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Volumn 17, Issue 9, 2013, Pages 473-485

Evaluation of normalization methods to pave the way towards large-scale LC-MS-based metabolomics profiling experiments

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANALYTICAL EQUIPMENT; ARTICLE; DATA ANALYSIS; LEISHMANIA DONOVANI; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; MASS SPECTROMETRY; MEASUREMENT; METABOLOMICS; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; STANDARD; STATISTICAL ANALYSIS;

EID: 84883685328     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2013.0010     Document Type: Article
Times cited : (93)

References (35)
  • 2
    • 0037225727 scopus 로고    scopus 로고
    • Contrast normalization of oligonucleotide arrays
    • Astrand M. (2003). Contrast normalization of oligonucleotide arrays. J Comput Biol 10, 95-102.
    • (2003) J Comput Biol , vol.10 , pp. 95-102
    • Astrand, M.1
  • 3
    • 84873899821 scopus 로고    scopus 로고
    • Bias, randomization, and ovarian proteomic data: A reply to Producers and Consumers"
    • Baggerly KA, Coombes KR, and Morris JS. (2005). Bias, randomization, and ovarian proteomic data: A reply to "Producers and Consumers". Cancer Informatics 1, 9-14.
    • (2005) Cancer Informatics , vol.1 , pp. 9-14
    • Baggerly, K.A.1    Coombes, K.R.2    Morris, J.S.3
  • 4
    • 30744460897 scopus 로고    scopus 로고
    • Large-scale human metabolomics studies: A strategy for data (pre-) processing and validation
    • Bijlsma S, Bobeldijk I, Verheij ER, et al. (2006). Large-scale human metabolomics studies: A strategy for data (pre-) processing and validation. Anal Chem 78, 567-574.
    • (2006) Anal Chem , vol.78 , pp. 567-574
    • Bijlsma, S.1    Bobeldijk, I.2    Verheij, E.R.3
  • 7
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • Cui X, and Churchill GA. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4, 210.
    • (2003) Genome Biol , vol.4 , pp. 210
    • Cui, X.1    Churchill, G.A.2
  • 8
    • 84887791432 scopus 로고    scopus 로고
    • A comprehensive evaluation of normalization methods for Illumina highthroughput RNA sequencing data analysis
    • doi: 10.1093/bib/bbs046
    • Dillies MA, Rau A, Aubert J, et al. (2012). A comprehensive evaluation of normalization methods for Illumina highthroughput RNA sequencing data analysis. Brief Bioinform. doi: 10.1093/bib/bbs046.
    • (2012) Brief Bioinform
    • Ma, D.1    Rau, A.2    Aubert, J.3
  • 9
    • 79959913950 scopus 로고    scopus 로고
    • Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry
    • Dunn WB, Broadhurst D, Begley P, et al. (2011). Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols 6, 1060-1083.
    • (2011) Nature Protocols , vol.6 , pp. 1060-1083
    • Dunn, W.B.1    Broadhurst, D.2    Begley, P.3
  • 11
    • 3242741850 scopus 로고    scopus 로고
    • Design of experiments: An efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry
    • Gullberg J, Jonsson P, Nordström A, Sjö ström M, and Moritz T. (2004). Design of experiments: An efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331, 283-295.
    • (2004) Anal Biochem , vol.331 , pp. 283-295
    • Gullberg, J.1    Jonsson, P.2    Nordström, A.3    Sjostrom, M.4    Moritz, T.5
  • 13
    • 0035749210 scopus 로고    scopus 로고
    • Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls
    • RESEARCH0055
    • Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, and Slonim DK. (2001). Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biol 2:RESEARCH0055
    • (2001) Genome Biol , vol.2
    • Hill, A.A.1    Brown, E.L.2    Whitley, M.Z.3    Tucker-Kellogg, G.4    Hunter, C.P.5    Slonim, D.K.6
  • 15
    • 84860361428 scopus 로고    scopus 로고
