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Volumn 15, Issue 18, 2015, Pages 3140-3151

In-depth evaluation of software tools for data-independent acquisition based label-free quantification

Author keywords

Bioinformatics; Data independent acquisition; Ion mobility separation; Label free quantification

Indexed keywords

PROTEIN; PEPTIDE FRAGMENT; PROTEOME;

EID: 84941747213     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400396     Document Type: Article
Times cited : (52)

References (41)
  • 1
    • 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
  • 2
    • 63049084861 scopus 로고    scopus 로고
    • The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS
    • Geromanos, S. J., Vissers, J. P. C., Silva, J.C., Dorschel, C. A. et al., The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009, 9, 1683-1695.
    • (2009) Proteomics , vol.9 , pp. 1683-1695
    • Geromanos, S.J.1    Vissers, J.P.C.2    Silva, J.C.3    Dorschel, C.A.4
  • 3
    • 79953719716 scopus 로고    scopus 로고
    • More than 100000 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 100000 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, 1785-1793.
    • (2011) J. Proteome Res. , vol.10 , pp. 1785-1793
    • Michalski, A.1    Cox, J.2    Mann, M.3
  • 4
    • 84861897793 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics and network biology
    • Bensimon, A., Heck, A. J. R., Aebersold, R., Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem. 2012, 81, 379-405.
    • (2012) Annu. Rev. Biochem , vol.81 , pp. 379-405
    • Bensimon, A.1    Heck, A.J.R.2    Aebersold, R.3
  • 5
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm, M., Schlegl, J., Hahne, H., Moghaddas Gholami, A. et al., Mass-spectrometry-based draft of the human proteome. Nature 2014, 509, 582-587.
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1    Schlegl, J.2    Hahne, H.3    Moghaddas Gholami, A.4
  • 6
    • 84864987862 scopus 로고    scopus 로고
    • The use of selected reaction monitoring in quantitative proteomics
    • Holman, S. W., Sims, P. F. G., Eyers, C. E., The use of selected reaction monitoring in quantitative proteomics. Bioanalysis 2012, 4, 1763-1786.
    • (2012) Bioanalysis , vol.4 , pp. 1763-1786
    • Holman, S.W.1    Sims, P.F.G.2    Eyers, C.E.3
  • 7
    • 20144388265 scopus 로고    scopus 로고
    • Quantitative proteomic analysis by accurate mass retention time pairs
    • Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
    • (2005) Anal. Chem. , vol.77 , pp. 2187-2200
    • Silva, J.C.1    Denny, R.2    Dorschel, C.A.3    Gorenstein, M.4
  • 8
    • 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
    • Gillet, L. C., Navarro, P., Tate, S., Röst, H. 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 2012, 11, O111.016717.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. O111016717
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Röst, H.4
  • 9
    • 84895071750 scopus 로고    scopus 로고
    • Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
    • Distler, U., Kuharev, J., Navarro, P., Levin, Y. et al., Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat. Methods 2014, 11, 167-170.
    • (2014) Nat. Methods , vol.11 , pp. 167-170
    • Distler, U.1    Kuharev, J.2    Navarro, P.3    Levin, Y.4
  • 10
    • 84896767479 scopus 로고    scopus 로고
    • General statistical framework for quantitative proteomics by stable isotope labeling
    • Navarro, P., Trevisan-Herraz, M., Bonzon-Kulichenko, E., Núñez, E. et al., General statistical framework for quantitative proteomics by stable isotope labeling. J. Proteome Res. 2014, 13, 1234-1247.
    • (2014) J. Proteome Res. , vol.13 , pp. 1234-1247
    • Navarro, P.1    Trevisan-Herraz, M.2    Bonzon-Kulichenko, E.3    Núñez, E.4
  • 11
    • 79961202534 scopus 로고    scopus 로고
    • The importance of the digest: proteolysis and absolute quantification in proteomics
    • Brownridge, P., Beynon, R. J., The importance of the digest: proteolysis and absolute quantification in proteomics. Methods 2011, 54, 351-360.
    • (2011) Methods , vol.54 , pp. 351-360
    • Brownridge, P.1    Beynon, R.J.2
  • 12
    • 79551500036 scopus 로고    scopus 로고
    • Less label, more free: approaches in label-free quantitative mass spectrometry
    • Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
    • (2011) Proteomics , vol.11 , pp. 535-553
    • Neilson, K.A.1    Ali, N.A.2    Muralidharan, S.3    Mirzaei, M.4
  • 13
    • 83055168515 scopus 로고    scopus 로고
    • Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach
    • M111007633
    • Carroll, K. M., Simpson, D. M., Eyers, C. E., Knight, C. G. et al., Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Mol. Cell. Proteomics 2011, 10, M111.007633.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Carroll, K.M.1    Simpson, D.M.2    Eyers, C.E.3    Knight, C.G.4
