메뉴 건너뛰기




Volumn 15, Issue 12, 2016, Pages 4722-4730

Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and Its Application to Kidney Tissue Substructures

Author keywords

automated; cortex; high pH fractionation; kidney proteome; label free; medulla; microgram sample amount; modified BCA assay; preconditioning; protein assay; TMT

Indexed keywords

PROTEOME;

EID: 85000786916     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.6b00889     Document Type: Article
Times cited : (38)

References (44)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422 (6928) 198-207 10.1038/nature01511
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 84871297843 scopus 로고    scopus 로고
    • Next-generation proteomics: Towards an integrative view of proteome dynamics
    • Altelaar, A. F. M.; Munoz, J.; Heck, A. J. R. Next-generation proteomics: towards an integrative view of proteome dynamics Nat. Rev. Genet. 2012, 14 (1) 35-48 10.1038/nrg3356
    • (2012) Nat. Rev. Genet. , vol.14 , Issue.1 , pp. 35-48
    • Altelaar, A.F.M.1    Munoz, J.2    Heck, A.J.R.3
  • 3
    • 84937704297 scopus 로고    scopus 로고
    • Classification of Large Cellular Populations and Discovery of Rare Cells Using Single Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
    • Ong, T.-H.; Kissick, D. J.; Jansson, E. T.; Comi, T. J.; Romanova, E. V.; Rubakhin, S. S.; Sweedler, J. V. Classification of Large Cellular Populations and Discovery of Rare Cells Using Single Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Anal. Chem. 2015, 87 (14) 7036-7042 10.1021/acs.analchem.5b01557
    • (2015) Anal. Chem. , vol.87 , Issue.14 , pp. 7036-7042
    • Ong, T.-H.1    Kissick, D.J.2    Jansson, E.T.3    Comi, T.J.4    Romanova, E.V.5    Rubakhin, S.S.6    Sweedler, J.V.7
  • 4
    • 79961226080 scopus 로고    scopus 로고
    • Mohammed, S. Highly Sensitive Proteome Analysis of FACS-Sorted Adult Colon Stem Cells
    • Di Palma, S.; Stange, D.; van de Wetering, M.; Clevers, H.; Heck, A. J. R.; Mohammed, S. Mohammed, S. Highly Sensitive Proteome Analysis of FACS-Sorted Adult Colon Stem Cells J. Proteome Res. 2011, 10 (8) 3814-3819 10.1021/pr200367p
    • (2011) J. Proteome Res. , vol.10 , Issue.8 , pp. 3814-3819
    • Di Palma, S.1    Stange, D.2    Van De Wetering, M.3    Clevers, H.4    Heck, A.J.R.5    Mohammed, S.6
  • 7
    • 79960011243 scopus 로고    scopus 로고
    • High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers
    • Wiśniewski, J. R.; Ostasiewicz, P.; Mann, M. High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers J. Proteome Res. 2011, 10 (7) 3040-3049 10.1021/pr200019m
    • (2011) J. Proteome Res. , vol.10 , Issue.7 , pp. 3040-3049
    • Wiśniewski, J.R.1    Ostasiewicz, P.2    Mann, M.3
  • 8
    • 79959958529 scopus 로고    scopus 로고
    • Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600)
    • Andrews, G. L.; Simons, B. L.; Young, J. B.; Hawkridge, A. M.; Muddiman, D. C. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600) Anal. Chem. 2011, 83 (13) 5442-5446 10.1021/ac200812d
    • (2011) Anal. Chem. , vol.83 , Issue.13 , pp. 5442-5446
    • Andrews, G.L.1    Simons, B.L.2    Young, J.B.3    Hawkridge, A.M.4    Muddiman, D.C.5
  • 10
    • 84915774615 scopus 로고    scopus 로고
    • Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer
    • Kelstrup, C. D.; Jersie-Christensen, R. R.; Batth, T. S.; Arrey, T. N.; Kuehn, A.; Kellmann, M.; Olsen, J. V. Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer J. Proteome Res. 2014, 13 (12) 6187-6195 10.1021/pr500985w
    • (2014) J. Proteome Res. , vol.13 , Issue.12 , pp. 6187-6195
    • Kelstrup, C.D.1    Jersie-Christensen, R.R.2    Batth, T.S.3    Arrey, T.N.4    Kuehn, A.5    Kellmann, M.6    Olsen, J.V.7
  • 14
    • 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
    • Köcher, 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) 2699-2704 10.1021/ac103243t
    • (2011) Anal. Chem. , vol.83 , Issue.7 , pp. 2699-2704
    • Köcher, T.1    Swart, R.2    Mechtler, K.3
  • 16
    • 84874082380 scopus 로고    scopus 로고
    • Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns
    • Yamana, R.; Iwasaki, M.; Wakabayashi, M.; Nakagawa, M.; Yamanaka, S.; Ishihama, Y. Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns J. Proteome Res. 2013, 12 (1) 214-221 10.1021/pr300837u
    • (2013) J. Proteome Res. , vol.12 , Issue.1 , pp. 214-221
    • Yamana, R.1    Iwasaki, M.2    Wakabayashi, M.3    Nakagawa, M.4    Yamanaka, S.5    Ishihama, Y.6
  • 17
    • 79952499962 scopus 로고    scopus 로고
    • Challenges in urine bioanalytical assays: Overcoming nonspecific binding
    • Ji, A. J.; Jiang, Z.; Livson, Y.; Davis, J. A.; Chu, J. X.; Weng, N. Challenges in urine bioanalytical assays: overcoming nonspecific binding Bioanalysis 2010, 2 (9) 1573-1586 10.4155/bio.10.114
    • (2010) Bioanalysis , vol.2 , Issue.9 , pp. 1573-1586
    • Ji, A.J.1    Jiang, Z.2    Livson, Y.3    Davis, J.A.4    Chu, J.X.5    Weng, N.6
  • 18
    • 84912103148 scopus 로고    scopus 로고
    • Micelle assisted thin-film solid phase microextraction: A new approach for determination of quaternary ammonium compounds in environmental samples
    • Boyacl, E.; Pawliszyn, J. Micelle assisted thin-film solid phase microextraction: a new approach for determination of quaternary ammonium compounds in environmental samples Anal. Chem. 2014, 86 (18) 8916-8921 10.1021/ac5015673
    • (2014) Anal. Chem. , vol.86 , Issue.18 , pp. 8916-8921
    • Boyacl, E.1    Pawliszyn, J.2
  • 21
    • 0037277179 scopus 로고    scopus 로고
    • Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome
    • Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome J. Proteome Res. 2003, 2 (1) 43-50 10.1021/pr025556v
    • (2003) J. Proteome Res. , vol.2 , Issue.1 , pp. 43-50
    • Peng, J.1    Elias, J.E.2    Thoreen, C.C.3    Licklider, L.J.4    Gygi, S.P.5
  • 22
    • 79955752894 scopus 로고    scopus 로고
    • Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
    • Wang, Y.; Yang, F.; Gritsenko, M. A.; Wang, Y.; Clauss, T.; Liu, T.; Shen, Y.; Monroe, M. E.; Lopez-Ferrer, D.; Reno, T. et al. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells Proteomics 2011, 11 (10) 2019-2026 10.1002/pmic.201000722
    • (2011) Proteomics , vol.11 , Issue.10 , pp. 2019-2026
    • Wang, Y.1    Yang, F.2    Gritsenko, M.A.3    Wang, Y.4    Clauss, T.5    Liu, T.6    Shen, Y.7    Monroe, M.E.8    Lopez-Ferrer, D.9    Reno, T.10
  • 23
    • 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. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19 (3) 242-247 10.1038/85686
    • (2001) Nat. Biotechnol. , vol.19 , Issue.3 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 25
    • 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 10.1021/ac0262560
    • (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
