메뉴 건너뛰기




Volumn 12, Issue 4, 2013, Pages 1628-1644

An automated pipeline for high-throughput label-free quantitative proteomics

Author keywords

algorithms; automation; bioinformatics software; label free; mass spectrometry; quantification

Indexed keywords

ISOTOPE;

EID: 84875928072     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300992u     Document Type: Article
Times cited : (142)

References (46)
  • 1
    • 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
  • 2
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5, 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 3
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-3567
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 5
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20, 1466-1467
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 6
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S.; Shu, H.; Frank, A.; Wang, L.-C.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra Anal. Chem. 2005, 77, 4626-4639
    • (2005) Anal. Chem. , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 7
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Tabb, D. L.; Fernando, C. G.; Chambers, M. C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis J. Proteome Res. 2007, 6, 654-661
    • (2007) J. Proteome Res. , vol.6 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 8
    • 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
  • 9
    • 35748972060 scopus 로고    scopus 로고
    • Semi-supervised learning for peptide identification from shotgun proteomics datasets
    • Käll, L.; Canterbury, J. D.; Weston, J.; Noble, W. S.; MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets Nat. Methods 2007, 4, 923-925
    • (2007) Nat. Methods , vol.4 , pp. 923-925
    • Käll, L.1    Canterbury, J.D.2    Weston, J.3    Noble, W.S.4    MacCoss, M.J.5
  • 10
    • 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
  • 12
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu, H.; Sadygov, R. G.; Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76, 4193-4201
    • (2004) Anal. Chem. , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates, J.R.3
  • 13
    • 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
  • 14
    • 84857986224 scopus 로고    scopus 로고
    • Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry
    • Ludwig, C.; Claassen, M.; Schmidt, A.; Aebersold, R. Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry Mol. Cell. Proteomics 2012, 11, M111.013987
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 111013987
    • Ludwig, C.1    Claassen, M.2    Schmidt, A.3    Aebersold, R.4
  • 15
    • 59149084542 scopus 로고    scopus 로고
    • Targeted proteomic strategy for clinical biomarker discovery
    • Schiess, R.; Wollscheid, B.; Aebersold, R. Targeted proteomic strategy for clinical biomarker discovery Mol. Oncol. 2009, 3, 33-44
    • (2009) Mol. Oncol. , vol.3 , pp. 33-44
    • Schiess, R.1    Wollscheid, B.2    Aebersold, R.3
  • 18
    • 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
  • 22
    • 80855134793 scopus 로고    scopus 로고
    • PATRIC: The comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
    • Gillespie, J. J. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species Infect. Immun. 2011, 79, 4286-4298
    • (2011) Infect. Immun. , vol.79 , pp. 4286-4298
    • Gillespie, J.J.1
  • 23
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; King, N.; Stein, S. E.; Aebersold, R. Development and validation of a spectral library searching method for peptide identification from MS/MS Proteomics 2007, 7, 655-667
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6    Aebersold, R.7
  • 27
    • 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
  • 28
    • 79961225176 scopus 로고    scopus 로고
    • Probabilistic consensus scoring improves tandem mass spectrometry peptide identification
    • Nahnsen, S.; Bertsch, A.; Rahnenführer, J.; Nordheim, A.; Kohlbacher, O. Probabilistic consensus scoring improves tandem mass spectrometry peptide identification J. Proteome Res. 2011, 10, 3332-3343
    • (2011) J. Proteome Res. , vol.10 , pp. 3332-3343
    • Nahnsen, S.1    Bertsch, A.2    Rahnenführer, J.3    Nordheim, A.4    Kohlbacher, O.5
  • 29
    • 78651082595 scopus 로고    scopus 로고
    • MzML - A community standard for mass spectrometry data
