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Volumn 75, Issue 12, 2012, Pages 3495-3513

Targeted proteome investigation via selected reaction monitoring mass spectrometry

Author keywords

Antibodies; Mass spectrometry; Proteome mapping; Proteomics; Selected Reaction Monitoring (SRM)

Indexed keywords

ANTIBODY; PROTEIN; PROTEOME;

EID: 84862173529     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.04.048     Document Type: Review
Times cited : (53)

References (145)
  • 2
    • 28844443172 scopus 로고    scopus 로고
    • Genome annotation past, present, and future: how to define an ORF at each locus
    • Brent M.R. Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res 2005, 15:1777-1786.
    • (2005) Genome Res , vol.15 , pp. 1777-1786
    • Brent, M.R.1
  • 3
    • 0042880980 scopus 로고    scopus 로고
    • Vertebrate gene predictions and the problem of large genes
    • Wang J., Li S., Zhang Y., Zheng H., Xu Z., Ye J., et al. Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 2003, 4:741-749.
    • (2003) Nat Rev Genet , vol.4 , pp. 741-749
    • Wang, J.1    Li, S.2    Zhang, Y.3    Zheng, H.4    Xu, Z.5    Ye, J.6
  • 4
    • 0036733640 scopus 로고    scopus 로고
    • Computational prediction of eukaryotic protein-coding genes
    • Zhang M.Q. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 2002, 3:698-709.
    • (2002) Nat Rev Genet , vol.3 , pp. 698-709
    • Zhang, M.Q.1
  • 5
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 6
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3    Khrebtukova, I.4    Zhang, L.5    Mayr, C.6
  • 7
    • 0034256020 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing: the logic of combinatorial control
    • Smith C.W., Valcarcel J. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci 2000, 25:381-388.
    • (2000) Trends Biochem Sci , vol.25 , pp. 381-388
    • Smith, C.W.1    Valcarcel, J.2
  • 8
    • 33745394130 scopus 로고    scopus 로고
    • Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes
    • Xing Y., Lee C. Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat Rev Genet 2006, 7:499-509.
    • (2006) Nat Rev Genet , vol.7 , pp. 499-509
    • Xing, Y.1    Lee, C.2
  • 10
    • 57449088165 scopus 로고    scopus 로고
    • Proteomics studies confirm the presence of alternative protein isoforms on a large scale
    • Tress M.L., Bodenmiller B., Aebersold R., Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biol 2008, 9:R162.
    • (2008) Genome Biol , vol.9
    • Tress, M.L.1    Bodenmiller, B.2    Aebersold, R.3    Valencia, A.4
  • 12
    • 62549126959 scopus 로고    scopus 로고
    • Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases
    • Ryu G.M., Song P., Kim K.W., Oh K.S., Park K.J., Kim J.H. Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases. Nucleic Acids Res 2009, 37:1297-1307.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1297-1307
    • Ryu, G.M.1    Song, P.2    Kim, K.W.3    Oh, K.S.4    Park, K.J.5    Kim, J.H.6
  • 13
    • 62649126517 scopus 로고    scopus 로고
    • Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae
    • Schacherer J., Shapiro J.A., Ruderfer D.M., Kruglyak L. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 2009, 458:342-345.
    • (2009) Nature , vol.458 , pp. 342-345
    • Schacherer, J.1    Shapiro, J.A.2    Ruderfer, D.M.3    Kruglyak, L.4
  • 14
    • 34547108086 scopus 로고    scopus 로고
    • Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
    • Clark R.M., Schweikert G., Toomajian C., Ossowski S., Zeller G., Shinn P., et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 2007, 317:338-342.
    • (2007) Science , vol.317 , pp. 338-342
    • Clark, R.M.1    Schweikert, G.2    Toomajian, C.3    Ossowski, S.4    Zeller, G.5    Shinn, P.6
  • 15
    • 34548295740 scopus 로고    scopus 로고
    • A sequence-based variation map of 8.27 million SNPs in inbred mouse strains
    • Frazer K.A., Eskin E., Kang H.M., Bogue M.A., Hinds D.A., Beilharz E.J., et al. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 2007, 448:1050-1053.
    • (2007) Nature , vol.448 , pp. 1050-1053
    • Frazer, K.A.1    Eskin, E.2    Kang, H.M.3    Bogue, M.A.4    Hinds, D.A.5    Beilharz, E.J.6
  • 16
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • Consortium G.P. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
    • Consortium, G.P.1
  • 17
    • 0037338365 scopus 로고    scopus 로고
    • Proteomic analysis of post-translational modifications
    • Mann M., Jensen O.N. Proteomic analysis of post-translational modifications. Nat Biotechnol 2003, 21:255-261.
    • (2003) Nat Biotechnol , vol.21 , pp. 255-261
    • Mann, M.1    Jensen, O.N.2
  • 18
    • 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, 80:273-299.
    • (2011) Annu Rev Biochem , vol.80 , pp. 273-299
    • Cox, J.1    Mann, M.2
  • 19
    • 70349131530 scopus 로고    scopus 로고
    • The phosphoproteomics data explosion
    • Lemeer S., Heck A.J. The phosphoproteomics data explosion. Curr Opin Chem Biol 2009, 13:414-420.
    • (2009) Curr Opin Chem Biol , vol.13 , pp. 414-420
    • Lemeer, S.1    Heck, A.J.2
  • 22
    • 0000508290 scopus 로고    scopus 로고
    • Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence
    • Roest Crollius H., Jaillon O., Bernot A., Dasilva C., Bouneau L., Fischer C., et al. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet 2000, 25:235-238.
