메뉴 건너뛰기




Volumn 15, Issue 3, 2016, Pages 809-814

Testing and Validation of Computational Methods for Mass Spectrometry

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; LIPIDOMICS; MASS SPECTROMETRY; METABOLOMICS; PRIORITY JOURNAL; PROTEOMICS; BIOLOGY; PROCEDURES; STANDARDS; VALIDATION STUDY;

EID: 84960364338     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00852     Document Type: Article
Times cited : (32)

References (38)
  • 1
    • 80555146719 scopus 로고    scopus 로고
    • Editorial: From Data to Results
    • Aebersold, R. Editorial: From Data to Results Mol. Cell. Proteomics 2011, 10, E111.014787 10.1074/mcp.E111.014787
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. E111014787
    • Aebersold, R.1
  • 2
    • 84929660072 scopus 로고    scopus 로고
    • Managing Expectations When Publishing Tools and Methods for Computational Proteomics
    • Martens, L.; Kohlbacher, O.; Weintraub, S. T. Managing Expectations When Publishing Tools and Methods for Computational Proteomics J. Proteome Res. 2015, 14, 2002-2004 10.1021/pr501318d
    • (2015) J. Proteome Res. , vol.14 , pp. 2002-2004
    • Martens, L.1    Kohlbacher, O.2    Weintraub, S.T.3
  • 3
    • 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, 1583-5 10.1093/bioinformatics/btt176
    • (2013) Bioinformatics , vol.29 , pp. 1583-1585
    • Smith, R.1    Ventura, D.2    Prince, J.T.3
  • 4
    • 84885639290 scopus 로고    scopus 로고
    • On representative and illustrative comparisons with real data in bioinformatics: Response to the letter to the editor by Smith et al
    • Boulesteix, A. L. On representative and illustrative comparisons with real data in bioinformatics: response to the letter to the editor by Smith et al Bioinformatics 2013, 29, 2664-6 10.1093/bioinformatics/btt458
    • (2013) Bioinformatics , vol.29 , pp. 2664-2666
    • Boulesteix, A.L.1
  • 5
    • 84876567454 scopus 로고    scopus 로고
    • A plea for neutral comparison studies in computational sciences
    • Boulesteix, A. L.; Lauer, S.; Eugster, M. J. A plea for neutral comparison studies in computational sciences PLoS One 2013, 8, e61562 10.1371/journal.pone.0061562
    • (2013) PLoS One , vol.8 , pp. e61562
    • Boulesteix, A.L.1    Lauer, S.2    Eugster, M.J.3
  • 6
    • 84929465279 scopus 로고    scopus 로고
    • Ten simple rules for reducing overoptimistic reporting in methodological computational research
    • Boulesteix, A. L. Ten simple rules for reducing overoptimistic reporting in methodological computational research PLoS Comput. Biol. 2015, 11, e1004191 10.1371/journal.pcbi.1004191
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004191
    • Boulesteix, A.L.1
  • 7
    • 84940653205 scopus 로고    scopus 로고
    • A Statistical Framework for Hypothesis Testing in Real Data Comparison Studies
    • Boulesteix, A.-L.; Hable, R.; Lauer, S.; Eugster, M. J. A. A Statistical Framework for Hypothesis Testing in Real Data Comparison Studies Am. Stat. 2015, 69, 201-212 10.1080/00031305.2015.1005128
    • (2015) Am. Stat. , vol.69 , pp. 201-212
    • Boulesteix, A.-L.1    Hable, R.2    Lauer, S.3    Eugster, M.J.A.4
  • 8
    • 84928989815 scopus 로고    scopus 로고
    • JAMSS: Proteomics mass spectrometry simulation in Java
    • Smith, R.; Prince, J. T. JAMSS: proteomics mass spectrometry simulation in Java Bioinformatics 2015, 31, 791-3 10.1093/bioinformatics/btu729
    • (2015) Bioinformatics , vol.31 , pp. 791-793
    • Smith, R.1    Prince, J.T.2
  • 9
    • 84890105363 scopus 로고    scopus 로고
    • Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data
    • Noyce, A. B.; Smith, R.; Dalgleish, J.; Taylor, R. M.; Erb, K. C.; Okuda, N.; Prince, J. T. Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data J. Proteome Res. 2013, 12, 5742-9 10.1021/pr400727e