    • Separating the wheat from the chaff: A prioritisation pipeline for the analysis of metabolomics datasets
    • Jankevics A, Merlo ME, de Vries M, Vonk RJ, Takano E, and Breitling R. (2012). Separating the wheat from the chaff: A prioritisation pipeline for the analysis of metabolomics datasets. Metabolomics 8, 29-36.
    • (2012) Metabolomics , vol.8 , pp. 29-36
    • Jankevics, A.1    Merlo, M.E.2    De Vries, M.3    Vonk, R.J.4    Takano, E.5    Breitling, R.6
  • 16
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson WE, Li C, and Rabinovic A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118.
    • (2007) Biostatistics , vol.8 , pp. 118
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 17
    • 84860359421 scopus 로고    scopus 로고
    • State-of-the-art data normalisation methods improve NMR-based metabolomic analysis
    • Kohl SM, Klein MS, Hochrein J, Oefner PJ, Spang R, and Gronwald W. (2011). State-of-the-art data normalisation methods improve NMR-based metabolomic analysis. Metabolomics 8, 146-160.
    • (2011) Metabolomics , vol.8 , pp. 146-160
    • Kohl, S.M.1    Klein, M.S.2    Hochrein, J.3    Oefner, P.J.4    Spang, R.5    Gronwald, W.6
  • 18
    • 34848914038 scopus 로고    scopus 로고
    • Capturing heterogeneity in gene expression studies by surrogate variable analysis
    • Leek JT, and Storey JD. (2007). Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics 3, e161.
    • (2007) PLoS Genetics , vol.3
    • Leek, J.T.1    Storey, J.D.2
  • 19
    • 65549139459 scopus 로고    scopus 로고
    • Data-driven normalization strategies for high-throughput quantitative RTPCR
    • Mar J, Kimura Y, Schroder K, et al. (2009). Data-driven normalization strategies for high-throughput quantitative RTPCR. BMC Bioinformat 10, 110.
    • (2009) BMC Bioinformat , vol.10 , pp. 110
    • Mar, J.1    Kimura, Y.2    Schroder, K.3
  • 20
    • 33748490271 scopus 로고    scopus 로고
    • Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping
    • Prince JT, and Marcotte EM. (2006). Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem 78, 6140-6152.
    • (2006) Anal Chem , vol.78 , pp. 6140-6152
    • Prince, J.T.1    Marcotte, E.M.2
  • 22
    • 70350095897 scopus 로고    scopus 로고
    • Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data
    • Redestig H, Fukushima A, Stenlund H, et al. (2009). Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Anal Chem 81, 7974-7980.
    • (2009) Anal Chem , vol.81 , pp. 7974-7980
    • Redestig, H.1    Fukushima, A.2    Stenlund, H.3
  • 23
    • 0036027086 scopus 로고    scopus 로고
    • An improved multiple internal standard normalisation for drift in LA-ICP-MS measurements
    • Ridder FD, Pintelon R, Schoukens J, Navez J, Andre L, and Dehairs F. (2002). An improved multiple internal standard normalisation for drift in LA-ICP-MS measurements. JAAS 17, 1461-1470.
    • (2002) JAAS , vol.17 , pp. 1461-1470
    • Ridder, F.D.1    Pintelon, R.2    Schoukens, J.3    Navez, J.4    Andre, L.5    Dehairs, F.6
  • 25
    • 79953267955 scopus 로고    scopus 로고
    • PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis
    • Scheltema R, Jankevics A, Jansen RC, Swertz MA, and Breitling R. (2011). PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis. Anal Chem 83, 2786-2793.
    • (2011) Anal Chem , vol.83 , pp. 2786-2793
    • Scheltema, R.1    Jankevics, A.2    Jansen, R.C.3    Ma, S.4    Breitling, R.5
  • 26
    • 77952851186 scopus 로고    scopus 로고
    • Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
    • Schmid R, Baum P, Ittrich C, et al. (2010). Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics 11: 349.
    • (2010) BMC Genomics , vol.11 , pp. 349
    • Schmid, R.1    Baum, P.2    Ittrich, C.3