    • (2000) Nat Genet , vol.25 , pp. 235-238
    • Roest Crollius, H.1    Jaillon, O.2    Bernot, A.3    Dasilva, C.4    Bouneau, L.5    Fischer, C.6
  • 25
    • 0035895513 scopus 로고    scopus 로고
    • Gene number. What if there are only 30,000 human genes?
    • Claverie J.M. Gene number. What if there are only 30,000 human genes?. Science (New York, NY) 2001, 291:1255-1257.
    • (2001) Science (New York, NY) , vol.291 , pp. 1255-1257
    • Claverie, J.M.1
  • 26
    • 0033385495 scopus 로고    scopus 로고
    • Evolution of transcriptional control from prokaryotic beginnings to eukaryotic complexities
    • Huang L., Guan R.J., Pardee A.B. Evolution of transcriptional control from prokaryotic beginnings to eukaryotic complexities. Crit Rev Eukaryot Gene Expr 1999, 9:175-182.
    • (1999) Crit Rev Eukaryot Gene Expr , vol.9 , pp. 175-182
    • Huang, L.1    Guan, R.J.2    Pardee, A.B.3
  • 27
    • 0033976523 scopus 로고    scopus 로고
    • Discovery and modeling of transcriptional regulatory regions
    • Fickett J.W., Wasserman W.W. Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol 2000, 11:19-24.
    • (2000) Curr Opin Biotechnol , vol.11 , pp. 19-24
    • Fickett, J.W.1    Wasserman, W.W.2
  • 28
    • 0035221502 scopus 로고    scopus 로고
    • Perspectives for mass spectrometry and functional proteomics
    • Godovac-Zimmermann J., Brown L.R. Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 2001, 20:1-57.
    • (2001) Mass Spectrom Rev , vol.20 , pp. 1-57
    • Godovac-Zimmermann, J.1    Brown, L.R.2
  • 29
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • Alberts B. The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 1998, 92:291-294.
    • (1998) Cell , vol.92 , pp. 291-294
    • Alberts, B.1
  • 31
    • 68949206409 scopus 로고    scopus 로고
    • Applying mass spectrometry-based proteomics to genetics, genomics and network biology
    • Gstaiger M., Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 2009, 10:617-627.
    • (2009) Nat Rev Genet , vol.10 , pp. 617-627
    • Gstaiger, M.1    Aebersold, R.2
  • 32
    • 77952956167 scopus 로고    scopus 로고
    • Decoding signalling networks by mass spectrometry-based proteomics
    • Choudhary C., Mann M. Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 2010, 11:427-439.
    • (2010) Nat Rev Mol Cell Biol , vol.11 , pp. 427-439
    • Choudhary, C.1    Mann, M.2
  • 33
    • 84862172680 scopus 로고    scopus 로고
    • Accessed 2012 Apr 26, ProteinAtlas
    • ProteinAtlas Accessed 2012 Apr 26. http://www.proteinatlas.org/.
  • 35
    • 63449121086 scopus 로고    scopus 로고
    • Generation and validation of affinity reagents on a proteome-wide level
    • Uhlen M., Hober S. Generation and validation of affinity reagents on a proteome-wide level. J Mol Recognit 2009, 22:57-64.
    • (2009) J Mol Recognit , vol.22 , pp. 57-64
    • Uhlen, M.1    Hober, S.2
  • 36
    • 84862177749 scopus 로고    scopus 로고
    • Antibody array analysis of labelled proteomes: how should we control specificity?
    • Holm A., Wu W., Lund-Johansen F. Antibody array analysis of labelled proteomes: how should we control specificity?. N Biotechnol 2011, 1-8.
    • (2011) N Biotechnol , pp. 1-8
    • Holm, A.1    Wu, W.2    Lund-Johansen, F.3
  • 37
    • 34548448107 scopus 로고    scopus 로고
    • Affinity reagent resources for human proteome detection: initiatives and perspectives
    • Stoevesandt O., Taussig M.J. Affinity reagent resources for human proteome detection: initiatives and perspectives. Proteomics 2007, 7:2738-2750.
    • (2007) Proteomics , vol.7 , pp. 2738-2750
    • Stoevesandt, O.1    Taussig, M.J.2
  • 38
    • 79959851876 scopus 로고    scopus 로고
    • A roadmap to generate renewable protein binders to the human proteome
    • Colwill K., Graslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods 2011, 8:551-558.
    • (2011) Nat Methods , vol.8 , pp. 551-558
    • Colwill, K.1    Graslund, S.2
  • 39
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 40
    • 77954523086 scopus 로고    scopus 로고
    • Options and considerations when selecting a quantitative proteomics strategy
    • Domon B., Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol 2010, 28:710-721.
    • (2010) Nat Biotechnol , vol.28 , pp. 710-721
    • Domon, B.1    Aebersold, R.2
  • 41
    • 33748168091 scopus 로고
    • Electrospray ion source. Another variation on the free-jet theme - The Journal of Physical Chemistry (ACS Publications)
    • Yamashita M., Fenn J.B. Electrospray ion source. Another variation on the free-jet theme - The Journal of Physical Chemistry (ACS Publications). J Phys Chem 1984, 88(20):4451-4459.
    • (1984) J Phys Chem , vol.88 , Issue.20 , pp. 4451-4459
    • Yamashita, M.1    Fenn, J.B.2
  • 42
    • 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, 246:64-71.
    • (1989) Science , vol.246 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 43
    • 0024289037 scopus 로고
    • Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons
    • Karas M., Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem Oct. 15 1988, 60(20):2299-2301.