  • 26
    • 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. R. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics Nat. Protoc. 2009, 4 (4) 484-494 10.1038/nprot.2009.21
    • (2009) Nat. Protoc. , vol.4 , Issue.4 , pp. 484-494
    • Boersema, P.J.1    Raijmakers, R.2    Lemeer, S.3    Mohammed, S.4    Heck, A.J.R.5
  • 27
    • 84930583084 scopus 로고    scopus 로고
    • Low-pH Solid-Phase Amino Labeling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis
    • Böhm, G.; Prefot, P.; Jung, S.; Selzer, S.; Mitra, V.; Britton, D.; Kuhn, K.; Pike, I.; Thompson, A. H. Low-pH Solid-Phase Amino Labeling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis J. Proteome Res. 2015, 14 (6) 2500-2510 10.1021/acs.jproteome.5b00072
    • (2015) J. Proteome Res. , vol.14 , Issue.6 , pp. 2500-2510
    • Böhm, G.1    Prefot, P.2    Jung, S.3    Selzer, S.4    Mitra, V.5    Britton, D.6    Kuhn, K.7    Pike, I.8    Thompson, A.H.9
  • 29
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5 (11) 976-989 10.1016/1044-0305(94)80016-2
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , Issue.11 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 30
    • 84976875034 scopus 로고    scopus 로고
    • PANTHER version 10: Expanded protein families and functions, and analysis tools
    • Mi, H.; Poudel, S.; Muruganujan, A.; Casagrande, J. T.; Thomas, P. D. PANTHER version 10: expanded protein families and functions, and analysis tools Nucleic Acids Res. 2016, 44 (D1) D336-D342 10.1093/nar/gkv1194
    • (2016) Nucleic Acids Res. , vol.44 , Issue.D1 , pp. D336-D342
    • Mi, H.1    Poudel, S.2    Muruganujan, A.3    Casagrande, J.T.4    Thomas, P.D.5
  • 31
    • 84949036104 scopus 로고    scopus 로고
    • Multiplexed, Proteome-wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains
    • Isasa, M.; Rose, C. M.; Elsasser, S.; Navarrete-Perea, J.; Paulo, J. A.; Finley, D. J.; Gygi, S. P. Multiplexed, Proteome-wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains J. Proteome Res. 2015, 14 (12) 5306-5317 10.1021/acs.jproteome.5b00802
    • (2015) J. Proteome Res. , vol.14 , Issue.12 , pp. 5306-5317
    • Isasa, M.1    Rose, C.M.2    Elsasser, S.3    Navarrete-Perea, J.4    Paulo, J.A.5    Finley, D.J.6    Gygi, S.P.7
  • 33
    • 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 (1) 248-254 10.1016/0003-2697(76)90527-3
    • (1976) Anal. Biochem. , vol.72 , Issue.1 , pp. 248-254
    • Bradford, M.M.1
  • 35
    • 36248958722 scopus 로고    scopus 로고
    • Protein Detection and Proteomics Technology
    • Spence, M. T. Z. Molecular Probes: Eugene, OR
    • Haughland, R. P. Protein Detection and Proteomics Technology. In A Guide to Fluorescent Probes and Labeling Technologies; Spence, M. T. Z., Ed.; Molecular Probes: Eugene, OR, 2005; pp 413-472.
    • (2005) A Guide to Fluorescent Probes and Labeling Technologies , pp. 413-472
    • Haughland, R.P.1
  • 36
    • 0043210665 scopus 로고    scopus 로고
    • Epicocconone, A Novel Fluorescent Compound from the Fungus Epicoccum nigrum
    • Bell, P. J. L.; Karuso, P. Epicocconone, A Novel Fluorescent Compound from the Fungus Epicoccum nigrum J. Am. Chem. Soc. 2003, 125 (31) 9304-9305 10.1021/ja035496+
    • (2003) J. Am. Chem. Soc. , vol.125 , Issue.31 , pp. 9304-9305
    • Bell, P.J.L.1    Karuso, P.2
  • 37
    • 0037386868 scopus 로고    scopus 로고
