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Volumn 11, Issue 5, 2016, Pages 993-1006

Six alternative proteases for mass spectrometry-based proteomics beyond trypsin

Author keywords

[No Author keywords available]

Indexed keywords

ARGC PROTEASE; ASPN PROTEASE; BOVINE SERUM ALBUMIN; CHYMOTRYPSIN; GLUC PROTEASE; LYSC PROTEASE; LYSN PROTEASE; PROTEINASE; TRYPSIN; UNCLASSIFIED DRUG; ESCHERICHIA COLI PROTEIN; PEPTIDE; PEPTIDE HYDROLASE;

EID: 84983486884     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2016.057     Document Type: Article
Times cited : (342)

References (48)
  • 1
    • 0142215475 scopus 로고    scopus 로고
    • Global analysis of protein expression in yeast
    • Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
    • (2003) Nature , vol.425 , pp. 737-741
    • Ghaemmaghami, S.1
  • 2
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy, L.M.F. et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008).
    • (2008) Nature , vol.455 , pp. 1251-1254
    • De Godoy, L.M.F.1
  • 3
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M.-S. et al. A draft map of the human proteome. Nature 509, 575-581 (2014).
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.-S.1
  • 4
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm, M. et al. Mass-spectrometry-based draft of the human proteome. Nature 509, 582-587 (2014).
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1
  • 5
    • 0033051101 scopus 로고    scopus 로고
    • Direct analysis of protein complexes using mass spectrometry
    • Link, A.J. et al. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682 (1999).
    • (1999) Nat. Biotechnol. , vol.17 , pp. 676-682
    • Link, A.J.1
  • 6
    • 0035582244 scopus 로고    scopus 로고
    • An automated multidimensional protein identification technology for shotgun proteomics
    • Wolters, D.A., Washburn, M.P. & Yates, J.R. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690 (2001).
    • (2001) Anal. Chem. , vol.73 , pp. 5683-5690
    • Wolters, D.A.1    Washburn, M.P.2    Yates, J.R.3
  • 7
    • 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. 14, 35-48 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 35-48
    • Altelaar, A.F.M.1    Munoz, J.2    Heck, A.J.R.3
  • 8
    • 67651173106 scopus 로고    scopus 로고
    • Proteomics by mass spectrometry: Approaches, advances, and applications
    • Yates, J.R., Ruse, C.I. & Nakorchevsky, A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11, 49-79 (2009).
    • (2009) Annu. Rev. Biomed. Eng. , vol.11 , pp. 49-79
    • Yates, J.R.1    Ruse, C.I.2    Nakorchevsky, A.3
  • 9
    • 84861897793 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics and network biology
    • Bensimon, A., Heck, A.J.R. & Aebersold, R. Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem. 81, 379-405 (2012).
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 379-405
    • Bensimon, A.1    Heck, A.J.R.2    Aebersold, R.3
  • 10
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 11
    • 77955876447 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics in cell biology
    • Walther, T.C. & Mann, M. Mass spectrometry-based proteomics in cell biology. J. Cell Biol. 190, 491-500 (2010).
    • (2010) J. Cell Biol. , vol.190 , pp. 491-500
    • Walther, T.C.1    Mann, M.2
  • 12
    • 84937245669 scopus 로고    scopus 로고
    • Proteomics beyond trypsin
    • Tsiatsiani, L. & Heck, A.J.R. Proteomics beyond trypsin. FEBS J. 282, 2612-2626 (2015).
    • (2015) FEBS J. , vol.282 , pp. 2612-2626
    • Tsiatsiani, L.1    Heck, A.J.R.2
  • 13
    • 84901945789 scopus 로고    scopus 로고
    • Confetti: A multiprotease map of the HeLa proteome for comprehensive proteomics
    • Guo, X., Trudgian, D.C., Lemoff, A., Yadavalli, S. & Mirzaei, H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Mol. Cell. Proteomics 13, 1573-1584 (2014).
