Data processing for mass spectrometry-based metabolomics

XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification

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Metabolomics—the link between genotypes and phenotypes

Fiehn, O. (2002) · Plant Molecular Biology · doi:10.1023/a:1013713905833 · Cited by 3,445 · see citing works

The Statistical Analysis of Compositional Data

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Metabolomics — the link between genotypes and phenotypes

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Metabolomics by numbers: acquiring and understanding global metabolite data

Goodacre, R., Vaidyanathan, S., Dunn, W. B., Harrigan, G. G., & Kell, D. B. (2004) · Trends in biotechnology · doi:10.1016/j.tibtech.2004.03.007 · Cited by 1,262 · see citing works

Quantitative Analysis of Urine Vapor and Breath by Gas-Liquid Partition Chromatography

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A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations

Raamsdonk, L. M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M. C., BERDEN, J. A., Brindle, K. M., Kell, D. B., Rowland, J. J., et al. (2001) · Nature Biotechnology · doi:10.1038/83496 · Cited by 1,005 · see citing works

Large-Scale Human Metabolomics Studies: A Strategy for Data (Pre-) Processing and Validation

Bijlsma, S., Bobeldijk, I., Verheij, E. R., Ramaker, R., Kochhar, S., Macdonald, I. A., van Ommen, B., & Smilde, A. K. (2005) · Analytical Chemistry · doi:10.1021/ac051495j · Cited by 869 · see citing works

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data

Katajamaa, M., Miettinen, J., & Orešič, M. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btk039 · Cited by 836 · see citing works

An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data

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A common open representation of mass spectrometry data and its application to proteomics research

Pedrioli, P. G. A., Eng, J. K., Hubley, R. M., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B. S., Nilsson, E. J., Angeletti, R. H., Apweiler, R., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt1031 · Cited by 782 · see citing works

Potential of metabolomics as a functional genomics tool

Bino, R. J., Hall, R. D., Fiehn, O., Kopka, J., Saito, K., Draper, J., Nikolau, B. J., Mendes, P., Roessner, U., Beale, M. H., et al. (2004) · Trends in Plant Science · doi:10.1016/j.tplants.2004.07.004 · Cited by 781 · see citing works

Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping

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Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data

Tomasi, G., van den Berg, F. W. J., & Andersson, C. A. (2004) · Journal of Chemometrics · doi:10.1002/cem.859 · Cited by 709 · see citing works

Quantification of Proteins and Metabolites by Mass Spectrometry without Isotopic Labeling or Spiked Standards

Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T. A., Hill, L. R., Norton, S. M., Kumar, P., Anderle, M., & Becker, C. H. (2003) · Analytical Chemistry · doi:10.1021/ac026468x · Cited by 654 · see citing works

Parametric Time Warping

Eilers, P. H. C. (2003) · Analytical Chemistry · doi:10.1021/ac034800e · Cited by 637 · see citing works

Metabolomics: Current technologies and future trends

Hollywood, K. A., Brison, D. R., & Goodacre, R. (2006) · PROTEOMICS · doi:10.1002/pmic.200600106 · Cited by 595 · see citing works

A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles

Tikunov, Y. M., Lommen, A., Vos, C. H. R. D., Verhoeven, H. A., Bino, R. J., Hall, R. D., & Bovy, A. G. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.105.068130 · Cited by 511 · see citing works

Plant metabolomics: from holistic hope, to hype, to hot topic

Hall, R. D. (2006) · New Phytologist · doi:10.1111/j.1469-8137.2005.01632.x · Cited by 507 · see citing works

The genetics of plant metabolism

Keurentjes, J. J. B., Fu, J., de Vos, C. H. R., Lommen, A., Hall, R. D., Bino, R. J., van der Plas, L. H. W., Jansen, R. C., Vreugdenhil, D., & Koornneef, M. (2006) · Nature Genetics · doi:10.1038/ng1815 · Cited by 499 · see citing works

A comprehensive urinary metabolomic approach for identifying kidney cancer

Kind, T., Tolstikov, V., Fiehn, O., & Weiss, R. H. (2007) · Analytical Biochemistry · doi:10.1016/j.ab.2007.01.028 · Cited by 449 · see citing works

Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards

Wu, L., Mashego, M. R., van Dam, J. C., Proell, A. M., Vinke, J. L., Ras, C., van Winden, W. A., van Gulik, W. M., & Heijnen, J. J. (2004) · Analytical Biochemistry · doi:10.1016/j.ab.2004.09.001 · Cited by 423 · see citing works

Acquired Obesity Is Associated with Changes in the Serum Lipidomic Profile Independent of Genetic Effects – A Monozygotic Twin Study

Pietiläinen, K. H., Sysi‐Aho, M., Rissanen, A., Seppänen‐Laakso, T., Yki‐Järvinen, H., Kaprio, J. A., & Orešič, M. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000218 · Cited by 415 · see citing works

Metabolomics technology and bioinformatics

Shulaev, V. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbl012 · Cited by 409 · see citing works

Processing methods for differential analysis of LC/MS profile data

Katajamaa, M., & Orešič, M. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-179 · Cited by 400 · see citing works

Normalization method for metabolomics data using optimal selection of multiple internal standards

Sysi‐Aho, M., Katajamaa, M., Yetukuri, L., & Orešič, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-93 · Cited by 358 · see citing works

Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells

Rischer, H., Orešič, M., Seppänen‐Laakso, T., Katajamaa, M., Lammertyn, F., Ardiles-Diaz, W., Montagu, M. C. E. V., Inzé, D., Oksman‐Caldentey, K., & Goossens, A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601027103 · Cited by 325 · see citing works

Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry

Listgarten, J., & Emili, A. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500005-mcp200 · Cited by 296 · see citing works

A proposed framework for the description of plant metabolomics experiments and their results

JENKINS, H. A., Hardy, N. W., Beckmann, M., Draper, J., SMITH, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R. D., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt1041 · Cited by 285 · see citing works

Metabolite fingerprinting: detecting biological features by independent component analysis

Scholz, M., Gatzek, S., Sterling, A., Fiehn, O., & Selbig, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth270 · Cited by 278 · see citing works

MET-IDEA: Data Extraction Tool for Mass Spectrometry-Based Metabolomics

Broeckling, C. D., Reddy, I. R., Duran, A. L., Zhao, X., & Sumner, L. W. (2006) · Analytical Chemistry · doi:10.1021/ac0521596 · Cited by 275 · see citing works

Nonlinear Data Alignment for UPLC−MS and HPLC−MS Based Metabolomics: Quantitative Analysis of Endogenous and Exogenous Metabolites in Human Serum

Nordström, A., O’Maille, G., Qin, C., & Siuzdak, G. E. (2006) · Analytical Chemistry · doi:10.1021/ac060245f · Cited by 273 · see citing works

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., Randolph, T. R., Wang, P., May, D., Eng, J. K., Fang, R., Lin, C., et al. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl276 · Cited by 265 · see citing works

The role of analytical sciences in medical systems biology

van der Greef, J., Stroobant, P., & van der Heijden, R. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.08.013 · Cited by 263 · see citing works

Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping

Prince, J. T., & Marcotte, E. M. (2006) · Analytical Chemistry · doi:10.1021/ac0605344 · Cited by 259 · see citing works

Software Tools for Analysis of Mass Spectrometric Lipidome Data

Haimi, P., Uphoff, A., Hermansson, M., & Somerharju, P. J. (2006) · Analytical Chemistry · doi:10.1021/ac061390w · Cited by 230 · see citing works

A Systems Biology Strategy Reveals Biological Pathways and Plasma Biomarker Candidates for Potentially Toxic Statin-Induced Changes in Muscle

Laaksonen, R., Katajamaa, M., Päivä, H., Sysi‐Aho, M., Saarinen, L., Junni, P., Lütjohann, D., Smet, J., Coster, R. V., Seppänen‐Laakso, T., et al. (2006) · PLoS ONE · doi:10.1371/journal.pone.0000097 · Cited by 223 · see citing works

The light‐hyperresponsive high pigment‐2dg mutation of tomato: alterations in the fruit metabolome

Bino, R. J., Vos, C. H. R. D., Lieberman, M., Hall, R. D., Bovy, A. G., Jonker, H. H., Tikunov, Y. M., Lommen, A., Moco, S., & Levin, I. (2005) · New Phytologist · doi:10.1111/j.1469-8137.2005.01362.x · Cited by 223 · see citing works

Comprehensive Label-Free Method for the Relative Quantification of Proteins from Biological Samples

