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Volumn 13, Issue 12, 2014, Pages 5888-5897

ICan: An optimized ion-current-based quantification procedure with enhanced quantitative accuracy and sensitivity in biomarker discovery

Author keywords

ion current; label free; normalization; protein ratio determination; quantitative proteomics

Indexed keywords

BIOLOGICAL MARKER; PROTEIN; BOVINE SERUM ALBUMIN; ESCHERICHIA COLI PROTEIN; PROTEOME;

EID: 84915820357     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr5008224     Document Type: Article
Times cited : (19)

References (44)
  • 3
    • 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.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 2002, 1 (5) 376-386
    • (2002) Mol. Cell. Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 5
    • 23044504789 scopus 로고    scopus 로고
    • Guidelines for the routine application of the peptide hits technique
    • Gao, J.; Friedrichs, M. S.; Dongre, A. R.; Opiteck, G. J. Guidelines for the routine application of the peptide hits technique J. Am. Soc. Mass Spectrom. 2005, 16 (8) 1231-1238
    • (2005) J. Am. Soc. Mass Spectrom. , vol.16 , Issue.8 , pp. 1231-1238
    • Gao, J.1    Friedrichs, M.S.2    Dongre, A.R.3    Opiteck, G.J.4
  • 6
    • 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., 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76 (14) 4193-4201
    • (2004) Anal. Chem. , vol.76 , Issue.14 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates, J.R.3
  • 7
    • 6044226889 scopus 로고    scopus 로고
    • Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures
    • Wiener, M. C.; Sachs, J. R.; Deyanova, E. G.; Yates, N. A. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures Anal. Chem. 2004, 76 (20) 6085-6096
    • (2004) Anal. Chem. , vol.76 , Issue.20 , pp. 6085-6096
    • Wiener, M.C.1    Sachs, J.R.2    Deyanova, E.G.3    Yates, N.A.4
  • 8
    • 0037106398 scopus 로고    scopus 로고
    • Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry
    • Bondarenko, P. V.; Chelius, D.; Shaler, T. A. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry Anal. Chem. 2002, 74 (18) 4741-4749
    • (2002) Anal. Chem. , vol.74 , Issue.18 , pp. 4741-4749
    • Bondarenko, P.V.1    Chelius, D.2    Shaler, T.A.3
  • 9
  • 10
    • 38649095599 scopus 로고    scopus 로고
    • An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
    • Mueller, L. N.; Brusniak, M. Y.; Mani, D. R.; Aebersold, R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data J. Proteome Res. 2008, 7 (1) 51-61
    • (2008) J. Proteome Res. , vol.7 , Issue.1 , pp. 51-61
    • Mueller, L.N.1    Brusniak, M.Y.2    Mani, D.R.3    Aebersold, R.4
  • 12
    • 84899854225 scopus 로고    scopus 로고
    • Reproducible Ion-Current-Based Approach for 24-Plex Comparison of the Tissue Proteomes of Hibernating versus Normal Myocardium in Swine Models
    • Qu, J.; Young, R.; Page, B. J.; Shen, X.; Tata, N.; Li, J.; Duan, X.; Fallavollita, J. A.; Canty, J. M., Jr. Reproducible Ion-Current-Based Approach for 24-Plex Comparison of the Tissue Proteomes of Hibernating versus Normal Myocardium in Swine Models J. Proteome Res. 2014, 13 (5) 2571-2584
    • (2014) J. Proteome Res. , vol.13 , Issue.5 , pp. 2571-2584
    • Qu, J.1    Young, R.2    Page, B.J.3    Shen, X.4    Tata, N.5    Li, J.6    Duan, X.7    Fallavollita, J.A.8    Canty, J.M.9
  • 13
    • 84898719933 scopus 로고    scopus 로고
    • Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data
    • Tu, C.; Li, J.; Sheng, Q.; Zhang, M.; Qu, J. Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data J. Proteome Res. 2014, 13 (4) 2069-2079
    • (2014) J. Proteome Res. , vol.13 , Issue.4 , pp. 2069-2079
    • Tu, C.1    Li, J.2    Sheng, Q.3    Zhang, M.4    Qu, J.5
  • 15
    • 84899740206 scopus 로고    scopus 로고
    • Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data
    • Rudnick, P. A.; Wang, X.; Yan, X.; Sedransk, N.; Stein, S. E. Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data Mol. Cell. Proteomics 2014, 13 (5) 1341-1351
