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Volumn 10, Issue 7, 2011, Pages 2922-2929

MSSimulator: Simulation of mass spectrometry data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MSSIMULATOR; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUALITY CONTROL; SIMULATOR;

EID: 79959943230     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200155f     Document Type: Article
Times cited : (36)

References (32)
  • 1
    • 18744384734 scopus 로고    scopus 로고
    • Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
    • DOI 10.1093/bioinformatics/bti254
    • Morris, J. S.; Coombes, K. R.; Koomen, J.; Baggerly, K. A.; Kobayashi, R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum Bioinformatics 2005, 21, 1764-75 (Pubitemid 40674202)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1764-1775
    • Morris, J.S.1    Coombes, K.R.2    Koomen, J.3    Baggerly, K.A.4    Kobayashi, R.5
  • 2
    • 18744410496 scopus 로고    scopus 로고
    • Understanding the characteristics of mass spectrometry data through the use of simulation
    • Coombes, K. R.; Koomen, J. M.; Baggerly, K. A.; Morris, J. S.; Kobayashi, R. Understanding the characteristics of mass spectrometry data through the use of simulation Cancer Inform. 2005, 1, 41-52
    • (2005) Cancer Inform. , vol.1 , pp. 41-52
    • Coombes, K.R.1    Koomen, J.M.2    Baggerly, K.A.3    Morris, J.S.4    Kobayashi, R.5
  • 5
    • 60549117342 scopus 로고    scopus 로고
    • Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
    • Yang, C.; He, Z.; Yu, W. Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis BMC Bioinform. 2009, 10, 4
    • (2009) BMC Bioinform. , vol.10 , pp. 4
    • Yang, C.1    He, Z.2    Yu, W.3
  • 8
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • DOI 10.1002/pmic.200300744
    • Creasy, D. M.; Cottrell, J. S. Unimod: Protein modifications for mass spectrometry Proteomics 2004, 4, 1534-6 (Pubitemid 38738312)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 9
    • 33846632267 scopus 로고    scopus 로고
    • Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics
    • DOI 10.1021/pr060507u
    • Siepen, J. A.; Keevil, E.-J.; Knight, D.; Hubbard, S. J. Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics J. Proteome Res. 2007, 6, 399-408 (Pubitemid 46173693)
    • (2007) Journal of Proteome Research , vol.6 , Issue.1 , pp. 399-408
    • Siepen, J.A.1    Keevil, E.-J.2    Knight, D.3    Hubbard, S.J.4
  • 11
    • 39849105680 scopus 로고    scopus 로고
    • Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics
    • Pfeifer, N.; Leinenbach, A.; Huber, C. G.; Kohlbacher, O. Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics BMC Bioinform. 2007, 8, 468
    • (2007) BMC Bioinform. , vol.8 , pp. 468
    • Pfeifer, N.1    Leinenbach, A.2    Huber, C.G.3    Kohlbacher, O.4
  • 12
    • 0035957820 scopus 로고    scopus 로고
    • A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks
    • DOI 10.1016/S0021-9673(01)00594-5, PII S0021967301005945
    • 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 (Pubitemid 32289320)
    • (2001) Journal of Chromatography A , vol.915 , Issue.1-2 , pp. 1-13
    • Lan, K.1    Jorgenson, J.W.2
  • 13
    • 0025830123 scopus 로고
    • Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem
    • Kubinyi, H. Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem Anal. Chim. Acta 1991, 247, 107-19
    • (1991) Anal. Chim. Acta , vol.247 , pp. 107-19
    • Kubinyi, H.1
  • 16
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • DOI 10.1021/ac049951b
    • Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides Anal. Chem. 2004, 76, 3908-22 (Pubitemid 38943659)
    • (2004) Analytical Chemistry , vol.76 , Issue.14 , pp. 3908-3922
    • Zhang, Z.1
  • 18
    • 51249111303 scopus 로고    scopus 로고
    • A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
    • Zhou, C.; Bowler, L. D.; Feng, J. A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data BMC Bioinform. 2008, 9, 325
