메뉴 건너뛰기




Volumn 12, Issue 1, 2013, Pages 214-221

Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns

Author keywords

IPS cell; Monolithic silica column; One shot proteomics; Shotgun proteomics

Indexed keywords

PROTEOME; SILICON DIOXIDE;

EID: 84874082380     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300837u     Document Type: Article
Times cited : (50)

References (41)
  • 2
    • 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, 273-99.
    • (2011) Annu. Rev. Biochem. , vol.80 , pp. 273-299
    • Cox, J.1    Mann, M.2
  • 3
    • 33644861546 scopus 로고    scopus 로고
    • Immobilized pH gradient isoelectric focusing as a firstdimension separation in shotgun proteomics
    • Cargile, B. J.; Sevinsky, J. R.; Essader, A. S.; Stephenson, J. L.; Bundy, J. L. Immobilized pH gradient isoelectric focusing as a firstdimension separation in shotgun proteomics. J. Biomol. Tech. 2005, 16 (3), 181-9.
    • (2005) J. Biomol. Tech. , vol.16 , Issue.3 , pp. 181-189
    • Cargile, B.J.1    Sevinsky, J.R.2    Essader, A.S.3    Stephenson, J.L.4    Bundy, J.L.5
  • 4
    • 26444539668 scopus 로고    scopus 로고
    • Orthogonality of separation in two-dimensional liquid chromatography
    • Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of separation in two-dimensional liquid chromatography. Anal. Chem. 2005, 77 (19), 6426-34.
    • (2005) Anal. Chem. , vol.77 , Issue.19 , pp. 6426-6434
    • Gilar, M.1    Olivova, P.2    Daly, A.E.3    Gebler, J.C.4
  • 8
    • 84857938446 scopus 로고    scopus 로고
    • Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    • Geiger, T.; Wehner, A.; Schaab, C.; Cox, J.; Mann, M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell. Proteomics 2012, 11 (3), M111.014050.
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.3
    • Geiger, T.1    Wehner, A.2    Schaab, C.3    Cox, J.4    Mann, M.5
  • 9
    • 70349777613 scopus 로고    scopus 로고
    • Optimizing the peak capacity per unit time in one-dimensional and offline two-dimensional liquid chromatography for the separation of complex peptide samples
    • Eeltink, S.; Dolman, S.; Swart, R.; Ursem, M.; Schoenmakers, P. J. Optimizing the peak capacity per unit time in one-dimensional and offline two-dimensional liquid chromatography for the separation of complex peptide samples. J. Chromatogr., A 2009, 1216 (44), 7368-74.
    • (2009) J. Chromatogr., A , vol.1216 , Issue.44 , pp. 7368-7374
    • Eeltink, S.1    Dolman, S.2    Swart, R.3    Ursem, M.4    Schoenmakers, P.J.5
  • 10
    • 11444269089 scopus 로고    scopus 로고
    • The Use of micrometer-sized particles in ultrahigh pressure liquid chromatography
    • Jerkovich, A. D.; Mellors, J. S.; Jorgenson, J. W. The Use of micrometer-sized particles in ultrahigh pressure liquid chromatography. LC-GC Eur. 2003, 16, 20-23.
    • (2003) LC-GC Eur. , vol.16 , pp. 20-23
    • Jerkovich, A.D.1    Mellors, J.S.2    Jorgenson, J.W.3
  • 11
    • 0033082675 scopus 로고    scopus 로고
    • Ultrahigh-pressure reversed-phase capillary liquid chromatography: Isocratic and gradient elution using columns packed with 1.0-micron particles
    • MacNair, J. E.; Patel, K. D.; Jorgenson, J. W. Ultrahigh-pressure reversed-phase capillary liquid chromatography: isocratic and gradient elution using columns packed with 1.0-micron particles. Anal. Chem. 1999, 71 (3), 700-8.
    • (1999) Anal. Chem. , vol.71 , Issue.3 , pp. 700-708
