메뉴 건너뛰기




Volumn 12, Issue 23-24, 2012, Pages 3475-3484

LFQuant: A label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data

Author keywords

Analysis tool; Bioinformatics; Extracted ion chromatogram; Fast; Label free quantification

Indexed keywords

ACCURACY; ARTICLE; DATA ANALYSIS; DATA BASE; FRACTIONATION; LIQUID CHROMATOGRAPHY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY;

EID: 84871259414     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200017     Document Type: Article
Times cited : (36)

References (42)
  • 1
    • 0037370373 scopus 로고    scopus 로고
    • Proteomics: the first decade and beyond
    • Patterson, S. D., Aebersold, R. H., Proteomics: the first decade and beyond. Nat. Genet. 2003, 33, 311-323.
    • (2003) Nat. Genet , vol.33 , pp. 311-323
    • Patterson, S.D.1    Aebersold, R.H.2
  • 2
    • 84863230118 scopus 로고    scopus 로고
    • Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos
    • Li, Z., Adams, R. M., Chourey, K., Hurst G. B. et al., Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J. Proteome Res. 2012, 11, 1582-1590.
    • (2012) J. Proteome Res , vol.11 , pp. 1582-1590
    • Li, Z.1    Adams, R.M.2    Chourey, K.3    Hurst, G.B.4
  • 3
    • 84865780879 scopus 로고    scopus 로고
    • Precision, proteome coverage and dynamic range of Arabidopsis proteome profiling using 15N metabolic labeling and label-free approaches
    • Arsova, B., Zauber, H., Schulze, W. X., Precision, proteome coverage and dynamic range of Arabidopsis proteome profiling using 15N metabolic labeling and label-free approaches. Mol. Cell Proteomics 2012, 11, 619-628.
    • (2012) Mol. Cell Proteomics , vol.11 , pp. 619-628
    • Arsova, B.1    Zauber, H.2    Schulze, W.X.3
  • 4
    • 79960436501 scopus 로고    scopus 로고
    • Global absolute quantification of a proteome: challenges in the deployment of a QconCAT strategy
    • Brownridge, P., Holman, S. W., Gaskell, S. J., Grant, C. M. et al., Global absolute quantification of a proteome: challenges in the deployment of a QconCAT strategy. Proteomics 2011, 11, 2957-2970.
    • (2011) Proteomics , vol.11 , pp. 2957-2970
    • Brownridge, P.1    Holman, S.W.2    Gaskell, S.J.3    Grant, C.M.4
  • 5
    • 41349096900 scopus 로고    scopus 로고
    • Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
    • Deutsch, E. W., Lam, H., Aebersold, R., Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol. Genomics 2008, 33, 18-25.
    • (2008) Physiol. Genomics , vol.33 , pp. 18-25
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 6
    • 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
  • 7
    • 33747180294 scopus 로고    scopus 로고
    • A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
    • Bellew, M., Coram, M., Fitzgibbon, M., Igra, M. et al., A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006, 22, 1902-1909.
    • (2006) Bioinformatics , vol.22 , pp. 1902-1909
    • Bellew, M.1    Coram, M.2    Fitzgibbon, M.3    Igra, M.4
  • 8
    • 33750615386 scopus 로고    scopus 로고
    • PEPPeR, a platform for experimental proteomic pattern recognition
    • Jaffe, J. D., Mani, D. R., Leptos, K. C., Church, G. M. et al., PEPPeR, a platform for experimental proteomic pattern recognition. Mol. Cell Proteomics 2006, 5, 1927-1941.
    • (2006) Mol. Cell Proteomics , vol.5 , pp. 1927-1941
    • Jaffe, J.D.1    Mani, D.R.2    Leptos, K.C.3    Church, G.M.4
  • 9
    • 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
  • 10
    • 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
  • 12
    • 79952549673 scopus 로고    scopus 로고
    • MRCQuant - an accurate LC-MS relative isotopic quantification algorithm on TOF instruments
    • Haskins, W. E., Petritis, K., Zhang, J., MRCQuant - an accurate LC-MS relative isotopic quantification algorithm on TOF instruments. BMC Bioinformatics 2011, 12, 74-85.
    • (2011) BMC Bioinformatics , vol.12 , pp. 74-85
    • Haskins, W.E.1    Petritis, K.2    Zhang, J.3
  • 13
    • 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. et al., 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, 1265-1272.
    • (2005) Mol. Cell Proteomics , vol.4 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4
  • 14
    • 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. et al., Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 2006, 5, 2339-2347.
    • (2006) J. Proteome Res , vol.5 , pp. 2339-2347
    • Zybailov, B.1    Mosley, A.L.2    Sardiu, M.E.3    Coleman, M.K.4
  • 15
    • 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
