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Volumn 13, Issue 6, 2014, Pages 1573-1584

Confetti: A multiprotease map of the HeLa proteome for comprehensive proteomics

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN; ELASTASE; PROTEINASE; PROTEOME; TRYPSIN; PEPTIDE; PEPTIDE FRAGMENT;

EID: 84901945789     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.035170     Document Type: Article
Times cited : (88)

References (39)
  • 1
    • 38349172005 scopus 로고    scopus 로고
    • Prediction of peptides observable by mass spectrometry applied at the experimental set level
    • Sanders, W. S., Bridges, S. M., McCarthy, F. M., Nanduri, B., and Burgess, S. C. (2007) Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics 8, S23
    • (2007) BMC Bioinformatics , vol.8
    • Sanders, W.S.1    Bridges, S.M.2    McCarthy, F.M.3    Nanduri, B.4    Burgess, S.C.5
  • 3
    • 79960258556 scopus 로고    scopus 로고
    • 100% protein sequence coverage: A modern form of surrealism in proteomics
    • Meyer, B., Papasotiriou, D. G., and Karas, M. (2011) 100% protein sequence coverage: a modern form of surrealism in proteomics. Amino Acids 41, 291-310
    • (2011) Amino Acids , vol.41 , pp. 291-310
    • Meyer, B.1    Papasotiriou, D.G.2    Karas, M.3
  • 4
    • 84871959637 scopus 로고    scopus 로고
    • Method of the Year 2012
    • Nature Methods
    • Nature Methods (2013) Method of the Year 2012. Nat. Methods 10, 1
    • (2013) Nat. Methods , vol.10 , pp. 1
  • 5
    • 84860856325 scopus 로고    scopus 로고
    • Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
    • Ebhardt, H. A., Sabido, E., Huttenhain, R., Collins, B., and Aebersold, R. (2012) Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. Proteomics 12, 1185-1193
    • (2012) Proteomics , vol.12 , pp. 1185-1193
    • Ebhardt, H.A.1    Sabido, E.2    Huttenhain, R.3    Collins, B.4    Aebersold, R.5
  • 7
    • 0037274605 scopus 로고    scopus 로고
    • Multiple enzymatic digestion for enhanced sequence coverage of proteins in complex proteomic mixtures using capillary LC with ion trap MS/MS
    • DOI 10.1021/pr025557n
    • Choudhary, G., Wu, S. L., Shieh, P., and Hancock, W. S. (2003) Multiple enzymatic digestion for enhanced sequence coverage of proteins in complex proteomic mixtures using capillary LC with ion trap MS/MS. J. Proteome Res. 2, 59-67 (Pubitemid 36207191)
    • (2003) Journal of Proteome Research , vol.2 , Issue.1 , pp. 59-67
    • Choudhary, G.1    Wu, S.-L.2    Shieh, P.3    Hancock, W.S.4
  • 8
    • 33748573295 scopus 로고    scopus 로고
    • Enhanced sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS/MS
    • DOI 10.1093/bfgp/ell026
    • Biringer, R. G., Amato, H., Harrington, M. G., Fonteh, A. N., Riggins, J. N., and Huhmer, A. F. (2006) Enhanced sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS/MS. Brief Funct. Genomic Proteomic 5, 144-153 (Pubitemid 46403007)
    • (2006) Briefings in Functional Genomics and Proteomics , vol.5 , Issue.2 , pp. 144-153
    • Biringer, R.G.1    Amato, H.2    Harrington, M.G.3    Fonteh, A.N.4    Riggins, J.N.5    Huhmer, A.F.R.6
  • 9
    • 77949786295 scopus 로고    scopus 로고
    • Value of using multiple proteases for large-scale mass spectrometry-based proteomics
    • Swaney, D. L., Wenger, C. D., and Coon, J. J. (2010) Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 9, 1323-1329
    • (2010) J. Proteome Res. , vol.9 , pp. 1323-1329
    • Swaney, D.L.1    Wenger, C.D.2    Coon, J.J.3
  • 11
    • 84858725817 scopus 로고    scopus 로고
    • Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis
    • Wisniewski, J. R., and Mann, M. (2012) Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal. Chem. 84, 2631-2637
    • (2012) Anal. Chem. , vol.84 , pp. 2631-2637
    • Wisniewski, J.R.1    Mann, M.2
  • 13
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • DOI 10.1093/bioinformatics/bth092
    • Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (Pubitemid 38931421)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 15
    • 84870926630 scopus 로고    scopus 로고
    • Cloud CPFP: A shotgun proteomics data analysis pipeline using cloud and high performance computing
    • Trudgian, D. C., and Mirzaei, H. (2012) Cloud CPFP: A shotgun proteomics data analysis pipeline using cloud and high performance computing. J. Proteome Res. 11, 6282-6290
    • (2012) J. Proteome Res. , vol.11 , pp. 6282-6290
    • Trudgian, D.C.1    Mirzaei, H.2
  • 16
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40, D71-75
    • (2012) Nucleic Acids Res , vol.40
  • 18
    • 33745561205 scopus 로고    scopus 로고
    • An introduction to variable and feature selection
    • Guyon, I., and Elisseeff, A. (2003) An introduction to variable and feature selection. J. Mach. Learn. Res. 3, 1157-1182
    • (2003) J. Mach. Learn. Res. , vol.3 , pp. 1157-1182