    • Martens, L. mzML-a community standard for mass spectrometry data Mol. Cell. Proteomics 2011, 10, R110.000133
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. 110000133
    • Martens, L.1
  • 31
    • 84863609997 scopus 로고    scopus 로고
    • TOPPAS: A graphical workflow editor for the analysis of high-throughput proteomics data
    • Junker, J.; Bielow, C.; Bertsch, A.; Sturm, M.; Reinert, K.; Kohlbacher, O. TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data J. Proteome Res. 2012, 11, 3914-3920
    • (2012) J. Proteome Res. , vol.11 , pp. 3914-3920
    • Junker, J.1    Bielow, C.2    Bertsch, A.3    Sturm, M.4    Reinert, K.5    Kohlbacher, O.6
  • 33
    • 84875918606 scopus 로고    scopus 로고
    • Ph.D. thesis, Universität Tübingen: Tübingen, Germany.
    • Sturm, M. Ph.D. thesis, Universität Tübingen: Tübingen, Germany, 2010.
    • (2010)
    • Sturm, M.1
  • 34
    • 58149209843 scopus 로고
    • Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions
    • Senko, M. W.; Beu, S. C.; McLafferty, F. W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions J. Am. Soc. Mass Spectrom. 1995, 6, 229-233
    • (1995) J. Am. Soc. Mass Spectrom. , vol.6 , pp. 229-233
    • Senko, M.W.1    Beu, S.C.2    McLafferty, F.W.3
  • 35
    • 0035957820 scopus 로고    scopus 로고
    • A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks
    • Lan, K.; Jorgenson, J. W. A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks J. Chromatogr., A 2001, 915, 1-13
    • (2001) J. Chromatogr., A , vol.915 , pp. 1-13
    • Lan, K.1    Jorgenson, J.W.2
  • 37
    • 42149105642 scopus 로고    scopus 로고
    • Time-series alignment by non-negative multiple generalized canonical correlation analysis
    • Fischer, B.; Roth, V.; Buhmann, J. M. Time-series alignment by non-negative multiple generalized canonical correlation analysis BMC Bioinf. 2007, 8 (Suppl 10) S4
    • (2007) BMC Bioinf. , vol.8 , Issue.SUPPL. 10 , pp. 4
    • Fischer, B.1    Roth, V.2    Buhmann, J.M.3
  • 38
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • Smith, C. A.; Want, E. J.; O'Maille, G.; Abagyan, R.; Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal. Chem. 2006, 78, 779-787
    • (2006) Anal. Chem. , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 39
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • Heyer, L. J.; Kruglyak, S.; Yooseph, S. Exploring expression data: identification and analysis of coexpressed genes Genome Res. 1999, 9, 1106-1115
    • (1999) Genome Res. , vol.9 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 41
    • 68449102172 scopus 로고    scopus 로고
    • Proteomewide cellular protein concentrations of the human pathogen Leptospira interrogans
    • Malmström, J.; Beck, M.; Schmidt, A.; Lange, V.; Deutsch, E. W.; Aebersold, R. Proteomewide cellular protein concentrations of the human pathogen Leptospira interrogans Nature 2009, 460, 762-765
    • (2009) Nature , vol.460 , pp. 762-765
    • Malmström, J.1    Beck, M.2    Schmidt, A.3    Lange, V.4    Deutsch, E.W.5    Aebersold, R.6
  • 42
    • 38649129079 scopus 로고    scopus 로고
    • Posterior error probabilities and false discovery rates: Two sides of the same coin
    • Käll, L.; Storey, J. D.; MacCoss, M. J.; Noble, W. S. Posterior error probabilities and false discovery rates: two sides of the same coin J. Proteome Res. 2008, 7, 40-44
    • (2008) J. Proteome Res. , vol.7 , pp. 40-44
    • Käll, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 43
    • 67650733220 scopus 로고    scopus 로고
    • Highly accelerated feature detection in proteomics data sets using modern graphics processing units
    • Hussong, R.; Gregorius, B.; Tholey, A.; Hildebrandt, A. Highly accelerated feature detection in proteomics data sets using modern graphics processing units Bioinformatics 2009, 25, 1937-1943
    • (2009) Bioinformatics , vol.25 , pp. 1937-1943
    • Hussong, R.1    Gregorius, B.2    Tholey, A.3    Hildebrandt, A.4
  • 44
    • 67650388499 scopus 로고    scopus 로고
    • TOPPView: An open-source viewer for mass spectrometry data
    • Sturm, M.; Kohlbacher, O. TOPPView: an open-source viewer for mass spectrometry data J. Proteome Res. 2009, 8, 3760-3763
    • (2009) J. Proteome Res. , vol.8 , pp. 3760-3763
    • Sturm, M.1    Kohlbacher, O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.