  • 15
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhäusser, B., Busse, D., Li, N., Dittmar, G. et al., Global quantification of mammalian gene expression control. Nature 2011, 473, 337-342.
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhäusser, B.1    Busse, D.2    Li, N.3    Dittmar, G.4
  • 16
    • 79959963697 scopus 로고    scopus 로고
    • RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification
    • Colaert, N., Gevaert, K., Martens, L., RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification. J. Proteome Res. 2011, 10, 3183-3189.
    • (2011) J. Proteome Res , vol.10 , pp. 3183-3189
    • Colaert, N.1    Gevaert, K.2    Martens, L.3
  • 18
    • 84898665956 scopus 로고    scopus 로고
    • OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
    • Röst, H. L., Rosenberger, G., Navarro, P., Gillet, L. et al., OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat. Biotechnol. 2014, 32, 219-23.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 219-223
    • Röst, H.L.1    Rosenberger, G.2    Navarro, P.3    Gillet, L.4
  • 19
    • 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. 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
  • 20
    • 84892877597 scopus 로고    scopus 로고
    • Exploring skyline for both MS(E)-based label-free proteomics and HRMS quantitation of small molecules
    • Liu, S., Chen, X., Yan, Z., Qin, S. et al., Exploring skyline for both MS(E)-based label-free proteomics and HRMS quantitation of small molecules. Proteomics 2014, 14, 169-180.
    • (2014) Proteomics , vol.14 , pp. 169-180
    • Liu, S.1    Chen, X.2    Yan, Z.3    Qin, S.4
  • 21
    • 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.
    • (2013) J. Proteome Res , vol.12 , pp. 2340-2353
    • Bond, N.J.1    Shliaha, P.V.2    Lilley, K.S.3    Gatto, L.4
  • 22
    • 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
  • 23
    • 42249108173 scopus 로고    scopus 로고
    • OpenMS - an open-source software framework for mass spectrometry
    • Sturm, M., Bertsch, A., Gröpl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163.
    • (2008) BMC Bioinformatics , vol.9 , pp. 163
    • Sturm, M.1    Bertsch, A.2    Gröpl, C.3    Hildebrandt, A.4
  • 24
    • 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
  • 25
    • 35348965139 scopus 로고    scopus 로고
    • SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling
    • Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S. et al., SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 2007, 7, 3470-3480.
    • (2007) Proteomics , vol.7 , pp. 3470-3480
    • Mueller, L.N.1    Rinner, O.2    Schmidt, A.3    Letarte, S.4
  • 26
    • 84890571201 scopus 로고    scopus 로고
    • Data processing methods and quality control strategies for label-free LC-MS protein quantification
    • Sandin, M., Teleman, J., Malmström, J., Levander, F., Data processing methods and quality control strategies for label-free LC-MS protein quantification. Biochim. Biophys. Acta 2014, 1844, 29-41.
    • (2014) Biochim. Biophys. Acta , vol.1844 , pp. 29-41
    • Sandin, M.1    Teleman, J.2    Malmström, J.3    Levander, F.4
  • 27
    • 54349106196 scopus 로고    scopus 로고
    • Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
    • Lange, E., Tautenhahn, R., Neumann, S., Gröpl, C., Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics 2008, 9, 375.
    • (2008) BMC Bioinformatics , vol.9 , pp. 375
    • Lange, E.1    Tautenhahn, R.2    Neumann, S.3    Gröpl, C.4
  • 28
    • 27644543078 scopus 로고    scopus 로고
    • Comparison of label-free methods for quantifying human proteins by shotgun proteomics
    • Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G. et al., Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4, 1487-1502.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1487-1502
    • Old, W.M.1    Meyer-Arendt, K.2    Aveline-Wolf, L.3    Pierce, K.G.4
  • 29
    • 78249241486 scopus 로고    scopus 로고
    • Evaluation for computational platforms of LC-MS based label-free quantitative proteomics: a global view
    • Zhang, R., Barton, A., Brittenden, J., Huang, J. T. J., Crowther, D., Evaluation for computational platforms of LC-MS based label-free quantitative proteomics: a global view. J. Proteomics Bioinform. 2010, 03, 260-265.
    • (2010) J. Proteomics Bioinform , vol.3 , pp. 260-265
    • Zhang, R.1    Barton, A.2    Brittenden, J.3    Huang, J.T.J.4    Crowther, D.5
  • 30
    • 84975194477 scopus 로고    scopus 로고
    • Digestion and depletion of abundant proteins improves proteomic coverage