    • (1988) Anal Chem , vol.60 , Issue.20 , pp. 2299-2301
    • Karas, M.1    Hillenkamp, F.2
  • 44
    • 54049090766 scopus 로고    scopus 로고
    • Selected reaction monitoring for quantitative proteomics: a tutorial
    • Lange V., Picotti P., Domon B., Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008, 4:222.
    • (2008) Mol Syst Biol , vol.4 , pp. 222
    • Lange, V.1    Picotti, P.2    Domon, B.3    Aebersold, R.4
  • 45
    • 77957990113 scopus 로고    scopus 로고
    • Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
    • Geiger T., Cox J., Mann M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol Cell Proteomics 2010, 9:2252-2261.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2252-2261
    • Geiger, T.1    Cox, J.2    Mann, M.3
  • 46
    • 84861860481 scopus 로고    scopus 로고
    • Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis
    • in press.
    • Gillet LC, Navarro P, Tate S, Roest H, Selevsek N, Reiter L, et al. Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics in press.
    • Mol Cell Proteomics
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Roest, H.4    Selevsek, N.5    Reiter, L.6
  • 48
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Venable J.D., Dong M.Q., Wohlschlegel J., Dillin A., Yates J.R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 2004, 1:39-45.
    • (2004) Nat Methods , vol.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 49
    • 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, 2:43-50.
    • (2003) J Proteome Res , vol.2 , pp. 43-50
    • Peng, J.1    Elias, J.E.2    Thoreen, C.C.3    Licklider, L.J.4    Gygi, S.P.5
  • 50
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias J.E., Gygi S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 51
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii A.I., Vitek O., Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007, 4:787-797.
    • (2007) Nat Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 52
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 53
    • 79952379394 scopus 로고    scopus 로고
    • Proteome coverage prediction for integrated proteomics datasets
    • Claassen M., Aebersold R., Buhmann J.M. Proteome coverage prediction for integrated proteomics datasets. J Comput Biol 2011, 18:283-293.
    • (2011) J Comput Biol , vol.18 , pp. 283-293
    • Claassen, M.1    Aebersold, R.2    Buhmann, J.M.3
  • 54
    • 72149093828 scopus 로고    scopus 로고
    • Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry
    • Reiter L., Claassen M., Schrimpf S.P., Jovanovic M., Schmidt A., Buhmann J.M., et al. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics 2009, 8:2405-2417.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2405-2417
    • Reiter, L.1    Claassen, M.2    Schrimpf, S.P.3    Jovanovic, M.4    Schmidt, A.5    Buhmann, J.M.6
  • 55
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii A.I., Keller A., Kolker E., Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003, 75:4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 56
    • 80053387432 scopus 로고    scopus 로고
    • IProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    • (007690)
    • Shteynberg D., Deutsch E.W., Lam H., Eng J.K., Sun Z., Tasman N., et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics 2011, 10:M111. (007690).
    • (2011) Mol Cell Proteomics , vol.10
    • Shteynberg, D.1    Deutsch, E.W.2    Lam, H.3    Eng, J.K.4    Sun, Z.5    Tasman, N.6
  • 57
    • 34848903890 scopus 로고    scopus 로고
    • The implications of proteolytic background for shotgun proteomics
    • Picotti P., Aebersold R., Domon B. The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics 2007, 6:1589-1598.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1589-1598
    • Picotti, P.1    Aebersold, R.2    Domon, B.3
  • 60
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26:1367-1372.
    • (2008) Nat Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 62
    • 67249117201 scopus 로고    scopus 로고
    • Proteomics: from technology developments to biological applications
    • Abu-Farha M., Elisma F., Zhou H., Tian R., Zhou H., Asmer M.S., et al. Proteomics: from technology developments to biological applications. Anal Chem 2009, 81:4585-4599.
    • (2009) Anal Chem , vol.81 , pp. 4585-4599
    • Abu-Farha, M.1    Elisma, F.2    Zhou, H.3    Tian, R.4    Zhou, H.5    Asmer, M.S.6
  • 63
    • 0034652301 scopus 로고    scopus 로고
    • Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry
    • Gatlin C.L., Eng J.K., Cross S.T., Detter J.C., Yates J.R. Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal Chem 2000, 72:757-763.
    • (2000) Anal Chem , vol.72 , pp. 757-763
    • Gatlin, C.L.1    Eng, J.K.2    Cross, S.T.3    Detter, J.C.4    Yates, J.R.5
  • 64
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual J.F., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178.
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3    Hirozane-Kishikawa, T.4    Dricot, A.5    Li, N.6
  • 65
    • 33645708138 scopus 로고    scopus 로고
    • Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    • Nesvizhskii A.I., Roos F.F., Grossmann J., Vogelzang M., Eddes J.S., Gruissem W., et al. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 2006, 5:652-670.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.I.1    Roos, F.F.2    Grossmann, J.3    Vogelzang, M.4    Eddes, J.S.5    Gruissem, W.6
  • 66
    • 34250873383 scopus 로고    scopus 로고
    • Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data
    • Bunger M.K., Cargile B.J., Sevinsky J.R., Deyanova E., Yates N.A., Hendrickson R.C., et al. Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data. J Proteome Res 2007, 6:2331-2340.
    • (2007) J Proteome Res , vol.6 , pp. 2331-2340
    • Bunger, M.K.1    Cargile, B.J.2    Sevinsky, J.R.3    Deyanova, E.4    Yates, N.A.5    Hendrickson, R.C.6
  • 67
    • 79955555530 scopus 로고    scopus 로고
    • Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
    • Brosch M., Saunders G.I., Frankish A., Collins M.O., Yu L., Wright J., et al. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res 2011, 21:756-767.
