메뉴 건너뛰기




Volumn 12, Issue 12, 2013, Pages 5742-5749

Mspire-simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data

Author keywords

mass spectroscopy; model; mspire; proteomics; simulation; simulator

Indexed keywords

ALGORITHM; ARTICLE; DEVICES; GOLD STANDARD; LIQUID CHROMATOGRAPHY; MACHINE LEARNING; MASS SPECTROMETRY; PREDICTION; PRIORITY JOURNAL; PROTEOMICS; SIMULATOR; AMINO ACID SEQUENCE; ANIMAL; BOVINAE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; HUMAN; MOLECULAR GENETICS; PROCEDURES; STANDARD; STANDARDS; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA;

EID: 84890105363     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400727e     Document Type: Article
Times cited : (17)

References (25)
  • 1
    • 79953719716 scopus 로고    scopus 로고
    • More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC-MS/MS
    • Michalski, A.; Cox, J.; Mann, M. More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC-MS/MS J. Proteome Res. 2011, 10 (4) 1785-1793
    • (2011) J. Proteome Res. , vol.10 , Issue.4 , pp. 1785-1793
    • Michalski, A.1    Cox, J.2    Mann, M.3
  • 2
    • 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 (12) 1367-1372
    • (2008) Nat. Biotechnol. , vol.26 , Issue.12 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 3
    • 84867045160 scopus 로고    scopus 로고
    • Current challenges in software solutions for mass spectrometry-based quantitative proteomics
    • Cappadona, S.; Baker, P.; Cutillas, P.; Heck, A. R.; Breukelen, B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics Amino Acids 2012, 43 (3) 1087-1108
    • (2012) Amino Acids , vol.43 , Issue.3 , pp. 1087-1108
    • Cappadona, S.1    Baker, P.2    Cutillas, P.3    Heck, A.R.4    Breukelen, B.5
  • 4
    • 67049132416 scopus 로고    scopus 로고
    • Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
    • Prakash, A.; Tomazela, D. M.; Frewen, B.; MacLean, B.; Merrihew, G.; Peterman, S.; MacCoss, M. J. Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development J. Proteome Res. 2009, 8 (6) 2733-2739
    • (2009) J. Proteome Res. , vol.8 , Issue.6 , pp. 2733-2739
    • Prakash, A.1    Tomazela, D.M.2    Frewen, B.3    MacLean, B.4    Merrihew, G.5    Peterman, S.6    MacCoss, M.J.7
  • 5
    • 84865778501 scopus 로고    scopus 로고
    • Application of Parallel Hybrid Algorithm in Massively Parallel GPGPU - The Improved Effective and Efficient Method for Calculating Coulombic Interactions in Simulations of Many Ions with SIMION
    • Saito, K.; Koizumi, E.; Koizumi, H. Application of Parallel Hybrid Algorithm in Massively Parallel GPGPU-The Improved Effective and Efficient Method for Calculating Coulombic Interactions in Simulations of Many Ions with SIMION J. Am. Soc. Mass Spectrom. 2012, 23 (9) 1609-1615
    • (2012) J. Am. Soc. Mass Spectrom. , vol.23 , Issue.9 , pp. 1609-1615
    • Saito, K.1    Koizumi, E.2    Koizumi, H.3
  • 7
    • 55349093999 scopus 로고    scopus 로고
    • LC-MSsim - A simulation software for liquid chromatography mass spectrometry data
    • Schulz-Trieglaff, O.; Pfeifer, N.; Gropl, C.; Kohlbacher, O.; Reinert, K. LC-MSsim-a simulation software for liquid chromatography mass spectrometry data BMC Bioinf. 2008, 9 (1) 423
    • (2008) BMC Bioinf. , vol.9 , Issue.1 , pp. 423
    • Schulz-Trieglaff, O.1    Pfeifer, N.2    Gropl, C.3    Kohlbacher, O.4    Reinert, K.5
  • 8
    • 79959943230 scopus 로고    scopus 로고
    • MSSimulator: Simulation of Mass Spectrometry Data
    • Bielow, C.; Aiche, S.; Andreotti, S.; Reinert, K. MSSimulator: Simulation of Mass Spectrometry Data J. Proteome Res. 2011, 10 (7) 2922-2929
    • (2011) J. Proteome Res. , vol.10 , Issue.7 , pp. 2922-2929
    • Bielow, C.1    Aiche, S.2    Andreotti, S.3    Reinert, K.4