    • (2013) J. Proteome Res. , vol.12 , pp. 5742-5749
    • Noyce, A.B.1    Smith, R.2    Dalgleish, J.3    Taylor, R.M.4    Erb, K.C.5    Okuda, N.6    Prince, J.T.7
  • 10
    • 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, 2922-9 10.1021/pr200155f
    • (2011) J. Proteome Res. , vol.10 , pp. 2922-2929
    • Bielow, C.1    Aiche, S.2    Andreotti, S.3    Reinert, K.4
  • 11
    • 55349093999 scopus 로고    scopus 로고
    • LC-MSsim - A simulation software for liquid chromatography mass spectrometry data
    • Schulz-Trieglaff, O.; Pfeifer, N.; Gröpl, C.; Kohlbacher, O.; Reinert, K. LC-MSsim - A simulation software for liquid chromatography mass spectrometry data BMC Bioinf. 2008, 9, 423 10.1186/1471-2105-9-423
    • (2008) BMC Bioinf. , vol.9 , pp. 423
    • Schulz-Trieglaff, O.1    Pfeifer, N.2    Gröpl, C.3    Kohlbacher, O.4    Reinert, K.5
  • 15
    • 84978008004 scopus 로고    scopus 로고
    • Terence's Stuff: Does it work in practice?
    • Speed, T. P. Terence's Stuff: Does it work in practice? IMS Bull. 2012, 41, 9
    • (2012) IMS Bull. , vol.41 , pp. 9
    • Speed, T.P.1
  • 16
    • 62549163396 scopus 로고    scopus 로고
    • Papers on normalization, variable selection, classification or clustering of microarray data
    • Rocke, D. M.; Ideker, T.; Troyanskaya, O.; Quackenbush, J.; Dopazo, J. Papers on normalization, variable selection, classification or clustering of microarray data Bioinformatics 2009, 25, 701-702 10.1093/bioinformatics/btp038
    • (2009) Bioinformatics , vol.25 , pp. 701-702
    • Rocke, D.M.1    Ideker, T.2    Troyanskaya, O.3    Quackenbush, J.4    Dopazo, J.5
  • 17
    • 84879391561 scopus 로고    scopus 로고
    • Improving qualitative and quantitative performance for MS(E)-based label-free proteomics
    • Bond, N. J.; Shliaha, P. V.; Lilley, K. S.; Gatto, L. Improving qualitative and quantitative performance for MS(E)-based label-free proteomics J. Proteome Res. 2013, 12, 2340-53 10.1021/pr300776t
    • (2013) J. Proteome Res. , vol.12 , pp. 2340-2353
    • Bond, N.J.1    Shliaha, P.V.2    Lilley, K.S.3    Gatto, L.4
  • 18
    • 84938750115 scopus 로고    scopus 로고
    • EBprot: Statistical analysis of labeling-based quantitative proteomics data
    • Koh, H. W.; Swa, H. L.; Fermin, D.; Ler, S. G.; Gunaratne, J.; Choi, H. EBprot: Statistical analysis of labeling-based quantitative proteomics data Proteomics 2015, 15, 2580-91 10.1002/pmic.201400620
    • (2015) Proteomics , vol.15 , pp. 2580-2591
    • Koh, H.W.1    Swa, H.L.2    Fermin, D.3    Ler, S.G.4    Gunaratne, J.5    Choi, H.6
  • 19
    • 80155124832 scopus 로고    scopus 로고
    • MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
    • Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics Nat. Methods 2011, 8, 937-40 10.1038/nmeth.1714
    • (2011) Nat. Methods , vol.8 , pp. 937-940
    • Ting, L.1    Rad, R.2    Gygi, S.P.3    Haas, W.4
  • 20
    • 84941747213 scopus 로고    scopus 로고
    • In-depth evaluation of software tools for data-independent acquisition based label-free quantification
    • Kuharev, J.; Navarro, P.; Distler, U.; Jahn, O.; Tenzer, S. In-depth evaluation of software tools for data-independent acquisition based label-free quantification Proteomics 2015, 15, 3140 10.1002/pmic.201400396
    • (2015) Proteomics , vol.15 , pp. 3140
    • Kuharev, J.1    Navarro, P.2    Distler, U.3    Jahn, O.4    Tenzer, S.5
  • 22
    • 84888266922 scopus 로고    scopus 로고
    • Assessing computational methods for transcription factor target gene identification based on ChIP-seq data
    • Sikora-Wohlfeld, W.; Ackermann, M.; Christodoulou, E. G.; Singaravelu, K.; Beyer, A. Assessing computational methods for transcription factor target gene identification based on ChIP-seq data PLoS Comput. Biol. 2013, 9, e1003342 10.1371/journal.pcbi.1003342