    • Guyon, I.1    Elisseeff, A.2
  • 19
    • 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., and Mann, M. (2009) Combination of fasp and stagetip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 8, 5674-5678
    • (2009) J. Proteome Res. , vol.8 , pp. 5674-5678
    • Wisniewski, J.R.1    Zougman, A.2    Mann, M.3
  • 20
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • DOI 10.1021/pr0604054
    • Tabb, D. L., Fernando, C. G., and Chambers, M. C. (2007) MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 6, 654-661 (Pubitemid 46340169)
    • (2007) Journal of Proteome Research , vol.6 , Issue.2 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 22
    • 77957339566 scopus 로고    scopus 로고
    • Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
    • Serang, O., MacCoss, M. J., and Noble, W. S. (2010) Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J. Proteome Res. 9, 5346-5357
    • (2010) J. Proteome Res. , vol.9 , pp. 5346-5357
    • Serang, O.1    MacCoss, M.J.2    Noble, W.S.3
  • 23
    • 70349213754 scopus 로고    scopus 로고
    • A bayesian approach to protein inference problem in shotgun proteomics
    • Li, Y. F., Arnold, R. J., Li, Y., Radivojac, P., Sheng, Q., and Tang, H. (2009) A bayesian approach to protein inference problem in shotgun proteomics. J. Comput. Biol. 16, 1183-1193
    • (2009) J. Comput. Biol. , vol.16 , pp. 1183-1193
    • Li, Y.F.1    Arnold, R.J.2    Li, Y.3    Radivojac, P.4    Sheng, Q.5    Tang, H.6
  • 24
    • 34948874252 scopus 로고    scopus 로고
    • Proteomic parsimony through bipartite graph analysis improves accuracy and transparency
    • DOI 10.1021/pr070230d
    • Zhang, B., Chambers, M. C., and Tabb, D. L. (2007) Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J. Proteome Res. 6, 3549-3557 (Pubitemid 47522746)
    • (2007) Journal of Proteome Research , vol.6 , Issue.9 , pp. 3549-3557
    • Zhang, B.1    Chambers, M.C.2    Tabb, D.L.3
  • 28
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team (2005) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
    • (2005) R: A Language and Environment for Statistical Computing
  • 29
    • 84883278190 scopus 로고    scopus 로고
    • Characterization of a high field Orbitrap mass spectrometer for proteome analysis
    • Pachl, F., Ruprecht, B., Lemeer, S., and Kuster, B. (2013) Characterization of a high field Orbitrap mass spectrometer for proteome analysis. Proteomics 13, 2552-2562
    • (2013) Proteomics , vol.13 , pp. 2552-2562
    • Pachl, F.1    Ruprecht, B.2    Lemeer, S.3    Kuster, B.4
  • 31
    • 56149086397 scopus 로고    scopus 로고
    • Decision tree-driven tandem mass spectrometry for shotgun proteomics
    • Swaney, D. L., McAlister, G. C., and Coon, J. J. (2008) Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5, 959-964
    • (2008) Nat. Methods , vol.5 , pp. 959-964
    • Swaney, D.L.1    McAlister, G.C.2    Coon, J.J.3
  • 32
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J., and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 33
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden, E., Navon, R., Steinfeld, I., Lipson, D., and Yakhini, Z. (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10, 48
    • (2009) BMC Bioinformatics , vol.10 , pp. 48
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 34
    • 84868327851 scopus 로고    scopus 로고
    • Large-scale quantitative assessment of different insolution protein digestion protocols reveals superior cleavage efficiency of tandem lys-c/trypsin proteolysis over trypsin digestion
    • Glatter, T., Ludwig, C., Ahrne, E., Aebersold, R., Heck, A. J. R., and Schmidt, A. (2012) Large-scale quantitative assessment of different insolution protein digestion protocols reveals superior cleavage efficiency of tandem lys-c/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11, 5145-5156
    • (2012) J. Proteome Res. , vol.11 , pp. 5145-5156
    • Glatter, T.1    Ludwig, C.2    Ahrne, E.3    Aebersold, R.4    Heck, A.J.R.5    Schmidt, A.6
  • 37
    • 8844233567 scopus 로고    scopus 로고
    • Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA)
    • DOI 10.1021/pr034086h
    • Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., and Pearson, T. W. (2004) Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome Res. 3, 235-244 (Pubitemid 38500990)
    • (2004) Journal of Proteome Research , vol.3 , Issue.2 , pp. 235-244
    • Anderson, N.L.1    Anderson, N.G.2    Haines, L.R.3    Hardie, D.B.4    Olafson, R.W.5    Pearson, T.W.6
  • 39
    • 77449108855 scopus 로고    scopus 로고
    • The PeptideAtlas Project
    • Deutsch, E. W. (2010) The PeptideAtlas Project. Methods Mol. Biol. 604, 285-296
    • (2010) Methods Mol. Biol. , vol.604 , pp. 285-296
    • Deutsch, E.W.1


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