    • (2011) Genome Res , vol.21 , pp. 756-767
    • Brosch, M.1    Saunders, G.I.2    Frankish, A.3    Collins, M.O.4    Yu, L.5    Wright, J.6
  • 68
    • 84865448443 scopus 로고    scopus 로고
    • Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function
    • in press.
    • Ezkurdia I, Del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, et al. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol Biol Evol in press.
    • Mol Biol Evol
    • Ezkurdia, I.1    Del Pozo, A.2    Frankish, A.3    Rodriguez, J.M.4    Harrow, J.5    Ashman, K.6
  • 70
    • 79955925635 scopus 로고    scopus 로고
    • Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data
    • Severing E.I., van Dijk A.D., van Ham R.C. Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data. BMC Plant Biol 2011, 11:82.
    • (2011) BMC Plant Biol , vol.11 , pp. 82
    • Severing, E.I.1    van Dijk, A.D.2    van Ham, R.C.3
  • 71
    • 79960057974 scopus 로고    scopus 로고
    • Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms
    • Chang K.Y., Muddiman D.C. Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms. BMC Genomics 2011, 12:358.
    • (2011) BMC Genomics , vol.12 , pp. 358
    • Chang, K.Y.1    Muddiman, D.C.2
  • 72
    • 78650850279 scopus 로고    scopus 로고
    • The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment
    • Ning K., Nesvizhskii A.I. The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. BMC Bioinformatics 2010, 11(Suppl. 11):S14.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 11
    • Ning, K.1    Nesvizhskii, A.I.2
  • 73
    • 79959875909 scopus 로고    scopus 로고
    • De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
    • Adamidi C., Wang Y., Gruen D., Mastrobuoni G., You X., Tolle D., et al. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res 2011, 21:1193-1200.
    • (2011) Genome Res , vol.21 , pp. 1193-1200
    • Adamidi, C.1    Wang, Y.2    Gruen, D.3    Mastrobuoni, G.4    You, X.5    Tolle, D.6
  • 74
    • 78650642557 scopus 로고    scopus 로고
    • Defining the transcriptome and proteome in three functionally different human cell lines
    • Lundberg E., Fagerberg L., Klevebring D., Matic I., Geiger T., Cox J., et al. Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol 2010, 6:450.
    • (2010) Mol Syst Biol , vol.6 , pp. 450
    • Lundberg, E.1    Fagerberg, L.2    Klevebring, D.3    Matic, I.4    Geiger, T.5    Cox, J.6
  • 75
    • 84863011504 scopus 로고    scopus 로고
    • Protein identification using customized protein sequence databases derived from RNA-Seq data
    • Wang X., Slebos R.J., Wang D., Halvey P.J., Tabb D.L., Liebler D.C., et al. Protein identification using customized protein sequence databases derived from RNA-Seq data. J Proteome Res 2012, 11:1009-1017.
    • (2012) J Proteome Res , vol.11 , pp. 1009-1017
    • Wang, X.1    Slebos, R.J.2    Wang, D.3    Halvey, P.J.4    Tabb, D.L.5    Liebler, D.C.6
  • 77
    • 20144381803 scopus 로고    scopus 로고
    • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    • Desiere F., Deutsch E.W., Nesvizhskii A.I., Mallick P., King N.L., Eng J.K., et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 2005, 6:R9.
    • (2005) Genome Biol , vol.6
    • Desiere, F.1    Deutsch, E.W.2    Nesvizhskii, A.I.3    Mallick, P.4    King, N.L.5    Eng, J.K.6
  • 78
    • 0942287072 scopus 로고    scopus 로고
    • Proteogenomic mapping as a complementary method to perform genome annotation
    • Jaffe J.D., Berg H.C., Church G.M. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 2004, 4:59-77.
    • (2004) Proteomics , vol.4 , pp. 59-77
    • Jaffe, J.D.1    Berg, H.C.2    Church, G.M.3
  • 79
    • 0035350894 scopus 로고    scopus 로고
    • Mass spectrometry allows direct identification of proteins in large genomes
    • Kuster B., Mortensen P., Andersen J.S., Mann M. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 2001, 1:641-650.
    • (2001) Proteomics , vol.1 , pp. 641-650
    • Kuster, B.1    Mortensen, P.2    Andersen, J.S.3    Mann, M.4
  • 80
    • 0037015610 scopus 로고    scopus 로고
    • Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry
    • Lasonder E., Ishihama Y., Andersen J.S., Vermunt A.M., Pain A., Sauerwein R.W., et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 2002, 419:537-542.
    • (2002) Nature , vol.419 , pp. 537-542
    • Lasonder, E.1    Ishihama, Y.2    Andersen, J.S.3    Vermunt, A.M.4    Pain, A.5    Sauerwein, R.W.6
  • 81
    • 53549100731 scopus 로고    scopus 로고
    • Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
    • Merrihew G.E., Davis C., Ewing B., Williams G., Kall L., Frewen B.E., et al. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 2008, 18:1660-1669.
    • (2008) Genome Res , vol.18 , pp. 1660-1669
    • Merrihew, G.E.1    Davis, C.2    Ewing, B.3    Williams, G.4    Kall, L.5    Frewen, B.E.6
  • 82
    • 0033167908 scopus 로고    scopus 로고
    • Nucleotide sequence databases: a gold mine for biologists
    • Pandey A., Lewitter F. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem Sci 1999, 24:276-280.