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 1573-1584
    • Guo, X.1    Trudgian, D.C.2    Lemoff, A.3    Yadavalli, S.4    Mirzaei, H.5
  • 14
    • 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. 9, 1323-1329 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 1323-1329
    • Swaney, D.L.1    Wenger, C.D.2    Coon, J.J.3
  • 15
    • 84895528737 scopus 로고    scopus 로고
    • Expanding proteome coverage with orthogonal-specificity α-lytic proteases
    • Meyer, J.G. et al. Expanding proteome coverage with orthogonal-specificity α-lytic proteases. Mol. Cell. Proteomics 13, 823-835 (2014).
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 823-835
    • Meyer, J.G.1
  • 16
    • 78149422253 scopus 로고    scopus 로고
    • Pressurized pepsin digestion in proteomics: An automatable alternative to trypsin for integrated top-down bottom-up proteomics
    • M110.001479
    • López-Ferrer, D. et al. Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics. Mol. Cell. Proteomics 10, M110.001479 (2011).
    • (2011) Mol. Cell. Proteomics , vol.10
    • López-Ferrer, D.1
  • 17
    • 84860641083 scopus 로고    scopus 로고
    • Improve the coverage for the analysis of phosphoproteome of HeLa cells by a tandem digestion approach
    • Bian, Y. et al. Improve the coverage for the analysis of phosphoproteome of HeLa cells by a tandem digestion approach. J. Proteome Res. 11, 2828-2837 (2012).
    • (2012) J. Proteome Res. , vol.11 , pp. 2828-2837
    • Bian, Y.1
  • 18
    • 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
    • Choudhary, G., Wu, S.-L., Shieh, P. & Hancock, W.S. 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 (2003).
    • (2003) J. Proteome Res. , vol.2 , pp. 59-67
    • Choudhary, G.1    Wu, S.-L.2    Shieh, P.3    Hancock, W.S.4
  • 19
    • 84925027070 scopus 로고    scopus 로고
    • LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification
    • Huesgen, P.F. et al. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. Nat. Methods 12, 55-58 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 55-58
    • Huesgen, P.F.1
  • 20
    • 84861990031 scopus 로고    scopus 로고
    • Protease bias in absolute protein quantitation
    • Peng, M. et al. Protease bias in absolute protein quantitation. Nat. Methods 9, 524-525 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 524-525
    • Peng, M.1
  • 21
    • 77956520064 scopus 로고    scopus 로고
    • Proteome-wide protein concentrations in the human heart
    • Aye, T.T. et al. Proteome-wide protein concentrations in the human heart. Mol. Biosyst. 6, 1917-1927 (2010).
    • (2010) Mol. Biosyst. , vol.6 , pp. 1917-1927
    • Aye, T.T.1
  • 22
    • 84899010486 scopus 로고    scopus 로고
    • Adenovirus composition, proteolysis, and disassembly studied by in-depth qualitative and quantitative proteomics
    • Benevento, M. et al. Adenovirus composition, proteolysis, and disassembly studied by in-depth qualitative and quantitative proteomics. J. Biol. Chem. 289, 11421-11430 (2014).
    • (2014) J. Biol. Chem. , vol.289 , pp. 11421-11430
    • Benevento, M.1
  • 23
    • 84890231620 scopus 로고    scopus 로고
    • Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis
    • Low, T.Y. et al. Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. Cell Rep. 5, 1469-1478 (2013).
    • (2013) Cell Rep. , vol.5 , pp. 1469-1478
    • Low, T.Y.1
  • 24
    • 66349106471 scopus 로고    scopus 로고
    • Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach
    • Gauci, S. et al. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal. Chem. 81, 4493-4501 (2009).
    • (2009) Anal. Chem. , vol.81 , pp. 4493-4501
    • Gauci, S.1
  • 25
    • 43949146287 scopus 로고    scopus 로고
    • Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites
    • Mohammed, S. et al. Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites. Anal. Chem. 80, 3584-3592 (2008).
    • (2008) Anal. Chem. , vol.80 , pp. 3584-3592
    • Mohammed, S.1
  • 26
    • 84929457709 scopus 로고    scopus 로고
    • One-hour proteome analysis in yeast
    • Richards, A.L. et al. One-hour proteome analysis in yeast. Nat. Protoc. 10, 701-714 (2015).
    • (2015) Nat. Protoc. , vol.10 , pp. 701-714
    • Richards, A.L.1
  • 27
    • 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. 19, 242-247 (2001).
    • (2001) Nat. Biotechnol. , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 28
    • 33644856320 scopus 로고    scopus 로고
    • Effects of modified digestion schemes on the identification of proteins from complex mixtures
    • Klammer, A.A. & MacCoss, M.J. Effects of modified digestion schemes on the identification of proteins from complex mixtures. J. Proteome Res. 5, 695-700 (2006).
    • (2006) J. Proteome Res. , vol.5 , pp. 695-700
    • Klammer, A.A.1    MacCoss, M.J.2
  • 29
    • 84893286158 scopus 로고    scopus 로고
    • Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis
    • Wu, X., Xiong, E., Wang, W., Scali, M. & Cresti, M. Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis. Nat. Protoc. 9, 362-374 (2014).
    • (2014) Nat. Protoc. , vol.9 , pp. 362-374
    • Wu, X.1    Xiong, E.2    Wang, W.3    Scali, M.4    Cresti, M.5
  • 30
    • 25644460465 scopus 로고    scopus 로고
    • Artifactual isoform profile modification following treatment of human plasma or serum with protease inhibitor, monitored by 2-dimensional electrophoresis and mass spectrometry
    • Schuchard, M.D. et al. Artifactual isoform profile modification following treatment of human plasma or serum with protease inhibitor, monitored by 2-dimensional electrophoresis and mass spectrometry. Biotechniques 39, 239-247 (2005).
    • (2005) Biotechniques , vol.39 , pp. 239-247
    • Schuchard, M.D.1
  • 31
    • 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. 2, 1896-1906 (2007).
    • (2007) Nat. Protoc. , vol.2 , pp. 1896-1906
    • Rappsilber, J.1    Mann, M.2    Ishihama, Y.3
  • 32
    • 51249118496 scopus 로고    scopus 로고
    • Interferences and contaminants encountered in modern mass spectrometry
    • Keller, B.O., Sui, J., Young, A.B. & Whittal, R.M. Interferences and contaminants encountered in modern mass spectrometry. Anal. Chim. Acta 627, 71-81 (2008).
    • (2008) Anal. Chim. Acta , vol.627 , pp. 71-81
    • Keller, B.O.1    Sui, J.2    Young, A.B.3    Whittal, R.M.4
  • 33
    • 36749068401 scopus 로고    scopus 로고
    • Performance characteristics of electron transfer dissociation mass spectrometry
    • Good, D.M., Wirtala, M., McAlister, G.C. & Coon, J.J. Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics 6, 1942-1951 (2007).
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1942-1951
    • Good, D.M.1    Wirtala, M.2    McAlister, G.C.3    Coon, J.J.4
  • 34
    • 33847782587 scopus 로고    scopus 로고
    • Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry
    • Molina, H., Horn, D.M., Tang, N., Mathivanan, S. & Pandey, A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 104, 2199-2204 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 2199-2204
    • Molina, H.1    Horn, D.M.2    Tang, N.3    Mathivanan, S.4    Pandey, A.5
  • 35
    • 84893846021 scopus 로고    scopus 로고
    • Cleaved and missed sites for trypsin, lys-C, and lys-N can be predicted with high confidence on the basis of sequence context
    • Gershon, P.D. Cleaved and missed sites for trypsin, lys-C, and lys-N can be predicted with high confidence on the basis of sequence context. J. Proteome Res. 13, 702-709 (2014).
    • (2014) J. Proteome Res. , vol.13 , pp. 702-709
    • Gershon, P.D.1
  • 36
    • 84937629707 scopus 로고    scopus 로고