    • Development and characterization of the NanoOrange protein quantitation assay: A fluorescence-based assay of proteins in solution
    • Jones, L. J.; Haugland, R. P.; Singer, V. L. Development and characterization of the NanoOrange protein quantitation assay: a fluorescence-based assay of proteins in solution Biotechniques 2003, 34 (4) 856-858
    • (2003) Biotechniques , vol.34 , Issue.4 , pp. 856-858
    • Jones, L.J.1    Haugland, R.P.2    Singer, V.L.3
  • 38
    • 84866973333 scopus 로고    scopus 로고
    • Investigation and reduction of sub-microgram peptide loss using molecular weight cut-off fractionation prior to mass spectrometric analysis
    • Cunningham, R.; Wang, J.; Wellner, D.; Li, L. Investigation and reduction of sub-microgram peptide loss using molecular weight cut-off fractionation prior to mass spectrometric analysis J. Mass Spectrom. 2012, 47 (10) 1327-1332 10.1002/jms.3069
    • (2012) J. Mass Spectrom. , vol.47 , Issue.10 , pp. 1327-1332
    • Cunningham, R.1    Wang, J.2    Wellner, D.3    Li, L.4
  • 39
    • 52649181646 scopus 로고    scopus 로고
    • Mohammed, S. Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue-specific diversity
    • Raijmakers, R.; Berkers, C. R.; de Jong, A.; Ovaa, H.; Heck, A. J. R.; Mohammed, S. Mohammed, S. Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue-specific diversity Mol. Cell. Proteomics 2008, 7 (9) 1755-1762 10.1074/mcp.M800093-MCP200
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.9 , pp. 1755-1762
    • Raijmakers, R.1    Berkers, C.R.2    De Jong, A.3    Ovaa, H.4    Heck, A.J.R.5    Mohammed, S.6
  • 40
    • 84905388250 scopus 로고    scopus 로고
    • Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma
    • Dayon, L.; Núñez Galindo, A.; Corthésy, J.; Cominetti, O.; Kussmann, M. Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma J. Proteome Res. 2014, 13 (8) 3837-3845 10.1021/pr500635f
    • (2014) J. Proteome Res. , vol.13 , Issue.8 , pp. 3837-3845
    • Dayon, L.1    Núñez Galindo, A.2    Corthésy, J.3    Cominetti, O.4    Kussmann, M.5
  • 41
    • 34548183872 scopus 로고    scopus 로고
    • Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
    • Rappsilber, J.; Mann, M.; Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips Nat. Protoc. 2007, 2 (8) 1896-1906 10.1038/nprot.2007.261
    • (2007) Nat. Protoc. , vol.2 , Issue.8 , pp. 1896-1906
    • Rappsilber, J.1    Mann, M.2    Ishihama, Y.3
  • 42
    • 84885407972 scopus 로고    scopus 로고
    • In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation
    • Han, D.; Moon, S.; Kim, Y.; Kim, J.; Jin, J.; Kim, Y. In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation Proteomics 2013, 13 (20) 2984-2988 10.1002/pmic.201300091
    • (2013) Proteomics , vol.13 , Issue.20 , pp. 2984-2988
    • Han, D.1    Moon, S.2    Kim, Y.3    Kim, J.4    Jin, J.5    Kim, Y.6
  • 44
    • 84968764310 scopus 로고    scopus 로고
    • Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling
    • Chen, W.; Wang, S.; Adhikari, S.; Deng, Z.; Wang, L.; Chen, L.; Ke, M.; Yang, P.; Tian, R. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling Anal. Chem. 2016, 88 (9) 4864-4871 10.1021/acs.analchem.6b00631
    • (2016) Anal. Chem. , vol.88 , Issue.9 , pp. 4864-4871
    • Chen, W.1    Wang, S.2    Adhikari, S.3    Deng, Z.4    Wang, L.5    Chen, L.6    Ke, M.7    Yang, P.8    Tian, R.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.