    • (1999) Trends Biochem Sci , vol.24 , pp. 276-280
    • Pandey, A.1    Lewitter, F.2
  • 83
    • 61649112956 scopus 로고    scopus 로고
    • The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
    • Loevenich S.N., Brunner E., King N.L., Deutsch E.W., Stein S.E., Aebersold R., et al. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics 2009, 10:59.
    • (2009) BMC Bioinformatics , vol.10 , pp. 59
    • Loevenich, S.N.1    Brunner, E.2    King, N.L.3    Deutsch, E.W.4    Stein, S.E.5    Aebersold, R.6
  • 84
    • 48249147316 scopus 로고    scopus 로고
    • High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
    • de Souza G.A., Malen H., Softeland T., Saelensminde G., Prasad S., Jonassen I., et al. High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example. BMC Genomics 2008, 9:316.
    • (2008) BMC Genomics , vol.9 , pp. 316
    • de Souza, G.A.1    Malen, H.2    Softeland, T.3    Saelensminde, G.4    Prasad, S.5    Jonassen, I.6
  • 86
    • 2942598149 scopus 로고    scopus 로고
    • PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation
    • Hornbeck P.V., Chabra I., Kornhauser J.M., Skrzypek E., Zhang B. PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 2004, 4:1551-1561.
    • (2004) Proteomics , vol.4 , pp. 1551-1561
    • Hornbeck, P.V.1    Chabra, I.2    Kornhauser, J.M.3    Skrzypek, E.4    Zhang, B.5
  • 87
    • 78651277460 scopus 로고    scopus 로고
    • PHOSIDA 2011: the posttranslational modification database
    • Gnad F., Gunawardena J., Mann M. PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res 2011, 39:D253-D260.
    • (2011) Nucleic Acids Res , vol.39
    • Gnad, F.1    Gunawardena, J.2    Mann, M.3
  • 88
    • 35348839586 scopus 로고    scopus 로고
    • PhosphoPep - a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
    • Bodenmiller B., Malmstrom J., Gerrits B., Campbell D., Lam H., Schmidt A., et al. PhosphoPep - a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol Syst Biol 2007, 3:139.
    • (2007) Mol Syst Biol , vol.3 , pp. 139
    • Bodenmiller, B.1    Malmstrom, J.2    Gerrits, B.3    Campbell, D.4    Lam, H.5    Schmidt, A.6
  • 89
    • 84862232378 scopus 로고    scopus 로고
    • Accessed 2012 Apr 26, UniProt
    • UniProt Accessed 2012 Apr 26. http://www.uniprot.org/.
  • 90
    • 77952778270 scopus 로고    scopus 로고
    • Prediction of posttranslational modification of proteins from their amino acid sequence
    • Eisenhaber B., Eisenhaber F. Prediction of posttranslational modification of proteins from their amino acid sequence. Methods Mol Biol 2010, 609:365-384.
    • (2010) Methods Mol Biol , vol.609 , pp. 365-384
    • Eisenhaber, B.1    Eisenhaber, F.2
  • 91
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer J.C., Cantley L.C., Yaffe M.B. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 2003, 31:3635-3641.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 92
    • 77449103113 scopus 로고    scopus 로고
    • Identification, analysis, and prediction of protein ubiquitination sites
    • Radivojac P., Vacic V., Haynes C., Cocklin R.R., Mohan A., Heyen J.W., et al. Identification, analysis, and prediction of protein ubiquitination sites. Proteins 2010, 78:365-380.
    • (2010) Proteins , vol.78 , pp. 365-380
    • Radivojac, P.1    Vacic, V.2    Haynes, C.3    Cocklin, R.R.4    Mohan, A.5    Heyen, J.W.6
  • 93
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 94
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    • Majoros W.H., Pertea M., Salzberg S.L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 2004, 20:2878-2879.
    • (2004) Bioinformatics , vol.20 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 95
    • 23144452801 scopus 로고    scopus 로고
    • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
    • Besemer J., Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 2005, 33:W451-W454.
    • (2005) Nucleic Acids Res , vol.33
    • Besemer, J.1    Borodovsky, M.2
  • 96
    • 79959829720 scopus 로고    scopus 로고
    • Widespread RNA and DNA sequence differences in the human transcriptome
    • Li M., Wang I.X., Li Y., Bruzel A., Richards A.L., Toung J.M., et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011, 333:53-58.
    • (2011) Science , vol.333 , pp. 53-58
    • Li, M.1    Wang, I.X.2    Li, Y.3    Bruzel, A.4    Richards, A.L.5    Toung, J.M.6
  • 97
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick P., Schirle M., Chen S.S., Flory M.R., Lee H., Martin D., et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 2007, 25:125-131.
    • (2007) Nat Biotechnol , vol.25 , pp. 125-131
    • Mallick, P.1    Schirle, M.2    Chen, S.S.3    Flory, M.R.4    Lee, H.5    Martin, D.6
  • 98
    • 79951499644 scopus 로고    scopus 로고
    • Too many roads not taken
    • Edwards A., Isserlin R., Bader G., Frye S. Too many roads not taken. Nature Feb. 10 2011, 470(7333):163-165.
    • (2011) Nature , vol.470 , Issue.7333 , pp. 163-165
    • Edwards, A.1    Isserlin, R.2    Bader, G.3    Frye, S.4
  • 99
    • 43549101411 scopus 로고    scopus 로고
    • Alternative binding proteins: affibody binding proteins developed from a small three-helix bundle scaffold
    • Nygren P.A. Alternative binding proteins: affibody binding proteins developed from a small three-helix bundle scaffold. FEBS J 2008, 275:2668-2676.
