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Volumn 13, Issue 3-4, 2013, Pages 493-503

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

Author keywords

Label free; Peak intensity; Protein quantification; Relative

Indexed keywords

HUMAN; LIMIT OF QUANTITATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PLASMA; PRIORITY JOURNAL; PROTEOMICS; REVIEW;

EID: 84873987395     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200269     Document Type: Review
Times cited : (72)

References (27)
  • 1
    • 33644524918 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics turns quantitative
    • Ong, S. E., Mann, M., Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1, 252-262.
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 4
    • 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
    • Noble, W.S.1    MacCoss, M.J.2
  • 5
    • 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
  • 6
    • 84865542140 scopus 로고    scopus 로고
    • Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli
    • Arike, L., Valgepea, K., Peil, L., Nahku, R. et al., Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J. Proteomics 2012, 75, 5437-5448.
    • (2012) J. Proteomics , vol.75 , pp. 5437-5448
    • Arike, L.1    Valgepea, K.2    Peil, L.3    Nahku, R.4
  • 8
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu, P., Vogel, C., Wang, R., Yao, X., Marcotte, E. M., Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25, 117-124.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 9
    • 80052347088 scopus 로고    scopus 로고
    • Bioinformatics challenges in mass spectrometry-driven proteomics
    • Martens, L., Bioinformatics challenges in mass spectrometry-driven proteomics. Methods Mol. Biol. 2011, 753, 359-371.
    • (2011) Methods Mol. Biol. , vol.753 , pp. 359-371
    • Martens, L.1
  • 10
    • 84859611662 scopus 로고    scopus 로고
    • Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data
    • Ning, K., Fermin, D., Nesvizhskii, A. I., Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J. Proteome Res. 2012, 11, 2261-2271.
    • (2012) J. Proteome Res. , vol.11 , pp. 2261-2271
    • Ning, K.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 11
    • 77954464041 scopus 로고    scopus 로고
    • Proteomics: a pragmatic perspective
    • Mallick, P., Kuster, B., Proteomics: a pragmatic perspective. Nat. Biotechnol. 2010, 28, 695-709.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 695-709
    • Mallick, P.1    Kuster, B.2
  • 12
    • 51649090147 scopus 로고    scopus 로고
    • A computational strategy to analyze label-free temporal bottom-up proteomics data
    • Du, X., Callister, S. J., Manes, N. P., Adkins, J. N. et al., A computational strategy to analyze label-free temporal bottom-up proteomics data. J. Proteome Res. 2008, 7, 2595-2604.
    • (2008) J. Proteome Res. , vol.7 , pp. 2595-2604
    • Du, X.1    Callister, S.J.2    Manes, N.P.3    Adkins, J.N.4
  • 13
    • 84859350735 scopus 로고    scopus 로고
    • Accurate mass spectrometry based protein quantification via shared peptides
    • Dost, B., Bandeira, N., Li, X., Shen, Z. et al., Accurate mass spectrometry based protein quantification via shared peptides. J. Comput. Biol. 2012, 19, 337-348.
    • (2012) J. Comput. Biol. , vol.19 , pp. 337-348
    • Dost, B.1    Bandeira, N.2    Li, X.3    Shen, Z.4
  • 14
    • 60849086516 scopus 로고    scopus 로고
    • Absolute protein quantification by LC/MS(E) for global analysis of salicylic acid-induced plant protein secretion responses
    • Cheng, F. Y., Blackburn, K., Lin, Y. M., Goshe, M. B., Williamson, J. D., Absolute protein quantification by LC/MS(E) for global analysis of salicylic acid-induced plant protein secretion responses. J. Proteome Res. 2009, 8, 82-93.
    • (2009) J. Proteome Res. , vol.8 , pp. 82-93
    • Cheng, F.Y.1    Blackburn, K.2    Lin, Y.M.3    Goshe, M.B.4    Williamson, J.D.5
  • 15
    • 46249116675 scopus 로고    scopus 로고
    • DAnTE: a statistical tool for quantitative analysis of -omics data
    • Polpitiya, A., Qian, W., Jaitly, N., Petyuk, V. et al., DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics 2008, 24, 1556-1558.
    • (2008) Bioinformatics , vol.24 , pp. 1556-1558
    • Polpitiya, A.1    Qian, W.2    Jaitly, N.3    Petyuk, V.4
  • 16
    • 68549137863 scopus 로고    scopus 로고
    • A statistical framework for protein quantitation in bottom-up MS-based proteomics
    • Karpievitch, Y., Stanley, J., Taverner, T., Huang, J. et al., A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics 2009, 25, 2028-2034.
    • (2009) Bioinformatics , vol.25 , pp. 2028-2034