  • 9
    • 56649123516 scopus 로고    scopus 로고
    • Mspire: Mass spectrometry proteomics in Ruby
    • Prince, J. T.; Marcotte, E. M. mspire: mass spectrometry proteomics in Ruby Bioinformatics 2008, 24 (23) 2796-2797
    • (2008) Bioinformatics , vol.24 , Issue.23 , pp. 2796-2797
    • Prince, J.T.1    Marcotte, E.M.2
  • 11
    • 60649089559 scopus 로고    scopus 로고
    • Highly sensitive feature detection for high resolution LC/MS
    • Tautenhahn, R.; Bottcher, C.; Neumann, S. Highly sensitive feature detection for high resolution LC/MS BMC Bioinf. 2008, 9 (1) 504
    • (2008) BMC Bioinf. , vol.9 , Issue.1 , pp. 504
    • Tautenhahn, R.1    Bottcher, C.2    Neumann, S.3
  • 12
    • 84867045160 scopus 로고    scopus 로고
    • Current challenges in software solutions for mass spectrometry-based quantitative proteomics
    • Cappadona, S.; Baker, P. R.; Cutillas, P. R.; Heck, A. J. R.; van Breukelen, B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics Amino Acids 2012, 43, 1087-1108
    • (2012) Amino Acids , vol.43 , pp. 1087-1108
    • Cappadona, S.1    Baker, P.R.2    Cutillas, P.R.3    Heck, A.J.R.4    Van Breukelen, B.5
  • 14
    • 84957622513 scopus 로고    scopus 로고
    • Generating Rule Sets from Model Trees
    • Foo, N. Springer: Berlin
    • Holmes, G.; Hall, M.; Prank, E., Generating Rule Sets from Model Trees. In Advanced Topics in Artificial Intelligence; Foo, N., Ed.; Springer: Berlin, 1999; Vol. 1747, pp 1-12.
    • (1999) Advanced Topics in Artificial Intelligence , vol.1747 , pp. 1-12
    • Holmes, G.1    Hall, M.2    Prank, E.3
  • 16
    • 0030180572 scopus 로고    scopus 로고
    • Ultrahigh-Speed Calculation of Isotope Distributions
    • Rockwood, A. L.; Van Orden, S. L. Ultrahigh-Speed Calculation of Isotope Distributions Anal. Chem. 1996, 68 (13) 2027-2030
    • (1996) Anal. Chem. , vol.68 , Issue.13 , pp. 2027-2030
    • Rockwood, A.L.1    Van Orden, S.L.2
  • 17
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: Open source software for rapid proteomics tools development
    • Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P. ProteoWizard: open source software for rapid proteomics tools development Bioinformatics 2008, 24 (21) 2534-2536
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 18
    • 84878882380 scopus 로고    scopus 로고
    • Novel algorithms and the benefits of comparative validation
    • Smith, R.; Ventura, D.; Prince, J. T. Novel algorithms and the benefits of comparative validation Bioinformatics 2013, 29 (12) 1583-1585
    • (2013) Bioinformatics , vol.29 , Issue.12 , pp. 1583-1585
    • Smith, R.1    Ventura, D.2    Prince, J.T.3
  • 19
    • 84890102618 scopus 로고    scopus 로고
    • Controlling for Confounding Variables in MS-omics Protocol: Why Modularity Matters
    • 10.1093/bib/bbt049
    • Smith, R.; Ventura, D.; Prince, J. T. Controlling for Confounding Variables in MS-omics Protocol: Why Modularity Matters Briefings Bioinf. 2013, 10.1093/bib/bbt049
    • (2013) Briefings Bioinf.
    • Smith, R.1    Ventura, D.2    Prince, J.T.3
  • 20
    • 84897366782 scopus 로고    scopus 로고
    • Statistical Agglomeration: Peak Summarization for Direct Infusion Lipidomics
    • 10.1093/bioinformatics/btt376
    • Smith, R.; Anthonymuthu, T. S.; Ventura, D.; Prince, J. T. Statistical Agglomeration: Peak Summarization for Direct Infusion Lipidomics Bioinformatics 2013, 10.1093/bioinformatics/btt376
    • (2013) Bioinformatics
    • Smith, R.1    Anthonymuthu, T.S.2    Ventura, D.3    Prince, J.T.4
  • 25
    • 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 (7) 3760-3763
    • (2009) J Proteome Res , vol.8 , Issue.7 , pp. 3760-3763
    • Sturm, M.1    Kohlbacher, O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.