    • (2008) FEBS J , vol.275 , pp. 2668-2676
    • Nygren, P.A.1
  • 100
    • 60149089005 scopus 로고    scopus 로고
    • Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy
    • Du J., Bernasconi P., Clauser K.R., Mani D.R., Finn S.P., Beroukhim R., et al. Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat Biotechnol 2009, 27:77-83.
    • (2009) Nat Biotechnol , vol.27 , pp. 77-83
    • Du, J.1    Bernasconi, P.2    Clauser, K.R.3    Mani, D.R.4    Finn, S.P.5    Beroukhim, R.6
  • 101
    • 8844233567 scopus 로고    scopus 로고
    • Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA)
    • Anderson N.L., Anderson N.G., Haines L.R., Hardie D.B., Olafson R.W., Pearson T.W. Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J Proteome Res 2004, 3:235-244.
    • (2004) J Proteome Res , vol.3 , 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
  • 102
    • 78149323414 scopus 로고    scopus 로고
    • Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays
    • Schwenk J.M., Igel U., Neiman M., Langen H., Becker C., Bjartell A., et al. Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays. Mol Cell Proteomics 2010, 9:2497-2507.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2497-2507
    • Schwenk, J.M.1    Igel, U.2    Neiman, M.3    Langen, H.4    Becker, C.5    Bjartell, A.6
  • 103
    • 57049106891 scopus 로고    scopus 로고
    • An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures
    • Schmidt A., Gehlenborg N., Bodenmiller B., Mueller L.N., Campbell D., Mueller M., et al. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol Cell Proteomics 2008, 7:2138-2150.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 2138-2150
    • Schmidt, A.1    Gehlenborg, N.2    Bodenmiller, B.3    Mueller, L.N.4    Campbell, D.5    Mueller, M.6
  • 105
    • 0030329981 scopus 로고    scopus 로고
    • SPOT synthesis. Epitope analysis with arrays of synthetic peptides prepared on cellulose membranes
    • Frank R., Overwin H. SPOT synthesis. Epitope analysis with arrays of synthetic peptides prepared on cellulose membranes. Methods Mol Biol 1996, 66:149-169.
    • (1996) Methods Mol Biol , vol.66 , pp. 149-169
    • Frank, R.1    Overwin, H.2
  • 106
    • 74049131716 scopus 로고    scopus 로고
    • High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
    • Picotti P., Rinner O., Stallmach R., Dautel F., Farrah T., Domon B., et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods 2010, 7:43-46.
    • (2010) Nat Methods , vol.7 , pp. 43-46
    • Picotti, P.1    Rinner, O.2    Stallmach, R.3    Dautel, F.4    Farrah, T.5    Domon, B.6
  • 107
    • 39049175370 scopus 로고    scopus 로고
    • Protein identification by tandem mass spectrometry and sequence database searching
    • Nesvizhskii A.I. Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol Biol 2007, 367:87-119.
    • (2007) Methods Mol Biol , vol.367 , pp. 87-119
    • Nesvizhskii, A.I.1
  • 108
    • 78650355102 scopus 로고    scopus 로고
    • Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry
    • Maclean B., Tomazela D.M., Abbatiello S.E., Zhang S., Whiteaker J.R., Paulovich A.G., et al. Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Anal Chem 2010, 82:10116-10124.
    • (2010) Anal Chem , vol.82 , pp. 10116-10124
    • Maclean, B.1    Tomazela, D.M.2    Abbatiello, S.E.3    Zhang, S.4    Whiteaker, J.R.5    Paulovich, A.G.6
  • 109
    • 79951536939 scopus 로고    scopus 로고
    • Collision energy optimization of b- and y-ions for multiple reaction monitoring mass spectrometry
    • Holstein Sherwood C.A., Gafken P.R., Martin D.B. Collision energy optimization of b- and y-ions for multiple reaction monitoring mass spectrometry. J Proteome Res 2011, 10:231-240.
    • (2011) J Proteome Res , vol.10 , pp. 231-240
    • Holstein Sherwood, C.A.1    Gafken, P.R.2    Martin, D.B.3
  • 110
    • 35348863892 scopus 로고    scopus 로고
    • High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites
    • Stahl-Zeng J., Lange V., Ossola R., Eckhardt K., Krek W., Aebersold R., et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 2007, 6:1809-1817.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1809-1817
    • Stahl-Zeng, J.1    Lange, V.2    Ossola, R.3    Eckhardt, K.4    Krek, W.5    Aebersold, R.6
  • 112
    • 84862232375 scopus 로고    scopus 로고
    • Accessed 2012 Apr 26, SRMAtlas
    • SRMAtlas Accessed 2012 Apr 26. http://www.srmatlas.org/.
  • 113
    • 77449108855 scopus 로고    scopus 로고
    • The PeptideAtlas Project
    • Deutsch E.W. The PeptideAtlas Project. Methods Mol Biol 2010, 604:285-296.
    • (2010) Methods Mol Biol , vol.604 , pp. 285-296
    • Deutsch, E.W.1
  • 114
    • 77949695871 scopus 로고    scopus 로고
    • Free computational resources for designing selected reaction monitoring transitions
    • Cham Mead J.A., Bianco L., Bessant C. Free computational resources for designing selected reaction monitoring transitions. Proteomics 2010, 10:1106-1126.