    • Karpievitch, Y.1    Stanley, J.2    Taverner, T.3    Huang, J.4
  • 17
    • 70449433751 scopus 로고    scopus 로고
    • Protein quantification in label-free LC-MS experiments
    • Clough, T., Key, M., Ott, I., Ragg, S. et al., Protein quantification in label-free LC-MS experiments. J. Proteome Res. 2009, 8, 5275-5284.
    • (2009) J. Proteome Res. , vol.8 , pp. 5275-5284
    • Clough, T.1    Key, M.2    Ott, I.3    Ragg, S.4
  • 18
    • 84873986846 scopus 로고    scopus 로고
    • MSstats: statistical protein quantification in label-free LC-MS experiments
    • R package, version 1.1 (July 11, 2012).
    • Clough, T., Vitek, O., MSstats: statistical protein quantification in label-free LC-MS experiments. 2011. R package, version 1.1 (July 11, 2012).
    • (2011)
    • Clough, T.1    Vitek, O.2
  • 19
    • 33746416664 scopus 로고    scopus 로고
    • All pre-diabetes is not the same: metabolic and vascular risks of impaired fasting glucose at 100 versus 110 mg/dl: the screening for impaired glucose tolerance study 1 (SIGT 1)
    • Phillips, L. S., Weintraub, W. S., Ziemer, D. C., Kolm, P. et al., All pre-diabetes is not the same: metabolic and vascular risks of impaired fasting glucose at 100 versus 110 mg/dl: the screening for impaired glucose tolerance study 1 (SIGT 1). Diabetes Care 2006, 29, 1405-1407.
    • (2006) Diabetes Care , vol.29 , pp. 1405-1407
    • Phillips, L.S.1    Weintraub, W.S.2    Ziemer, D.C.3    Kolm, P.4
  • 20
    • 82955187002 scopus 로고    scopus 로고
    • A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors
    • Webb-Robertson, B. J., Matzke, M. M., Jacobs, J. M., Pounds, J. G., Waters, K. M., A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors. Proteomics 2011, 11, 4736-4741.
    • (2011) Proteomics , vol.11 , pp. 4736-4741
    • Webb-Robertson, B.J.1    Matzke, M.M.2    Jacobs, J.M.3    Pounds, J.G.4    Waters, K.M.5
  • 21
    • 78149378686 scopus 로고    scopus 로고
    • Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data
    • Webb-Robertson, B. J., McCue, L. A., Waters, K. M., Matzke, M. M. et al., Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data. J. Proteome Res. 2010, 9, 5748-5756.
    • (2010) J. Proteome Res. , vol.9 , pp. 5748-5756
    • Webb-Robertson, B.J.1    McCue, L.A.2    Waters, K.M.3    Matzke, M.M.4
  • 22
    • 80053982558 scopus 로고    scopus 로고
    • Improved quality control processing of peptide-centric LC-MS proteomics data
    • Matzke, M. M., Waters, K. M., Metz, T. O., Jacobs, J. M. et al., Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics 2011, 27, 2866-2872.
    • (2011) Bioinformatics , vol.27 , pp. 2866-2872
    • Matzke, M.M.1    Waters, K.M.2    Metz, T.O.3    Jacobs, J.M.4
  • 23
    • 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
  • 24
    • 70349213754 scopus 로고    scopus 로고
    • A Bayesian approach to protein inference problem in shotgun proteomics
    • Li, Y. F., Arnold, R. J., Li, Y., Radivojac, P. et al., A Bayesian approach to protein inference problem in shotgun proteomics. J. Comput. Biol. 2009, 16, 1183-1193.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1183-1193
    • Li, Y.F.1    Arnold, R.J.2    Li, Y.3    Radivojac, P.4
  • 25
    • 84863517391 scopus 로고    scopus 로고
    • A hybrid approach to protein differential expression in mass spectrometry-based proteomics
    • Wang, X., Anderson, G. A., Smith, R. D., Dabney, A. R., A hybrid approach to protein differential expression in mass spectrometry-based proteomics. Bioinformatics 2012, 28, 1586-1591.
    • (2012) Bioinformatics , vol.28 , pp. 1586-1591
    • Wang, X.1    Anderson, G.A.2    Smith, R.D.3    Dabney, A.R.4
  • 26
    • 44149114239 scopus 로고    scopus 로고
    • Design and analysis of quantitative differential proteomics investigations using LC-MS technology
    • Bukham, Y., Dharsee, M., Ewing, R., Chu, P. et al., Design and analysis of quantitative differential proteomics investigations using LC-MS technology. J. Bioinform. Computat. Biol. 2008, 6, 107-123.
    • (2008) J. Bioinform. Computat. Biol. , vol.6 , pp. 107-123
    • Bukham, Y.1    Dharsee, M.2    Ewing, R.3    Chu, P.4
  • 27
    • 44449161040 scopus 로고    scopus 로고
    • Mixed-effects statistical model for comparative LC-MS proteomics studies
    • Daly, D., Anderson, K., Panisko, E., Purvine, S. et al., Mixed-effects statistical model for comparative LC-MS proteomics studies. J. Proteome Res. 2008, 7, 1209-1217.
    • (2008) J. Proteome Res. , vol.7 , pp. 1209-1217
    • Daly, D.1    Anderson, K.2    Panisko, E.3    Purvine, S.4


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