    • (2014) Mol. Cell. Proteomics , vol.13 , Issue.5 , pp. 1341-1351
    • Rudnick, P.A.1    Wang, X.2    Yan, X.3    Sedransk, N.4    Stein, S.E.5
  • 16
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang, Y. H.; Dudoit, S.; Luu, P.; Lin, D. M.; Peng, V.; Ngai, J.; Speed, T. P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 2002, 30 (4) e15
    • (2002) Nucleic Acids Res. , vol.30 , Issue.4 , pp. 15
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 17
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad, B. M.; Irizarry, R. A.; Astrand, M.; Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 2003, 19 (2) 185-193
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 18
    • 84878053091 scopus 로고    scopus 로고
    • Normalization and missing value imputation for label-free LC-MS analysis
    • Karpievitch, Y. V.; Dabney, A. R.; Smith, R. D. Normalization and missing value imputation for label-free LC-MS analysis BMC Bioinf. 2012, 13 (Suppl 16) S5
    • (2012) BMC Bioinf. , vol.13 , pp. 5
    • Karpievitch, Y.V.1    Dabney, A.R.2    Smith, R.D.3
  • 19
    • 71049194213 scopus 로고    scopus 로고
    • Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides
    • Kultima, K.; Nilsson, A.; Scholz, B.; Rossbach, U. L.; Falth, M.; Andren, P. E. Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides Mol. Cell. Proteomics 2009, 8 (10) 2285-2295
    • (2009) Mol. Cell. Proteomics , vol.8 , Issue.10 , pp. 2285-2295
    • Kultima, K.1    Nilsson, A.2    Scholz, B.3    Rossbach, U.L.4    Falth, M.5    Andren, P.E.6
  • 20
    • 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.; Nagaraj, N.; Mann, M. 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    Nagaraj, N.5    Mann, M.6
  • 21
    • 75249085783 scopus 로고    scopus 로고
    • Methods for combining peptide intensities to estimate relative protein abundance
    • Carrillo, B.; Yanofsky, C.; Laboissiere, S.; Nadon, R.; Kearney, R. E. Methods for combining peptide intensities to estimate relative protein abundance Bioinformatics 2010, 26 (1) 98-103
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 98-103
    • Carrillo, B.1    Yanofsky, C.2    Laboissiere, S.3    Nadon, R.4    Kearney, R.E.5
  • 23
    • 84875943685 scopus 로고    scopus 로고
    • Comparative study of targeted and label-free mass spectrometry methods for protein quantification
    • L, I. J.; Stoop, M. P.; Stingl, C.; Sillevis Smitt, P. A.; Luider, T. M.; Dekker, L. J. Comparative study of targeted and label-free mass spectrometry methods for protein quantification J. Proteome Res. 2013, 12 (4) 2005-2011
    • (2013) J. Proteome Res. , vol.12 , Issue.4 , pp. 2005-2011
    • Li, J.1    Stoop, M.P.2    Stingl, C.3    Sillevis Smitt, P.A.4    Luider, T.M.5    Dekker, L.J.6
  • 24
    • 41549117597 scopus 로고    scopus 로고
    • A quantitative analysis software tool for mass spectrometry-based proteomics
    • Park, S. K.; Venable, J. D.; Xu, T.; Yates, J. R., 3rd. A quantitative analysis software tool for mass spectrometry-based proteomics Nat. Methods 2008, 5 (4) 319-322
    • (2008) Nat. Methods , vol.5 , Issue.4 , pp. 319-322
    • Park, S.K.1    Venable, J.D.2    Xu, T.3    Yates, J.R.4
  • 25
    • 84870390546 scopus 로고    scopus 로고
    • An ion-current-based, comprehensive and reproducible proteomic strategy for comparative characterization of the cellular responses to novel anti-cancer agents in a prostate cell model
    • Tu, C.; Li, J.; Bu, Y.; Hangauer, D.; Qu, J. An ion-current-based, comprehensive and reproducible proteomic strategy for comparative characterization of the cellular responses to novel anti-cancer agents in a prostate cell model J. Proteomics 2012, 77, 187-201
    • (2012) J. Proteomics , vol.77 , pp. 187-201
    • Tu, C.1    Li, J.2    Bu, Y.3    Hangauer, D.4    Qu, J.5
  • 27
    • 33646564676 scopus 로고    scopus 로고
    • Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes
    • Wang, G.; Wu, W. W.; Zeng, W.; Chou, C. L.; Shen, R. F. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes J. Proteome Res. 2006, 5 (5) 1214-1223