    • (2010) Proteomics , vol.10 , pp. 1106-1126
    • Cham Mead, J.A.1    Bianco, L.2    Bessant, C.3
  • 115
    • 81155161026 scopus 로고    scopus 로고
    • A general strategy for studying multisite protein phosphorylation using label-free selected reaction monitoring mass spectrometry
    • Eissler C.L., Bremmer S.C., Martinez J.S., Parker L.L., Charbonneau H., Hall M.C. A general strategy for studying multisite protein phosphorylation using label-free selected reaction monitoring mass spectrometry. Anal Biochem 2011, 418:267-275.
    • (2011) Anal Biochem , vol.418 , pp. 267-275
    • Eissler, C.L.1    Bremmer, S.C.2    Martinez, J.S.3    Parker, L.L.4    Charbonneau, H.5    Hall, M.C.6
  • 117
    • 61849105469 scopus 로고    scopus 로고
    • Mass spectrometry based targeted protein quantification: methods and applications
    • Pan S., Aebersold R., Chen R., Rush J., Goodlett D.R., McIntosh M.W., et al. Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 2009, 8:787-797.
    • (2009) J Proteome Res , vol.8 , pp. 787-797
    • Pan, S.1    Aebersold, R.2    Chen, R.3    Rush, J.4    Goodlett, D.R.5    McIntosh, M.W.6
  • 118
    • 77951965920 scopus 로고    scopus 로고
    • Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
    • MacLean B., Tomazela D.M., Shulman N., Chambers M., Finney G.L., Frewen B., et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26:966-968.
    • (2010) Bioinformatics , vol.26 , pp. 966-968
    • MacLean, B.1    Tomazela, D.M.2    Shulman, N.3    Chambers, M.4    Finney, G.L.5    Frewen, B.6
  • 119
    • 43049090085 scopus 로고    scopus 로고
    • Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring
    • Lange V., Malmstrom J.A., Didion J., King N.L., Johansson B.P., Schafer J., et al. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics 2008, 7:1489-1500.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 1489-1500
    • Lange, V.1    Malmstrom, J.A.2    Didion, J.3    King, N.L.4    Johansson, B.P.5    Schafer, J.6
  • 121
    • 75749126208 scopus 로고    scopus 로고
    • Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry
    • Abbatiello S.E., Mani D.R., Keshishian H., Carr S.A. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin Chem 2010, 56:291-305.
    • (2010) Clin Chem , vol.56 , pp. 291-305
    • Abbatiello, S.E.1    Mani, D.R.2    Keshishian, H.3    Carr, S.A.4
  • 122
    • 84862172676 scopus 로고    scopus 로고
    • Accessed 2012 Apr 26, SRMCollider
    • SRMCollider Accessed 2012 Apr 26. http://www.srmcollider.org/.
  • 123
    • 84863900597 scopus 로고    scopus 로고
    • A computational tool to detect and avoid redundancy in selected reaction monitoring
    • in press.
    • Rost HL, Malmstrom L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics in press.
    • Mol Cell Proteomics
    • Rost, H.L.1    Malmstrom, L.2    Aebersold, R.3
  • 124
    • 79955595074 scopus 로고    scopus 로고
    • MProphet: automated data processing and statistical validation for large-scale SRM experiments
    • Reiter L., Rinner O., Picotti P., Huttenhain R., Beck M., Brusniak M.Y., et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods 2011, 8:430-435.
    • (2011) Nat Methods , vol.8 , pp. 430-435
    • Reiter, L.1    Rinner, O.2    Picotti, P.3    Huttenhain, R.4    Beck, M.5    Brusniak, M.Y.6
  • 125
    • 68749094119 scopus 로고    scopus 로고
    • Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
    • Picotti P., Bodenmiller B., Mueller L.N., Domon B., Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138:795-806.
    • (2009) Cell , vol.138 , pp. 795-806
    • Picotti, P.1    Bodenmiller, B.2    Mueller, L.N.3    Domon, B.4    Aebersold, R.5
  • 126
    • 79960245388 scopus 로고    scopus 로고
    • Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor
    • Bisson N., James D.A., Ivosev G., Tate S.A., Bonner R., Taylor L., et al. Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor. Nat Biotechnol 2011, 29:653-658.
    • (2011) Nat Biotechnol , vol.29 , pp. 653-658
    • Bisson, N.1    James, D.A.2    Ivosev, G.3    Tate, S.A.4    Bonner, R.5    Taylor, L.6
  • 127
    • 77957665187 scopus 로고    scopus 로고
    • A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans
    • Jovanovic M., Reiter L., Picotti P., Lange V., Bogan E., Hurschler B.A., et al. A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nat Methods 2010, 7:837-842.
    • (2010) Nat Methods , vol.7 , pp. 837-842
    • Jovanovic, M.1    Reiter, L.2    Picotti, P.3    Lange, V.4    Bogan, E.5    Hurschler, B.A.6
  • 128
    • 71649085644 scopus 로고    scopus 로고
    • Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies)
    • Zulak K.G., Lippert D.N., Kuzyk M.A., Domanski D., Chou T., Borchers C.H., et al. Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies). Plant J 2009, 60:1015-1030.
    • (2009) Plant J , vol.60 , pp. 1015-1030
    • Zulak, K.G.1    Lippert, D.N.2    Kuzyk, M.A.3    Domanski, D.4    Chou, T.5    Borchers, C.H.6
  • 129
    • 79551600149 scopus 로고    scopus 로고
    • Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
    • Costenoble R., Picotti P., Reiter L., Stallmach R., Heinemann M., Sauer U., et al. Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol Syst Biol 2011, 7:464.