Higgs, R. E., Knierman, M. D., Gelfanova, V., Butler, J. P., & Hale, J. E. (2005) · Journal of Proteome Research · doi:10.1021/pr050109b · Cited by 219 · see citing works

Automated Quantitative Analysis of Complex Lipidomes by Liquid Chromatography/Mass Spectrometry

Hermansson, M., Uphoff, A., Käkelä, R., & Somerharju, P. J. (2005) · Analytical Chemistry · doi:10.1021/ac048489s · Cited by 217 · see citing works

Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry

Radulovic, D., Jelveh, S., Ryu, S., Hamilton, T., Foss, E. J., Mao, Y., & Emili, A. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400061-mcp200 · Cited by 206 · see citing works

Metabolomics spectral formatting, alignment and conversion tools (MSFACTs)

Duran, A. L., Yang, J., Wang, L., & Sumner, L. W. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg315 · Cited by 190 · see citing works

A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry

Li, X., Yi, E. C., Kemp, C. J., Zhang, H., & Aebersold, R. H. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500141-mcp200 · Cited by 184 · see citing works

Application of Fast Fourier Transform Cross-Correlation for the Alignment of Large Chromatographic and Spectral Datasets

Wong, J. W. H., Durante, C., & Cartwright, H. (2005) · Analytical Chemistry · doi:10.1021/ac050619p · Cited by 176 · see citing works

Processing and classification of protein mass spectra

Hilario, M., Kalousis, A., Pellegrini, C., & Müller, M. (2006) · Mass Spectrometry Reviews · doi:10.1002/mas.20072 · Cited by 172 · see citing works

A comparison of three algorithms for chromatograms alignment

van Nederkassel, A. M., Daszykowski, M., Eilers, P. H. C., & Heyden, Y. V. (2006) · Journal of Chromatography A · doi:10.1016/j.chroma.2006.03.114 · Cited by 170 · see citing works

Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling

Birkemeyer, C., Luedemann, A., Wagner, C., Erban, A., & Kopka, J. (2004) · Trends in biotechnology · doi:10.1016/j.tibtech.2004.12.001 · Cited by 163 · see citing works

MathDAMP: a package for differential analysis of metabolite profiles

Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishi­oka, T., Robert, M., & Tomita, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-530 · Cited by 162 · see citing works

Robust Algorithm for Alignment of Liquid Chromatography−Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline

Jaitly, N., Monroe, M. E., Petyuk, V., Clauss, T. R., Adkins, J., & Smith, R. D. (2006) · Analytical Chemistry · doi:10.1021/ac052197p · Cited by 157 · see citing works

Statistical methods for comparing comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry results: Metabolomic analysis of mouse tissue extracts

Shellie, R. A., Welthagen, W., Zrostlı́ková, J., Spranger, J., Ristow, M., Fiehn, O., & Zimmermann, R. (2005) · Journal of Chromatography A · doi:10.1016/j.chroma.2005.05.088 · Cited by 151 · see citing works

MSight: An image analysis software for liquid chromatography‐mass spectrometry

Palagi, P. M., Walther, D., Quadroni, M., Catherinet, S., Burgess, J., Zimmermann‐Ivol, C. G., Sanchez, J., Binz, P., Hochstrasser, D. F., & Appel, R. D. (2005) · PROTEOMICS · doi:10.1002/pmic.200401244 · Cited by 140 · see citing works

A Comprehensive Two-Dimensional Retention Time Alignment Algorithm To Enhance Chemometric Analysis of Comprehensive Two-Dimensional Separation Data

Pierce, K. M., Wood, L., Wright, B. W., & Synovec, R. E. (2005) · Analytical Chemistry · doi:10.1021/ac0511142 · Cited by 132 · see citing works

Metabonomics with1H-NMR spectroscopy and liquid chromatography-mass spectrometry applied to the investigation of metabolic changes caused by gentamicin-induced nephrotoxicity in the rat

Lenz, E. M., Bright, J. D., Knight, R., Westwood, F. R., Davies, D. T., Major, H. J., & Wilson, I. D. (2005) · Biomarkers · doi:10.1080/13547500500094034 · Cited by 130 · see citing works

Proteome informatics I: Bioinformatics tools for processing experimental data

Palagi, P. M., Hernandez, P., Walther, D., & Appel, R. D. (2006) · PROTEOMICS · doi:10.1002/pmic.200600273 · Cited by 126 · see citing works