    • An augmented multiple-protease-based human phosphopeptide atlas
    • Giansanti, P. et al. An augmented multiple-protease-based human phosphopeptide atlas. Cell Rep. 11, 1834-43 (2015).
    • (2015) Cell Rep , vol.11 , pp. 1834-1843
    • Giansanti, P.1
  • 37
    • 0035416831 scopus 로고    scopus 로고
    • Overalkylation of a protein digest with iodoacetamide
    • Boja, E.S. & Fales, H.M. Overalkylation of a protein digest with iodoacetamide. Anal. Chem. 73, 3576-3582 (2001).
    • (2001) Anal. Chem. , vol.73 , pp. 3576-3582
    • Boja, E.S.1    Fales, H.M.2
  • 38
    • 0036067603 scopus 로고    scopus 로고
    • Nanoscale LC-MS(n): Technical design and applications to peptide and protein analysis
    • Meiring, H.D., van der Heeft, E., ten Hove, G.J. & de Jong, A.P.J.M. Nanoscale LC-MS(n): technical design and applications to peptide and protein analysis. J. Sep. Sci. 25, 557-568 (2002).
    • (2002) J. Sep. Sci. , vol.25 , pp. 557-568
    • Meiring, H.D.1    Van Der Heeft, E.2    Ten Hove, G.J.3    De Jong, A.P.J.M.4
  • 39
    • 84885012783 scopus 로고    scopus 로고
    • Large-scale identification of ubiquitination sites by mass spectrometry
    • Udeshi, N.D., Mertins, P., Svinkina, T. & Carr, S.A. Large-scale identification of ubiquitination sites by mass spectrometry. Nat. Protoc. 8, 1950-1960 (2013).
    • (2013) Nat. Protoc. , vol.8 , pp. 1950-1960
    • Udeshi, N.D.1    Mertins, P.2    Svinkina, T.3    Carr, S.A.4
  • 40
    • 84984933087 scopus 로고    scopus 로고
    • The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry
    • Villén, J., Gygi, S.P. & Villen, J. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat. Protoc. 3, 1630-1638 (2008).
    • (2008) Nat. Protoc. , vol.3 , pp. 1630-1638
    • Villén, J.1    Gygi, S.P.2    Villen, J.3
  • 41
    • 65249153010 scopus 로고    scopus 로고
    • Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N
    • Hohmann, L. et al. Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. J. Proteome Res. 8, 1415-1422 (2009).
    • (2009) J. Proteome Res. , vol.8 , pp. 1415-1422
    • Hohmann, L.1
  • 42
    • 77955442476 scopus 로고    scopus 로고
    • Evaluation of metalloendopeptidase Lys-N protease performance under different sample handling conditions
    • Taouatas, N., Heck, A.J.R. & Mohammed, S. Evaluation of metalloendopeptidase Lys-N protease performance under different sample handling conditions. J. Proteome Res. 9, 4282-4288 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 4282-4288
    • Taouatas, N.1    Heck, A.J.R.2    Mohammed, S.3
  • 43
    • 34548178909 scopus 로고    scopus 로고
    • In-gel digestion for mass spectrometric characterization of proteins and proteomes
    • Shevchenko, A., Tomas, H., Havlis, J., Olsen, J.V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856-2860 (2006).
    • (2006) Nat. Protoc. , vol.1 , pp. 2856-2860
    • Shevchenko, A.1    Tomas, H.2    Havlis, J.3    Olsen, J.V.4    Mann, M.5
  • 44
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wiśniewski, J.R. et al. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-352 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 352-359
    • Wiśniewski, J.R.1
  • 45
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick, P. et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (2007).
    • (2007) Nat. Biotechnol. , vol.25 , pp. 125-131
    • Mallick, P.1
  • 48
    • 84868115829 scopus 로고    scopus 로고
    • Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients
    • Köcher, T., Pichler, P., Swart, R. & Mechtler, K. Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat. Protoc. 7, 882-890 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 882-890
    • Köcher, T.1    Pichler, P.2    Swart, R.3    Mechtler, K.4


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