    • (2011) Mol Syst Biol , vol.7 , pp. 464
    • Costenoble, R.1    Picotti, P.2    Reiter, L.3    Stallmach, R.4    Heinemann, M.5    Sauer, U.6
  • 130
    • 34250722602 scopus 로고    scopus 로고
    • Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
    • Wolf-Yadlin A., Hautaniemi S., Lauffenburger D.A., White F.M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A 2007, 104:5860-5865.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 5860-5865
    • Wolf-Yadlin, A.1    Hautaniemi, S.2    Lauffenburger, D.A.3    White, F.M.4
  • 131
    • 77952082595 scopus 로고    scopus 로고
    • Measurement of protein phosphorylation stoichiometry by selected reaction monitoring mass spectrometry
    • Jin L.L., Tong J., Prakash A., Peterman S.M., St-Germain J.R., Taylor P., et al. Measurement of protein phosphorylation stoichiometry by selected reaction monitoring mass spectrometry. J Proteome Res 2010, 9:2752-2761.
    • (2010) J Proteome Res , vol.9 , pp. 2752-2761
    • Jin, L.L.1    Tong, J.2    Prakash, A.3    Peterman, S.M.4    St-Germain, J.R.5    Taylor, P.6
  • 132
    • 77954370179 scopus 로고    scopus 로고
    • A modified "cross-talk" between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation
    • Darwanto A., Curtis M.P., Schrag M., Kirsch W., Liu P., Xu G., et al. A modified "cross-talk" between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation. J Biol Chem 2010, 285:21868-21876.
    • (2010) J Biol Chem , vol.285 , pp. 21868-21876
    • Darwanto, A.1    Curtis, M.P.2    Schrag, M.3    Kirsch, W.4    Liu, P.5    Xu, G.6
  • 133
    • 84860869167 scopus 로고    scopus 로고
    • Using iRT, a normalized retention time for more targeted measurement of peptides
    • Escher C., Reiter L., Maclean B., Ossola R., Herzog F., Chilton J., et al. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics Apr. 2012, 12(8):1111-1121.
    • (2012) Proteomics , vol.12 , Issue.8 , pp. 1111-1121
    • Escher, C.1    Reiter, L.2    Maclean, B.3    Ossola, R.4    Herzog, F.5    Chilton, J.6
  • 134
    • 84862172677 scopus 로고    scopus 로고
    • Accessed 2012 Apr 26, Skyline
    • Skyline iRT Tutorial Accessed 2012 Apr 26. https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_irt.
    • iRT Tutorial
  • 135
    • 84862185335 scopus 로고    scopus 로고
    • Accessed 2012 Apr 26, Biognosys
    • Biognosys Accessed 2012 Apr 26. http://www.biognosys.ch/.
  • 136
    • 79955750055 scopus 로고    scopus 로고
    • Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
    • Bendall S.C., Simonds E.F., Qiu P., Amir el A.D., Krutzik P.O., Finck R., et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011, 332:687-696.
    • (2011) Science , vol.332 , pp. 687-696
    • Bendall, S.C.1    Simonds, E.F.2    Qiu, P.3    Amirel, A.D.4    Krutzik, P.O.5    Finck, R.6
  • 137
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov A.A., Solovyev V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000, 10:516-522.
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 138
    • 80052474629 scopus 로고    scopus 로고
    • The proteome of Mycoplasma pneumoniae, a supposedly "simple" cell
    • Catrein I., Herrmann R. The proteome of Mycoplasma pneumoniae, a supposedly "simple" cell. Proteomics 2011, 11:3614-3632.
    • (2011) Proteomics , vol.11 , pp. 3614-3632
    • Catrein, I.1    Herrmann, R.2
  • 140
    • 77956320089 scopus 로고    scopus 로고
    • Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions
    • Sun N., Pan C., Nickell S., Mann M., Baumeister W., Nagy I. Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. J Proteome Res 2010, 9:4839-4850.
    • (2010) J Proteome Res , vol.9 , pp. 4839-4850
    • Sun, N.1    Pan, C.2    Nickell, S.3    Mann, M.4    Baumeister, W.5    Nagy, I.6
  • 141
    • 77949517375 scopus 로고    scopus 로고
    • A proteomic view of an important human pathogen - towards the quantification of the entire Staphylococcus aureus proteome
    • Becher D., Hempel K., Sievers S., Zuhlke D., Pane-Farre J., Otto A., et al. A proteomic view of an important human pathogen - towards the quantification of the entire Staphylococcus aureus proteome. PLoS One 2009, 4:e8176.
    • (2009) PLoS One , vol.4
    • Becher, D.1    Hempel, K.2    Sievers, S.3    Zuhlke, D.4    Pane-Farre, J.5    Otto, A.6
  • 142
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy L.M., Olsen J.V., Cox J., Nielsen M.L., Hubner N.C., Frohlich F., et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455:1251-1254.
    • (2008) Nature , vol.455 , pp. 1251-1254
    • de Godoy, L.M.1    Olsen, J.V.2    Cox, J.3    Nielsen, M.L.4    Hubner, N.C.5    Frohlich, F.6
  • 143
  • 144
    • 77952980794 scopus 로고    scopus 로고
    • Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
    • Borchert N., Dieterich C., Krug K., Schutz W., Jung S., Nordheim A., et al. Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Res 2010, 20:837-846.
    • (2010) Genome Res , vol.20 , pp. 837-846
    • Borchert, N.1    Dieterich, C.2    Krug, K.3    Schutz, W.4    Jung, S.5    Nordheim, A.6


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