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Volumn 24, Issue , 2015, Pages 11-17

Proteome sequencing goes deep

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; SIGNAL PEPTIDE; TRYPSIN; PEPTIDE;

EID: 84909953725     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.10.017     Document Type: Review
Times cited : (84)

References (59)
  • 1
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn J.B., Mann M., Meng C.K., Wong S.F., Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 2464:64-71.
    • (1989) Science , vol.2464 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 2
    • 24644477568 scopus 로고
    • Matrix-assisted ultraviolet-laser desorption of nonvolatile compounds
    • Karas M., Bachmann D., Bahr U., Hillenkamp F. Matrix-assisted ultraviolet-laser desorption of nonvolatile compounds. Int J Mass Spectrom 1987, 78:53-68.
    • (1987) Int J Mass Spectrom , vol.78 , pp. 53-68
    • Karas, M.1    Bachmann, D.2    Bahr, U.3    Hillenkamp, F.4
  • 4
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of DNA elements (ENCODE)
    • A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011, 9:e1001046.
    • (2011) PLoS Biol , vol.9 , pp. e1001046
  • 6
    • 84874805815 scopus 로고    scopus 로고
    • The challenge of the proteome dynamic range and its implications for in-depth proteomics
    • Zubarev R.A. The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 2013, 13:723-726.
    • (2013) Proteomics , vol.13 , pp. 723-726
    • Zubarev, R.A.1
  • 8
    • 71549117585 scopus 로고    scopus 로고
    • Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
    • Wisniewski J.R., Zougman A., Mann M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 2009, 8:5674-5678.
    • (2009) J Proteome Res , vol.8 , pp. 5674-5678
    • Wisniewski, J.R.1    Zougman, A.2    Mann, M.3
  • 9
    • 57649187385 scopus 로고    scopus 로고
    • Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis
    • Hubner N.C., Ren S., Mann M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008, 8:4862-4872.
    • (2008) Proteomics , vol.8 , pp. 4862-4872
    • Hubner, N.C.1    Ren, S.2    Mann, M.3
  • 14
    • 84857938446 scopus 로고    scopus 로고
    • Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    • M111.014050
    • 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. M111.014050.
    • (2012) Mol Cell Proteomics , vol.11
    • Geiger, T.1    Wehner, A.2    Schaab, C.3    Cox, J.4    Mann, M.5
  • 19
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wisniewski J.R., Zougman A., Nagaraj N., Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009, 6:359-362.
    • (2009) Nat Methods , vol.6 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 21
    • 84895538371 scopus 로고    scopus 로고
    • Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells
    • Kulak N.A., Pichler G., Paron I., Nagaraj N., Mann M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods 2014, 11:319-324.
    • (2014) Nat Methods , vol.11 , pp. 319-324
    • Kulak, N.A.1    Pichler, G.2    Paron, I.3    Nagaraj, N.4    Mann, M.5
  • 22
    • 77949786295 scopus 로고    scopus 로고
    • Value of using multiple proteases for large-scale mass spectrometry-based proteomics
    • Swaney D.L., Wenger C.D., Coon J.J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res 2010, 9:1323-1329.
    • (2010) J Proteome Res , vol.9 , pp. 1323-1329
    • Swaney, D.L.1    Wenger, C.D.2    Coon, J.J.3
  • 24
    • 84858725817 scopus 로고    scopus 로고
    • Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis
    • Wisniewski J.R., Mann M. Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal Chem 2012, 84:2631-2637.
    • (2012) Anal Chem , vol.84 , pp. 2631-2637
    • Wisniewski, J.R.1    Mann, M.2
  • 25
    • 84901945789 scopus 로고    scopus 로고
    • Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics
    • Guo X.F., Trudgian D.C., Lemoff A., Yadavalli S., Mirzaei H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Mol Cell Proteomics 2014, 13:1573-1584.
    • (2014) Mol Cell Proteomics , vol.13 , pp. 1573-1584
    • Guo, X.F.1    Trudgian, D.C.2    Lemoff, A.3    Yadavalli, S.4    Mirzaei, H.5
  • 28
    • 84876314836 scopus 로고    scopus 로고
    • Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10000 proteins
    • Wisniewski J.R., Dus K., Mann M. Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10000 proteins. Proteomics Clin Appl 2013, 7:225-233.
    • (2013) Proteomics Clin Appl , vol.7 , pp. 225-233
    • Wisniewski, J.R.1    Dus, K.2    Mann, M.3
  • 30
    • 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, 83:5442-5446.
    • (2011) Anal Chem , vol.83 , pp. 5442-5446
    • Andrews, G.L.1    Simons, B.L.2    Young, J.B.3    Hawkridge, A.M.4    Muddiman, D.C.5
  • 32
    • 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
    • Kocher 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, 83:2699-2704.
    • (2011) Anal Chem , vol.83 , pp. 2699-2704
    • Kocher, T.1    Swart, R.2    Mechtler, K.3
  • 33
    • 84863700845 scopus 로고    scopus 로고
    • In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis
    • Cristobal A., Hennrich M.L., Giansanti P., Goerdayal S.S., Heck A.J.R., Mohammed S. In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis. Analyst 2012, 137:3541-3548.
    • (2012) Analyst , vol.137 , pp. 3541-3548
    • Cristobal, A.1    Hennrich, M.L.2    Giansanti, P.3    Goerdayal, S.S.4    Heck, A.J.R.5    Mohammed, S.6
  • 34
    • 84873038780 scopus 로고    scopus 로고
    • Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples
    • Hsieh E.J., Bereman M.S., Durand S., Valaskovic G.A., MacCoss M.J. Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples. J Am Soc Mass Spectrom 2013, 24:148-153.
    • (2013) J Am Soc Mass Spectrom , vol.24 , pp. 148-153
    • Hsieh, E.J.1    Bereman, M.S.2    Durand, S.3    Valaskovic, G.A.4    MacCoss, M.J.5
  • 35
    • 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, 1228:292-297.
    • (2012) J Chromatogr A , vol.1228 , pp. 292-297
    • Iwasaki, M.1    Sugiyama, N.2    Tanaka, N.3    Ishihama, Y.4
  • 36
    • 3042789073 scopus 로고    scopus 로고
    • Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
    • Syka J.E., Coon J.J., Schroeder M.J., Shabanowitz J., Hunt D.F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 2004, 101:9528-9533.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 9528-9533
    • Syka, J.E.1    Coon, J.J.2    Schroeder, M.J.3    Shabanowitz, J.4    Hunt, D.F.5
  • 38
    • 56149086397 scopus 로고    scopus 로고
    • Decision tree-driven tandem mass spectrometry for shotgun proteomics
    • Swaney D.L., McAlister G.C., Coon J.J. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 2008, 5:959-964.
    • (2008) Nat Methods , vol.5 , pp. 959-964
    • Swaney, D.L.1    McAlister, G.C.2    Coon, J.J.3
  • 42
    • 84895071750 scopus 로고    scopus 로고
    • Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
    • Distler U., Kuharev J., Navarro P., Levin Y., Schild H., Tenzer S. Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat Methods 2014, 11:167-170.
    • (2014) Nat Methods , vol.11 , pp. 167-170
    • Distler, U.1    Kuharev, J.2    Navarro, P.3    Levin, Y.4    Schild, H.5    Tenzer, S.6
  • 47
    • 84909600446 scopus 로고    scopus 로고
    • N-terminomics and proteogenomics, getting off to a good start
    • Hartmann E.M., Armengaud J. N-terminomics and proteogenomics, getting off to a good start. Proteomics 2014.
    • (2014) Proteomics
    • Hartmann, E.M.1    Armengaud, J.2
  • 48
    • 84881094423 scopus 로고    scopus 로고
    • Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq
    • Sheynkman G.M., Shortreed M.R., Frey B.L., Smith L.M. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol Cell Proteomics 2013, 12:2341-2353.
    • (2013) Mol Cell Proteomics , vol.12 , pp. 2341-2353
    • Sheynkman, G.M.1    Shortreed, M.R.2    Frey, B.L.3    Smith, L.M.4
  • 49
    • 84891818263 scopus 로고    scopus 로고
    • Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences
    • Sheynkman G.M., Shortreed M.R., Frey B.L., Scalf M., Smith L.M. Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J Proteome Res 2014, 13:228-240.
    • (2014) J Proteome Res , vol.13 , pp. 228-240
    • Sheynkman, G.M.1    Shortreed, M.R.2    Frey, B.L.3    Scalf, M.4    Smith, L.M.5
  • 51
    • 84907197082 scopus 로고    scopus 로고
    • MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction
    • Cox J., Hein M.Y., Luber C.A., Paron I., Nagaraj N., Mann M. MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction. Mol Cell Proteomics 2014, 13:2513-2526.
    • (2014) Mol Cell Proteomics , vol.13 , pp. 2513-2526
    • Cox, J.1    Hein, M.Y.2    Luber, C.A.3    Paron, I.4    Nagaraj, N.5    Mann, M.6
  • 54
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann M., Kulak N.A., Nagaraj N., Cox J. The coming age of complete, accurate, and ubiquitous proteomes. Mol Cell 2013, 49:583-590.
    • (2013) Mol Cell , vol.49 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3    Cox, J.4
  • 55
    • 84909960218 scopus 로고    scopus 로고
    • From the human genome to the human proteome
    • Munoz J., Heck A.J. From the human genome to the human proteome. Angew Chem Int Ed Engl 2014, 53:10864-10866.
    • (2014) Angew Chem Int Ed Engl , vol.53 , pp. 10864-10866
    • Munoz, J.1    Heck, A.J.2
  • 56
    • 84869393599 scopus 로고    scopus 로고
    • Uniting ENCODE with genome-wide proteomics
    • Paik Y.K., Hancock W.S. Uniting ENCODE with genome-wide proteomics. Nat Biotechnol 2012, 30:1065-1067.
    • (2012) Nat Biotechnol , vol.30 , pp. 1065-1067
    • Paik, Y.K.1    Hancock, W.S.2
  • 58
    • 84891786993 scopus 로고    scopus 로고
    • State of the human proteome in 2013 as viewed through peptideatlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven human proteome project
    • Farrah T., Deutsch E.W., Omenn G.S., Sun Z., Watts J.D., Yamamoto T., Shteynberg D., Harris M.M., Moritz R.L. State of the human proteome in 2013 as viewed through peptideatlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven human proteome project. J Proteome Res 2014, 13:60-75.
    • (2014) J Proteome Res , vol.13 , pp. 60-75
    • Farrah, T.1    Deutsch, E.W.2    Omenn, G.S.3    Sun, Z.4    Watts, J.D.5    Yamamoto, T.6    Shteynberg, D.7    Harris, M.M.8    Moritz, R.L.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.