    • MacNair, J.E.1    Patel, K.D.2    Jorgenson, J.W.3
  • 12
    • 21044443577 scopus 로고    scopus 로고
    • Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics
    • Shen, Y.; Zhang, R.; Moore, R. J.; Kim, J.; Metz, T. O.; Hixson, K. K.; Zhao, R.; Livesay, E. A.; Udseth, H. R.; Smith, R. D. Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics. Anal. Chem. 2005, 77 (10), 3090-100.
    • (2005) Anal. Chem. , vol.77 , Issue.10 , pp. 3090-3100
    • Shen, Y.1    Zhang, R.2    Moore, R.J.3    Kim, J.4    Metz, T.O.5    Hixson, K.K.6    Zhao, R.7    Livesay, E.A.8    Udseth, H.R.9    Smith, R.D.10
  • 15
    • 79953278916 scopus 로고    scopus 로고
    • Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides
    • Ko?cher, T.; Swart, R.; Mechtler, K. Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal. Chem. 2011, 83 (7), 2699-704.
    • (2011) Anal. Chem. , vol.83 , Issue.7 , pp. 2699-2704
    • Kocher, T.1    Swart, R.2    Mechtler, K.3
  • 21
    • 34748882992 scopus 로고    scopus 로고
    • Monolithic columns in high-performance liquid chromatography
    • discussion 100
    • Guiochon, G. Monolithic columns in high-performance liquid chromatography. J. Chromatogr., A 2007, 1168 (1-2), 101-68 discussion 100.
    • (2007) J. Chromatogr., A , vol.1168 , Issue.1-2 , pp. 101-168
    • Guiochon, G.1
  • 22
    • 84857036957 scopus 로고    scopus 로고
    • Comparison of the gradient kinetic performance of silica monolithic capillary columns with columns packed with 3 ?m porous and 2.7 ?m fused-core silica particles
    • Vaast, A.; Broeckhoven, K.; Dolman, S.; Desmet, G.; Eeltink, S. Comparison of the gradient kinetic performance of silica monolithic capillary columns with columns packed with 3 ?m porous and 2.7 ?m fused-core silica particles. J. Chromatogr., A 2012, 1228, 270-5.
    • (2012) J. Chromatogr., A , vol.1228 , pp. 270-275
    • Vaast, A.1    Broeckhoven, K.2    Dolman, S.3    Desmet, G.4    Eeltink, S.5
  • 23
    • 77950420818 scopus 로고    scopus 로고
    • One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale
    • Iwasaki, M.; Miwa, S.; Ikegami, T.; Tomita, M.; Tanaka, N.; Ishihama, Y. One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal. Chem. 2010, 82 (7), 2616-20.
    • (2010) Anal. Chem. , vol.82 , Issue.7 , pp. 2616-2620
    • Iwasaki, M.1    Miwa, S.2    Ikegami, T.3    Tomita, M.4    Tanaka, N.5    Ishihama, Y.6
  • 24
    • 84857059905 scopus 로고    scopus 로고
    • Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity
    • Iwasaki, M.; Sugiyama, N.; Tanaka, N.; Ishihama, Y. Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity. J. Chromatogr., A 2012, 1228, 292-7.
    • (2012) J. Chromatogr., A , vol.1228 , pp. 292-297
    • Iwasaki, M.1    Sugiyama, N.2    Tanaka, N.3    Ishihama, Y.4
  • 25
    • 36248966518 scopus 로고    scopus 로고
    • Induction of pluripotent stem cells from adult human fibroblasts by defined factors
    • Takahashi, K.; Tanabe, K.; Ohnuki, M.; Narita, M.; Ichisaka, T.; Tomoda, K.; Yamanaka, S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007, 131 (5), 861-72.
    • (2007) Cell , vol.131 , Issue.5 , pp. 861-872
    • Takahashi, K.1    Tanabe, K.2    Ohnuki, M.3    Narita, M.4    Ichisaka, T.5    Tomoda, K.6    Yamanaka, S.7
  • 28
    • 82455199147 scopus 로고    scopus 로고
    • Induced pluripotent stem cells-opportunities for disease modelling and drug discovery