    • (2006) J. Proteome Res. , vol.5 , Issue.5 , pp. 1214-1223
    • Wang, G.1    Wu, W.W.2    Zeng, W.3    Chou, C.L.4    Shen, R.F.5
  • 29
    • 67049119810 scopus 로고    scopus 로고
    • A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome
    • Duan, X.; Young, R.; Straubinger, R. M.; Page, B.; Cao, J.; Wang, H.; Yu, H.; Canty, J. M.; Qu, J. A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome J. Proteome Res. 2009, 8 (6) 2838-2850
    • (2009) J. Proteome Res. , vol.8 , Issue.6 , pp. 2838-2850
    • Duan, X.1    Young, R.2    Straubinger, R.M.3    Page, B.4    Cao, J.5    Wang, H.6    Yu, H.7    Canty, J.M.8    Qu, J.9
  • 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 (12) 1367-1372
    • (2008) Nat. Biotechnol. , vol.26 , Issue.12 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 32
  • 33
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations Nat. Methods 2005, 2 (9) 667-675
    • (2005) Nat. Methods , vol.2 , Issue.9 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4
  • 34
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth, G. K.; Speed, T. Normalization of cDNA microarray data Methods 2003, 31 (4) 265-273
    • (2003) Methods , vol.31 , Issue.4 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 35
    • 0002294347 scopus 로고
    • A simple sequentially rejective multiple test procedure
    • Holm, S. A simple sequentially rejective multiple test procedure Scand J. Stat. 1979, 6, 65-70
    • (1979) Scand J. Stat. , vol.6 , pp. 65-70
    • Holm, S.1
  • 36
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple tesing
    • Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple tesing J. R. Stat. Soc., Ser. B 1995, 57, 289-300
    • (1995) J. R. Stat. Soc., Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 39
    • 84864809026 scopus 로고    scopus 로고
    • Label-free quantification and shotgun analysis of complex proteomes by one-dimensional SDS-PAGE/NanoLC-MS: Evaluation for the large scale analysis of inflammatory human endothelial cells
    • Gautier, V.; Mouton-Barbosa, E.; Bouyssie, D.; Delcourt, N.; Beau, M.; Girard, J. P.; Cayrol, C.; Burlet-Schiltz, O.; Monsarrat, B.; Gonzalez de Peredo, A. Label-free quantification and shotgun analysis of complex proteomes by one-dimensional SDS-PAGE/NanoLC-MS: evaluation for the large scale analysis of inflammatory human endothelial cells Mol. Cell. Proteomics 2012, 11 (8) 527-539
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.8 , pp. 527-539
    • Gautier, V.1    Mouton-Barbosa, E.2    Bouyssie, D.3    Delcourt, N.4    Beau, M.5    Girard, J.P.6    Cayrol, C.7    Burlet-Schiltz, O.8    Monsarrat, B.9    Gonzalez De Peredo, A.10
  • 40
    • 84946031884 scopus 로고
    • Procedures for Detecting outlying Observations in Samples
    • Grubbs, F. Procedures for Detecting outlying Observations in Samples Technometrics 1969, 11 (1) 1-21
    • (1969) Technometrics , vol.11 , Issue.1 , pp. 1-21
    • Grubbs, F.1
  • 41
    • 33748319353 scopus 로고    scopus 로고
    • Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
    • Zybailov, B.; Mosley, A. L.; Sardiu, M. E.; Coleman, M. K.; Florens, L.; Washburn, M. P. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae J. Proteome Res. 2006, 5 (9) 2339-2347
    • (2006) J. Proteome Res. , vol.5 , Issue.9 , pp. 2339-2347
    • Zybailov, B.1    Mosley, A.L.2    Sardiu, M.E.3    Coleman, M.K.4    Florens, L.5    Washburn, M.P.6
  • 42
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol. Cell. Proteomics 2005, 4 (9) 1265-1272
    • (2005) Mol. Cell. Proteomics , vol.4 , Issue.9 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 43
    • 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.; Adamberg, K.; Vilu, R. Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli J. Proteomics 2012, 75 (17) 5437-5448
    • (2012) J. Proteomics , vol.75 , Issue.17 , pp. 5437-5448
    • Arike, L.1    Valgepea, K.2    Peil, L.3    Nahku, R.4    Adamberg, K.5    Vilu, R.6


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