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003342
    • Sikora-Wohlfeld, W.1    Ackermann, M.2    Christodoulou, E.G.3    Singaravelu, K.4    Beyer, A.5
  • 23
  • 24
    • 84937691256 scopus 로고    scopus 로고
    • Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
    • Kanitz, A.; Gypas, F.; Gruber, A. J.; Gruber, A. R.; Martin, G.; Zavolan, M. Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data Genome Biol. 2015, 16, 150 10.1186/s13059-015-0702-5
    • (2015) Genome Biol. , vol.16 , pp. 150
    • Kanitz, A.1    Gypas, F.2    Gruber, A.J.3    Gruber, A.R.4    Martin, G.5    Zavolan, M.6
  • 25
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M. I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biol. 2014, 15, 550 10.1186/s13059-014-0550-8
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 26
    • 84899504030 scopus 로고    scopus 로고
    • Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
    • Gatto, L.; Breckels, L. M.; Wieczorek, S.; Burger, T.; Lilley, K. S. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata Bioinformatics 2014, 30, 1322-4 10.1093/bioinformatics/btu013
    • (2014) Bioinformatics , vol.30 , pp. 1322-1324
    • Gatto, L.1    Breckels, L.M.2    Wieczorek, S.3    Burger, T.4    Lilley, K.S.5
  • 31
    • 10944232800 scopus 로고    scopus 로고
    • Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
    • Beyer, A.; Hollunder, J.; Nasheuer, H. P.; Wilhelm, T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale Mol. Cell. Proteomics 2004, 3, 1083-92 10.1074/mcp.M400099-MCP200
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1083-1092
    • Beyer, A.1    Hollunder, J.2    Nasheuer, H.P.3    Wilhelm, T.4
  • 32
    • 34047223024 scopus 로고    scopus 로고
    • Posttranscriptional expression regulation: What determines translation rates?
    • Brockmann, R.; Beyer, A.; Heinisch, J. J.; Wilhelm, T. Posttranscriptional expression regulation: what determines translation rates? PLoS Comput. Biol. 2007, 3, e57 10.1371/journal.pcbi.0030057
    • (2007) PLoS Comput. Biol. , vol.3 , pp. e57
    • Brockmann, R.1    Beyer, A.2    Heinisch, J.J.3    Wilhelm, T.4
  • 33
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • Vogel, C.; Marcotte, E. M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses Nat. Rev. Genet. 2012, 13, 227-32 10.1038/nrg3185
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 34
    • 84924347993 scopus 로고    scopus 로고
    • Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens
    • Jovanovic, M. et al. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens Science 2015, 347, 1259038 10.1126/science.1259038
    • (2015) Science , vol.347 , pp. 1259038
    • Jovanovic, M.1
  • 35
    • 84942905791 scopus 로고    scopus 로고
    • Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less
    • Serang, L.; Käll, O. Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less J. Proteome Res. 2015, 14, 4099-103 10.1021/acs.jproteome.5b00568
    • (2015) J. Proteome Res. , vol.14 , pp. 4099-4103
    • Serang, L.1    Käll, O.2
  • 36
  • 37
    • 81055124271 scopus 로고    scopus 로고
    • ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets
    • Frazee, A. C.; Langmead, B.; Leek, J. T. ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets BMC Bioinf. 2011, 12, 449 10.1186/1471-2105-12-449
    • (2011) BMC Bioinf. , vol.12 , pp. 449
    • Frazee, A.C.1    Langmead, B.2    Leek, J.T.3
  • 38
    • 84891796097 scopus 로고    scopus 로고
    • ProteomeXchange provides globally coordinated proteomics data submission and dissemination
    • Vizcaíno, J. A. et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nat. Biotechnol. 2014, 32, 223-6 10.1038/nbt.2839
    • (2014) Nat. Biotechnol. , vol.32 , pp. 223-226
    • Vizcaíno, J.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.