    • Grskovic, M.; Javaherian, A.; Strulovici, B.; Daley, G. Q. Induced pluripotent stem cells-opportunities for disease modelling and drug discovery. Nat. Rev. Drug Discovery 2011, 10 (12), 915-29.
    • (2011) Nat. Rev. Drug Discovery , vol.10 , Issue.12 , pp. 915-929
    • Grskovic, M.1    Javaherian, A.2    Strulovici, B.3    Daley, G.Q.4
  • 29
    • 79952846468 scopus 로고    scopus 로고
    • Progress in understanding reprogramming to the induced pluripotent state
    • Plath, K.; Lowry, W. E. Progress in understanding reprogramming to the induced pluripotent state. Nat. Rev. Genet. 2011, 12 (4), 253-65.
    • (2011) Nat. Rev. Genet. , vol.12 , Issue.4 , pp. 253-265
    • Plath, K.1    Lowry, W.E.2
  • 31
    • 82155179339 scopus 로고    scopus 로고
    • The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells
    • Munoz, J.; Low, T. Y.; Kok, Y. J.; Chin, A.; Frese, C. K.; Ding, V.; Choo, A.; Heck, A. J. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol. Syst. Biol. 2011, 7, 550.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 550
    • Munoz, J.1    Low, T.Y.2    Kok, Y.J.3    Chin, A.4    Frese, C.K.5    Ding, V.6    Choo, A.7    Heck, A.J.8
  • 34
    • 80054711609 scopus 로고    scopus 로고
    • Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines
    • Masuda, T.; Sugiyama, N.; Tomita, M.; Ishihama, Y. Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. Anal. Chem. 2011, 83 (20), 7698-703.
    • (2011) Anal. Chem. , vol.83 , Issue.20 , pp. 7698-7703
    • Masuda, T.1    Sugiyama, N.2    Tomita, M.3    Ishihama, Y.4
  • 35
    • 34548183872 scopus 로고    scopus 로고
    • Protocol for micropurification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
    • Rappsilber, J.; Mann, M.; Ishihama, Y. Protocol for micropurification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2007, 2 (8), 1896-906.
    • (2007) Nat. Protoc. , vol.2 , Issue.8 , pp. 1896-1906
    • Rappsilber, J.1    Mann, M.2    Ishihama, Y.3
  • 36
    • 84864302486 scopus 로고    scopus 로고
    • Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics
    • Helmy, M.; Sugiyama, N.; Tomita, M.; Ishihama, Y. Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics. Genes Cells 2012, 17 (8), 633-44.
    • (2012) Genes Cells , vol.17 , Issue.8 , pp. 633-644
    • Helmy, M.1    Sugiyama, N.2    Tomita, M.3    Ishihama, Y.4
  • 37
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • Nesvizhskii, A. I.; Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 2005, 4 (10), 1419-40.
    • (2005) Mol. Cell. Proteomics , vol.4 , Issue.10 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 38
    • 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.; Nagasu, T.; Rappsilber, J.; Mann, M. 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 (9), 1265-72.
    • (2005) Mol. Cell. Proteomics , vol.4 , Issue.9 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 39
    • 77949518999 scopus 로고    scopus 로고
    • EmPAI Calc-for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry
    • Shinoda, K.; Tomita, M.; Ishihama, Y. emPAI Calc-for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics 2010, 26 (4), 576-7.
    • (2010) Bioinformatics , vol.26 , Issue.4 , pp. 576-577
    • Shinoda, K.1    Tomita, M.2    Ishihama, Y.3
  • 41
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, d. W.; Sherman, B. T.; Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4 (1), 44-57.
    • (2009) Nat. Protoc. , vol.4 , Issue.1 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.