    • (2008) BMC Bioinform. , vol.9 , pp. 325
    • Zhou, C.1    Bowler, L.D.2    Feng, J.3
  • 19
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    • DOI 10.1038/nbt930
    • Elias, J. E.; Gibbons, F. D.; King, O. D.; Roth, F. P.; Gygi, S. P. Intensity-based protein identification by machine learning from a library of tandem mass spectra Nat. Biotechnol. 2004, 22, 214-9 (Pubitemid 38160538)
    • (2004) Nature Biotechnology , vol.22 , Issue.2 , pp. 214-219
    • Elias, J.E.1    Gibbons, F.D.2    King, O.D.3    Roth, F.P.4    Gygi, S.P.5
  • 20
    • 66749169317 scopus 로고    scopus 로고
    • Predicting intensity ranks of peptide fragment ions
    • Frank, A. M. Predicting intensity ranks of peptide fragment ions J. Proteome Res. 2009, 8, 2226-40
    • (2009) J. Proteome Res. , vol.8 , pp. 2226-40
    • Frank, A.M.1
  • 21
    • 69349092456 scopus 로고    scopus 로고
    • ETISEQ-an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics
    • Wong, J. W. H.; Schwahn, A. B.; Downard, K. M. ETISEQ-an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics BMC Bioinform. 2009, 10, 244
    • (2009) BMC Bioinform. , vol.10 , pp. 244
    • Wong, J.W.H.1    Schwahn, A.B.2    Downard, K.M.3
  • 22
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics 2004, 3, 1154-69
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1154-69
    • Ross, P.L.1
  • 23
    • 0036583926 scopus 로고    scopus 로고
    • Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics
    • Ong, S.-E. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics Mol. Cell. Proteomics 2002, 1, 376-86
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 376-86
    • Ong, S.-E.1
  • 25
    • 34547112014 scopus 로고    scopus 로고
    • 18O labeling with a correction for labeling efficiency
    • DOI 10.1074/mcp.T600029-MCP200
    • Ramos-Fernaindez, A.; López-Ferrer, D.; Vaizquez, J. Improved method for differential expression proteomics using trypsin-catalyzed 18O labeling with a correction for labeling efficiency Mol. Cell. Proteomics 2007, 6, 1274-86 (Pubitemid 47099235)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.7 , pp. 1274-1286
    • Ramos-Fernandez, A.1    Lopez-Ferrer, D.2    Vazquez, J.3
  • 26
    • 78651082595 scopus 로고    scopus 로고
    • MzML - A Community Standard for Mass Spectrometry Data
    • R110.000133
    • Martens, L. mzML-a Community Standard for Mass Spectrometry Data Mol. Cell. Proteomics 2010, R110.000133
    • (2010) Mol. Cell. Proteomics
    • Martens, L.1
  • 28
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
    • DOI 10.1038/nbt1001-946
    • Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat. Biotechnol. 2001, 19, 946-51 (Pubitemid 32947573)
    • (2001) Nature Biotechnology , vol.19 , Issue.10 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 29
    • 0344737959 scopus 로고    scopus 로고
    • Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry
    • DOI 10.1021/ac034633i
    • Li, X.-J.; Zhang, H.; Ranish, J. A.; Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry Anal. Chem. 2003, 75, 6648-57 (Pubitemid 37493927)
    • (2003) Analytical Chemistry , vol.75 , Issue.23 , pp. 6648-6657
    • Li, X.-J.1    Zhang, H.2    Ranish, J.A.3    Aebersold, R.4
  • 31
    • 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, 1367-72
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-72
    • Cox, J.1    Mann, M.2
  • 32
    • 34547727671 scopus 로고    scopus 로고
    • High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry
    • DOI 10.1021/ac0700833
    • Hoopmann, M. R.; Finney, G. L.; MacCoss, M. J. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry Anal. Chem. 2007, 79, 5620-32 (Pubitemid 47229808)
    • (2007) Analytical Chemistry , vol.79 , Issue.15 , pp. 5620-5632
    • Hoopmann, M.R.1    Finney, G.L.2    MacCoss, M.J.3


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