidosis Am. J. Physiol.: Renal Physiol. 2007, 292 (1) F140-7
    • (2007) Am. J. Physiol.: Renal Physiol. , vol.292 , Issue.1 , pp. 140-147
    • Curthoys, N.P.1    Taylor, L.2    Hoffert, J.D.3    Knepper, M.A.4
  • 27
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 1976, 72, 248-54
    • (1976) Anal. Biochem. , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 29
    • 84866124119 scopus 로고    scopus 로고
    • Comparison of one- and two-dimensional liquid chromatography approaches in the label-free quantitative analysis of Methylocella silvestris
    • Patel, N. A.; Crombie, A.; Slade, S. E.; Thalassinos, K.; Hughes, C.; Connolly, J. B.; Langridge, J.; Murrell, J. C.; Scrivens, J. H. Comparison of one- and two-dimensional liquid chromatography approaches in the label-free quantitative analysis of Methylocella silvestris J. Proteome Res. 2012, 11 (9) 4755-63
    • (2012) J. Proteome Res. , vol.11 , Issue.9 , pp. 4755-4763
    • Patel, N.A.1    Crombie, A.2    Slade, S.E.3    Thalassinos, K.4    Hughes, C.5    Connolly, J.B.6    Langridge, J.7    Murrell, J.C.8    Scrivens, J.H.9
  • 30
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74 (20) 5383-92
    • (2002) Anal. Chem. , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 31
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003, 75 (17) 4646-58
    • (2003) Anal. Chem. , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 32
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4 (3) 207-14
    • (2007) Nat. Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 34
  • 35
    • 66749171697 scopus 로고    scopus 로고
    • Statistical design of quantitative mass spectrometry-based proteomic experiments
    • Oberg, A. L.; Vitek, O. Statistical design of quantitative mass spectrometry-based proteomic experiments J. Proteome Res. 2009, 8 (5) 2144-56
    • (2009) J. Proteome Res. , vol.8 , Issue.5 , pp. 2144-2156
    • Oberg, A.L.1    Vitek, O.2
  • 36
    • 42049094894 scopus 로고    scopus 로고
    • Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments
    • Wong, J. W.; Sullivan, M. J.; Cagney, G. Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments Briefings Bioinf. 2008, 9 (2) 156-65
    • (2008) Briefings Bioinf. , vol.9 , Issue.2 , pp. 156-165
    • Wong, J.W.1    Sullivan, M.J.2    Cagney, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.