메뉴 건너뛰기




Volumn 129, Issue , 2015, Pages 121-126

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics

Author keywords

Continuously normalized spectral counts; Differential expression; Intensity; Missing data

Indexed keywords

ACCURACY; ARTICLE; CALIBRATION; ESCHERICHIA COLI; NONHUMAN; PARAMETERS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; STATISTICAL ANALYSIS; ALGORITHM; AMINO ACID SEQUENCE; CHEMISTRY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; METABOLISM; MOLECULAR GENETICS; PROCEDURES; SEQUENCE ANALYSIS; STAINING; STATISTICAL MODEL;

EID: 84945472903     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.07.036     Document Type: Article
Times cited : (52)

References (36)
  • 1
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii A.I., Vitek O., Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4(10):787-797.
    • (2007) Nat. Methods , vol.4 , Issue.10 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 2
    • 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 A., Pandey H., 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, A.5    Pandey, H.6    Mann, M.7
  • 5
    • 79953062776 scopus 로고    scopus 로고
    • Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis
    • Fermin D., Basrur V., Yocum A.K., Nesvizhskii A.I. Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics 2011, 11(7):1340-1345.
    • (2011) Proteomics , vol.11 , Issue.7 , pp. 1340-1345
    • Fermin, D.1    Basrur, V.2    Yocum, A.K.3    Nesvizhskii, A.I.4
  • 6
    • 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
  • 8
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Veneable J.D., Dong M.Q., Wohlschlegel J., Dillin A., Yates J.R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 2004, 1(1):39-45.
    • (2004) Nat. Methods , vol.1 , Issue.1 , pp. 39-45
    • Veneable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 10
    • 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 analaysis
    • O111.016717
    • Gillet L.C., Navarro P., Tate S., Röst H.L., Selevsek N., Reiter L., Bonner R., Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analaysis. Mol. Cell. Proteomics 2012, 11(6). (O111.016717).
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.6
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Röst, H.L.4    Selevsek, N.5    Reiter, L.6    Bonner, R.7    Aebersold, R.8
  • 12
    • 77954205753 scopus 로고    scopus 로고
    • PepC: proteomics software for identifying differentially expressed proteins based on spectral counting
    • Heinecke N.L., Pratt B.S., Vaisar T., Becker L. PepC: proteomics software for identifying differentially expressed proteins based on spectral counting. Bioinformatics 2010, 26(12):1574-1575.
    • (2010) Bioinformatics , vol.26 , Issue.12 , pp. 1574-1575
    • Heinecke, N.L.1    Pratt, B.S.2    Vaisar, T.3    Becker, L.4
  • 13
    • 77949519484 scopus 로고    scopus 로고
    • On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
    • Pham T.V., Piersma S.R., Warmoes M., Jimenez C.R. On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics 2010, 26(3):363-369.
    • (2010) Bioinformatics , vol.26 , Issue.3 , pp. 363-369
    • Pham, T.V.1    Piersma, S.R.2    Warmoes, M.3    Jimenez, C.R.4
  • 15
    • 58149299336 scopus 로고    scopus 로고
    • Significance analysis of spectral count data in label-free shotgun proteomics
    • Choi H., Fermin D., Nesvizhskii A.I. Significance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell. Proteomics 2008, 7(12):2373-2385.
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.12 , pp. 2373-2385
    • Choi, H.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 16
    • 80051643826 scopus 로고    scopus 로고
    • A Bayesian mixture model for comparative spectral count data in shotgun proteomics
    • (M110.007203)
    • Booth J.G., Eilertson K.E., Olinares P.D., Yu H. A Bayesian mixture model for comparative spectral count data in shotgun proteomics. Mol. Cell. Proteomics 2011, 10. (M110.007203).
    • (2011) Mol. Cell. Proteomics , vol.10
    • Booth, J.G.1    Eilertson, K.E.2    Olinares, P.D.3    Yu, H.4
  • 17
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Smyth G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 2004, 3(1):3.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3 , Issue.1 , pp. 3
    • Smyth, G.K.1
  • 20
    • 84907033616 scopus 로고    scopus 로고
    • MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
    • Choi M., Chang C.Y., Clough T., Broudy D., Killeen T., MacLean B.X., Vitek O. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 2014, 30(17):2524-2526.
    • (2014) Bioinformatics , vol.30 , Issue.17 , pp. 2524-2526
    • Choi, M.1    Chang, C.Y.2    Clough, T.3    Broudy, D.4    Killeen, T.5    MacLean, B.X.6    Vitek, O.7
  • 23
    • 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(4):2261-2271.
    • (2012) J. Proteome Res. , vol.11 , Issue.4 , pp. 2261-2271
    • Ning, K.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 24
    • 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. Proteome 2012, 75(17):5437-5448.
    • (2012) J. Proteome , 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
  • 25
    • 84883275474 scopus 로고    scopus 로고
    • Critical assessment of proteome-wide label-free absolute abundance estimation strategies
    • Ahrne E., Molzhan L., Glatter T., Schmidt A. Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 2013, 13(17):2567-2578.
    • (2013) Proteomics , vol.13 , Issue.17 , pp. 2567-2578
    • Ahrne, E.1    Molzhan, L.2    Glatter, T.3    Schmidt, A.4
  • 27
    • 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
  • 30
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings W.K. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970, 57(1):97-109.
    • (1970) Biometrika , vol.57 , Issue.1 , pp. 97-109
    • Hastings, W.K.1
  • 34
    • 79959734666 scopus 로고    scopus 로고
    • Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline
    • Trudgian D.C., Ridlova G., Fischer R., Mackeen M.M., Ternette N., Acuto O., Kessler B.M., Thomas B. Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline. Proteomics 2011, 26:2790-2797.
    • (2011) Proteomics , vol.26 , pp. 2790-2797
    • Trudgian, D.C.1    Ridlova, G.2    Fischer, R.3    Mackeen, M.M.4    Ternette, N.5    Acuto, O.6    Kessler, B.M.7    Thomas, B.8
  • 35
    • 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., Takeshi N., 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    Takeshi, N.5    Rappsilber, J.6    Mann, M.7
  • 36
    • 84926444106 scopus 로고    scopus 로고
    • MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer
    • Shalit T., Elinger D., Savidor A., Gabashvili A., Levin Y. MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer. J. Proteome Res. 2015, 14(4):1979-1986.
    • (2015) J. Proteome Res. , vol.14 , Issue.4 , pp. 1979-1986
    • Shalit, T.1    Elinger, D.2    Savidor, A.3    Gabashvili, A.4    Levin, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.