  • 27
    • 34347384910 scopus 로고    scopus 로고
    • Normalization method for metabolomics data using optimal selection of multiple internal standards
    • Sysi-Aho M, Katajamaa M, Yetukuri L, and Oresic M. (2007). Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformat 8, 93.
    • (2007) BMC Bioinformat , vol.8 , pp. 93
    • Sysi-Aho, M.1    Katajamaa, M.2    Yetukuri, L.3    Oresic, M.4
  • 28
    • 60649089559 scopus 로고    scopus 로고
    • Highly sensitive feature detection for high resolution LC/MS
    • Tautenhahn R, Bö ttcher C, and Neumann S. (2008). Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformat 9, 504.
    • (2008) BMC Bioinformat , vol.9 , pp. 504
    • Tautenhahn, R.1    Bö Ttcher, C.2    Neumann, S.3
  • 29
    • 78049351897 scopus 로고    scopus 로고
    • Towards an unbiased metabolic profiling of protozoan parasites: Optimization of a Leishmania sampling protocol for HILIC-orbitrap analysis
    • t'Kindt R., Jankevics A, Scheltema RA, et al. (2010a). Towards an unbiased metabolic profiling of protozoan parasites: Optimization of a Leishmania sampling protocol for HILIC-orbitrap analysis. Analyt Bioanal Chem. 398,2059-2069.
    • (2010) Analyt Bioanal Chem. , vol.398 , pp. 2059-2069
    • T'Kindt, R.1    Jankevics, A.2    Scheltema, R.A.3
  • 30
    • 78649776458 scopus 로고    scopus 로고
    • Metabolomics to unveil and understand phenotypic diversity between pathogen populations
    • t'Kindt R, Scheltema RA, Jankevics A, et al. (2010b). Metabolomics to unveil and understand phenotypic diversity between pathogen populations. Plos Neg Tropic Dis. 4, e904.
    • (2010) Plos Neg Tropic Dis. , vol.4
    • T'Kindt, R.1    Scheltema, R.A.2    Jankevics, A.3
  • 31
    • 65649108127 scopus 로고    scopus 로고
    • A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography
    • Valkenborg D, Thomas G, Krols L, Kas K, and Burzykowski T. (2009). A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography. J Mass Spectrom 44, 516-529.
    • (2009) J Mass Spectrom , vol.44 , pp. 516-529
    • Valkenborg, D.1    Thomas, G.2    Krols, L.3    Kas, K.4    Burzykowski, T.5
  • 32
    • 33747019547 scopus 로고    scopus 로고
    • Centering, scaling, and transformations: Improving the biological information content of metabolomics data
    • van den Berg RA, Hoefsloot HCJ, Westerhuis JA, Smilde AK, and van der werf MJ. (2006). Centering, scaling, and transformations: Improving the biological information content of metabolomics data. BMC Genom 7, 142.
    • (2006) BMC Genom , vol.7 , pp. 142
    • Van Den Berg, R.A.1    Hoefsloot, H.C.J.2    Westerhuis, J.A.3    Smilde, A.K.4    Van Der Werf, M.J.5
  • 33
    • 70449354965 scopus 로고    scopus 로고
    • Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping
    • van der Kloet FM, Bobeldijk I, Verheij ER, and Jellema RH. (2009). Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping. J Proteome Res 8, 5132-5141.
    • (2009) J Proteome Res , vol.8 , pp. 5132-5141
    • Van Der Kloet, F.M.1    Bobeldijk, I.2    Verheij, E.R.3    Jellema, R.H.4
  • 34
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • RESEARCH0034
    • Vandesompele J, De Preter K, Pattyn F, et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3, RESEARCH0034.
    • (2002) Genome Biol , vol.3
    • Vandesompele, J.1    De Preter, K.2    Pattyn, F.3
  • 35
    • 10744233766 scopus 로고    scopus 로고
    • Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
    • Wang W, Zhou H, Lin H, et al. (2003). Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75, 4818-4826.
    • (2003) Anal Chem , vol.75 , pp. 4818-4826
    • Wang, W.1    Zhou, H.2    Lin, H.3


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