  • 16
    • 74049132731 scopus 로고    scopus 로고
    • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
    • Griffin, N. M., Yu, J., Long, F., Oh, P. et al., Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat. Biotechnol. 2010, 28, 83-89.
    • (2010) Nat. Biotechnol , vol.28 , pp. 83-89
    • Griffin, N.M.1    Yu, J.2    Long, F.3    Oh, P.4
  • 18
    • 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
  • 19
    • 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, 1214-1223.
    • (2006) J. Proteome Res , vol.5 , pp. 1214-1223
    • Wang, G.1    Wu, W.W.2    Zeng, W.3    Chou, C.L.4    Shen, R.F.5
  • 20
    • 34848822499 scopus 로고    scopus 로고
    • Quantitative profile of five murine core proteomes using label-free functional proteomics
    • Cutillas P. R., Vanhaesebroeck B., Quantitative profile of five murine core proteomes using label-free functional proteomics. Mol. Cell Proteomics 2007, 6, 1560-1573.
    • (2007) Mol. Cell Proteomics , vol.6 , pp. 1560-1573
    • Cutillas, P.R.1    Vanhaesebroeck, B.2
  • 21
    • 76649139789 scopus 로고    scopus 로고
    • IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation
    • Tsou, C. C., Tsai, C. F., Tsui, Y. H., Sudhir, P. R. et al., IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol. Cell Proteomics 2010, 9, 131-144.
    • (2010) Mol. Cell Proteomics , vol.9 , pp. 131-144
    • Tsou, C.C.1    Tsai, C.F.2    Tsui, Y.H.3    Sudhir, P.R.4
  • 22
    • 80051817160 scopus 로고    scopus 로고
    • MassChroQ: a versatile tool for mass spectrometry quantification
    • Valot, B., Langella, O., Nano, E., Zivy, M., MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics 2011, 11, 3572-3577.
    • (2011) Proteomics , vol.11 , pp. 3572-3577
    • Valot, B.1    Langella, O.2    Nano, E.3    Zivy, M.4
  • 23
    • 63649096604 scopus 로고    scopus 로고
    • Relationship between sample loading amount and peptides identification and its effect on quantitative proteomics
    • Liu, K. H., Zhang, J. Y., Wang, J. L., Zhao, L. Y. et al., Relationship between sample loading amount and peptides identification and its effect on quantitative proteomics. Anal. Chem. 2009, 81, 1307-1314.
    • (2009) Anal. Chem , vol.81 , pp. 1307-1314
    • Liu, K.H.1    Zhang, J.Y.2    Wang, J.L.3    Zhao, L.Y.4
  • 24
    • 76749122411 scopus 로고    scopus 로고
    • Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses
    • Rudnick P. A., Clauser K. R., Kilpatrick L. E., Tchekhovskoi D. V. et al., Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 2010, 9, 225-241.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 225-241
    • Rudnick, P.A.1    Clauser, K.R.2    Kilpatrick, L.E.3    Tchekhovskoi, D.V.4
  • 25
    • 77949676526 scopus 로고    scopus 로고
    • A guide tour of the Trans-Proteomic Pipeline
    • Deutsch, E. W., Mendoza, L., Shtevnberg, D., Farrah, T. et al., A guide tour of the Trans-Proteomic Pipeline. Proteomics 2010, 10, 1150-1159.
    • (2010) Proteomics , vol.10 , pp. 1150-1159
    • Deutsch, E.W.1    Mendoza, L.2    Shtevnberg, D.3    Farrah, T.4
  • 26
    • 36549047947 scopus 로고    scopus 로고
    • A new strategy to filter out false positive identifications of peptides in SEQUEST database search results
    • Zhang, J. Y., Li, J., Xie, H. W., Zhu, Y. P. et al., A new strategy to filter out false positive identifications of peptides in SEQUEST database search results. Proteomics 2007, 7, 4036-4044.
    • (2007) Proteomics , vol.7 , pp. 4036-4044
    • Zhang, J.Y.1    Li, J.2    Xie, H.W.3    Zhu, Y.P.4
  • 27
    • 79952300022 scopus 로고    scopus 로고
    • A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision
    • Colaert, N., Vandekerckhove, J., Gevaert, K., Martens, L., A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision. Proteomics 2011, 11, 1110-1113.
    • (2011) Proteomics , vol.11 , pp. 1110-1113
    • Colaert, N.1    Vandekerckhove, J.2    Gevaert, K.3    Martens, L.4
  • 28
    • 79959734666 scopus 로고    scopus 로고
    • Comparison evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline
    • Trudqian, D. C., Ridlova, G., Fischer, R., Mackeen, M. M. et al., Comparison evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline. Proteomics 2011, 11, 2790-2797.
    • (2011) Proteomics , vol.11 , pp. 2790-2797
    • Trudqian, D.C.1    Ridlova, G.2    Fischer, R.3    Mackeen, M.M.4
  • 29
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 30
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K., McCormack, A. L., Yates, J. R., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 967-989.