    • Fonslow, B. R., Stein, B. D., Webb, K. J., Xu, T. et al., Digestion and depletion of abundant proteins improves proteomic coverage. Nat. Methods 2012, 1-5.
    • (2012) Nat. Methods , pp. 1-5
    • Fonslow, B.R.1    Stein, B.D.2    Webb, K.J.3    Xu, T.4
  • 31
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wiśniewski, J. R., Zougman, A., Nagaraj, N., Mann, M., Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-362.
    • (2009) Nat. Methods , vol.6 , pp. 359-362
    • Wiśniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 32
    • 84874762979 scopus 로고    scopus 로고
    • The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
    • Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A. et al., The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41, D1063-D1069.
    • (2013) Nucleic Acids Res , vol.41 , pp. D1063-D1069
    • Vizcaíno, J.A.1    Côté, R.G.2    Csordas, A.3    Dianes, J.A.4
  • 33
    • 84879367507 scopus 로고    scopus 로고
    • Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies
    • Shliaha, P. V, Bond, N. J., Gatto, L., Lilley, K. S., Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. J. Proteome Res. 2013, 12, 2323-2339.
    • (2013) J. Proteome Res. , vol.12 , pp. 2323-2339
    • Shliaha, P.V.1    Bond, N.J.2    Gatto, L.3    Lilley, K.S.4
  • 34
    • 84870322666 scopus 로고    scopus 로고
    • Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease
    • Erickson, A. R., Cantarel, B. L., Lamendella, R., Darzi, Y. et al., Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One 2012, 7, e49138.
    • (2012) PLoS One , vol.7 , pp. e49138
    • Erickson, A.R.1    Cantarel, B.L.2    Lamendella, R.3    Darzi, Y.4
  • 35
    • 84894259618 scopus 로고    scopus 로고
    • Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography-mass spectrometry workflow for biomarker discovery: use of product ion quantitation as an alternative data analysis
    • Daly, C. E., Ng, L.L., Hakimi, A., Willingale, R., Jones, D. J. L., Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography-mass spectrometry workflow for biomarker discovery: use of product ion quantitation as an alternative data analysis. Anal. Chem. 2014, 86, 1972-1979.
    • (2014) Anal. Chem. , vol.86 , pp. 1972-1979
    • Daly, C.E.1    Ng, L.L.2    Hakimi, A.3    Willingale, R.4    Jones, D.J.L.5
  • 36
    • 84883529394 scopus 로고    scopus 로고
    • Benchmarking stable isotope labeling based quantitative proteomics
    • Altelaar, A. F. M., Frese, C. K., Preisinger, C., Hennrich, M. L. et al., Benchmarking stable isotope labeling based quantitative proteomics. J. Proteomics 2013, 88, 14-26.
    • (2013) J. Proteomics , vol.88 , pp. 14-26
    • Altelaar, A.F.M.1    Frese, C.K.2    Preisinger, C.3    Hennrich, M.L.4
  • 37
    • 84907197082 scopus 로고    scopus 로고
    • MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction
    • Cox, J., Hein, M. Y., Luber, C. A., Paron, I. et al., MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction. Mol. Cell. Proteomics 2014, 13, 2513-2526.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 2513-2526
    • Cox, J.1    Hein, M.Y.2    Luber, C.A.3    Paron, I.4
  • 38
    • 84868028972 scopus 로고    scopus 로고
    • Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
    • Marguerat, S., Schmidt, A., Codlin, S., Chen, W. et al., Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 2012, 151, 671-683.
    • (2012) Cell , vol.151 , pp. 671-683
    • Marguerat, S.1    Schmidt, A.2    Codlin, S.3    Chen, W.4
  • 39
    • 84857476737 scopus 로고    scopus 로고
    • Computational and statistical analysis of protein mass spectrometry data
    • Noble, W. S., MacCoss, M. J., Computational and statistical analysis of protein mass spectrometry data. PLoS Comput. Biol. 2012, 8, e1002296.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002296
    • Noble, W.S.1    MacCoss, M.J.2
  • 40
    • 84873987395 scopus 로고    scopus 로고
    • A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments
    • Matzke, M. M., Brown, J. N., Gritsenko, M. A., Metz, T.O. et al., A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics 2013, 13, 493-503.
    • (2013) Proteomics , vol.13 , pp. 493-503
    • Matzke, M.M.1    Brown, J.N.2    Gritsenko, M.A.3    Metz, T.O.4
  • 41
    • 84914145820 scopus 로고    scopus 로고
    • An empirical bayesian random censoring threshold model improves detection of differentially abundant proteins
    • Koopmans, F., Cornelisse, L. N., Heskes, T., Dijkstra, T. M. H., An empirical bayesian random censoring threshold model improves detection of differentially abundant proteins. J. Proteome Res. 2014, 13, 3871-3880.
    • (2014) J. Proteome Res. , vol.13 , pp. 3871-3880
    • Koopmans, F.1    Cornelisse, L.N.2    Heskes, T.3    Dijkstra, T.M.H.4


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