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 967-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 31
    • 0141955057 scopus 로고    scopus 로고
    • A method for reducing the time required to match protein sequences with tandem mass spectra
    • Craig, R., Beavis, R. C., A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 2003, 17, 2310-2316.
    • (2003) Rapid Commun. Mass Spectrom , vol.17 , pp. 2310-2316
    • Craig, R.1    Beavis, R.C.2
  • 32
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 33
    • 63049091003 scopus 로고    scopus 로고
    • Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics
    • Zhang, J. Y., Ma, J., Dou, L., Wu, S. F. et al., Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics. Mol. Cell Proteomics 2009, 8, 547-557.
    • (2009) Mol. Cell Proteomics , vol.8 , pp. 547-557
    • Zhang, J.Y.1    Ma, J.2    Dou, L.3    Wu, S.F.4
  • 34
    • 78649657865 scopus 로고    scopus 로고
    • Improving the sensitivity of MASCOT search results validation by combining new features with Bayesian nonparametric model
    • Ma, J., Zhang, J. Y., Wu, S. F., Li, D. et al., Improving the sensitivity of MASCOT search results validation by combining new features with Bayesian nonparametric model. Proteomics 2010, 10, 4293-4300.
    • (2010) Proteomics , vol.10 , pp. 4293-4300
    • Ma, J.1    Zhang, J.Y.2    Wu, S.F.3    Li, D.4
  • 35
    • 76149132007 scopus 로고    scopus 로고
    • Comparison of database search strategies for high precursor mass accuracy MS/MS data
    • Hsieh, E. J., Hoopmann, M. R., MacLean, B., MacCoss, M. J., Comparison of database search strategies for high precursor mass accuracy MS/MS data. J. Proteome Res. 2010, 9, 1138-1143.
    • (2010) J. Proteome Res , vol.9 , pp. 1138-1143
    • Hsieh, E.J.1    Hoopmann, M.R.2    MacLean, B.3    MacCoss, M.J.4
  • 36
    • 33646894485 scopus 로고
    • A general approach to calculating isotopic distributions for mass spectrometry
    • Yergey, J. A., A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spectrom. Ion Phys. 1983, 52, 337-349.
    • (1983) Int. J. Mass Spectrom. Ion Phys , vol.52 , pp. 337-349
    • Yergey, J.A.1
  • 37
    • 79953719716 scopus 로고    scopus 로고
    • MJHGAore than 100,000 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., MJHGAore than 100, 000 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
  • 38
    • 76149142168 scopus 로고    scopus 로고
    • Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry
    • Tabb, D. L., Vega-Montoto, L., Rudnick, P. A., Variyath, A. M. et al., Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2010, 9, 761-776.
    • (2010) J. Proteome Res , vol.9 , pp. 761-776
    • Tabb, D.L.1    Vega-Montoto, L.2    Rudnick, P.A.3    Variyath, A.M.4
  • 39
    • 40549126588 scopus 로고    scopus 로고
    • Alignment of LC-MS images, with applications to biomarker discovery and protein identification
    • Vandenbogaert, M., Li-Thiao-Té, S., Kaltenbach, H. M., Zhang, R. et al., Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics 2008, 8, 650-672.
    • (2008) Proteomics , vol.8 , pp. 650-672
    • Vandenbogaert, M.1    Li-Thiao-Té, S.2    Kaltenbach, H.M.3    Zhang, R.4
  • 40
    • 84946263679 scopus 로고
    • Robust regression using iteratively reweighted least-squares
    • Holland, P. W., Welsch, R. E., Robust regression using iteratively reweighted least-squares. Commun. Statist.- Theor. Meth. 1977, A6: 813-827.
    • (1977) Commun. Statist.- Theor. Meth , vol.6 A , pp. 813-827
    • Holland, P.W.1    Welsch, R.E.2
  • 41
    • 79955101098 scopus 로고    scopus 로고
    • Reversible retention time alignment algorithm based on local regression
    • Chinese).
    • Li, L., Zhang, J. Y., Shi, X. J., Sun, H. C. et al., Reversible retention time alignment algorithm based on local regression. J. Central South Univ. (Sci. Tech.), 2011, 42, 100-105 (in Chinese).
    • (2011) J. Central South Univ. (Sci. Tech.) , vol.42 , pp. 100-105
    • Li, L.1    Zhang, J.Y.2    Shi, X.J.3    Sun, H.C.4
  • 42
    • 7044241344 scopus 로고    scopus 로고
    • DBParser: web-based software for shotgun proteomic data analyses
    • Yang, X., Dondeti, V., Dezube, R., Maynard, D. M. et al., DBParser: web-based software for shotgun proteomic data analyses. J. Proteome Res. 2004, 3, 1002-1008.
    • (2004) J. Proteome Res , vol.3 , pp. 1002-1008
    • Yang, X.1    Dondeti, V.2    Dezube, R.3    Maynard, D.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.