Optimization of NMR analysis of biological fluids for quantitative accuracy

Saude, E. J., Slupsky, C. M., & Sykes, B. D. (2006) · Metabolomics · doi:10.1007/s11306-006-0023-5 · Cited by 123 · see citing works

Computer methods in analytical mass spectrometry. Identification of an unknown compound in a catalog

Crawford, L., & Morrison, J. D. (1968) · Analytical Chemistry · doi:10.1021/ac60266a027 · Cited by 119 · see citing works

MapQuant: Open‐source software for large‐scale protein quantification

Leptos, K. C., Sarracino, D. A., Jaffe, J. D., Krastins, B., & Church, G. M. (2006) · PROTEOMICS · doi:10.1002/pmic.200500201 · Cited by 114 · see citing works

ChromAlign: A Two-Step Algorithmic Procedure for Time Alignment of Three-Dimensional LC−MS Chromatographic Surfaces

Sadygov, R. G., Martín-Maroto, F., & Hühmer, A. F. R. (2006) · Analytical Chemistry · doi:10.1021/ac060923y · Cited by 113 · see citing works

Signal Maps for Mass Spectrometry-based Comparative Proteomics

Prakash, A., Mallick, P., Whiteaker, J. R., Zhang, H., Paulovich, A. G., Flory, M. R., Lee, H., Aebersold, R. H., & Schwikowski, B. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500133-mcp200 · Cited by 111 · see citing works

New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data

Hastings, C. A., Norton, S. M., & Roy, S. (2002) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.600 · Cited by 101 · see citing works

Tools in Metabonomics: An Integrated Validation Approach for LC-MS Metabolic Profiling of Mercapturic Acids in Human Urine

Wagner, S., Scholz, K., Sieber, M., Kellert, M., & Völkel, W. (2007) · Analytical Chemistry · doi:10.1021/ac062153w · Cited by 91 · see citing works

Metabolomic approaches to phenotype characterization and applications to complex diseases

Orešič, M., Vidal‐Puig, A., & Hänninen, V. A. (2006) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.6.4.575 · Cited by 89 · see citing works

Difference detection in LC-MS data for protein biomarker discovery

Listgarten, J., Neal, R. M., Roweis, S. T., Wong, P., & Emili, A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl326 · Cited by 89 · see citing works

A bioinformatician's view of the metabolome

Nobeli, I., & Thornton, J. M. (2006) · BioEssays · doi:10.1002/bies.20414 · Cited by 86 · see citing works

A non-directed approach to the differential analysis of multiple LC–MS-derived metabolic profiles

Vorst, O., Vos, C. H. R. D., Lommen, A., Staps, R. V., Visser, R. G. F., Bino, R. J., & Hall, R. D. (2005) · Metabolomics · doi:10.1007/s11306-005-4432-7 · Cited by 82 · see citing works

Data pre-processing in liquid chromatography-mass spectrometry-based proteomics

Zhang, X., Asara, J. M., Adamec, J., Ouzzani, M., & Elmagarmid, A. K. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti660 · Cited by 79 · see citing works

Metabolic fingerprinting of rat urine by LC/MSPart 2. Data pretreatment methods for handling of complex data

Idborg, H., ZAMANI, L., Edlund, P., Schuppe‐Koistinen, I., & JACOBSSON, S. (2005) · Journal of Chromatography B · doi:10.1016/j.jchromb.2005.07.049 · Cited by 76 · see citing works

Algorithm for locating analytes of interest based on mass spectral similarity in GC × GC–TOF-MS data: analysis of metabolites in human infant urine

Sinha, A. E., Hope, J. L., Prazen, B. J., Nilsson, E. J., Jack, R. M., & Synovec, R. E. (2004) · Journal of Chromatography A · doi:10.1016/j.chroma.2004.08.064 · Cited by 76 · see citing works

Phenotype Characterisation Using Integrated Gene Transcript, Protein and Metabolite Profiling

Orešič, M., Clish, C. B., Davidov, E., Verheij, E., Vogels, J., Havekes, L., Neumann, E. K., Adourian, A., Naylor, S., van der Greef, J., et al. (2004) · Applied Bioinformatics · doi:10.2165/00822942-200403040-00002 · Cited by 69 · see citing works

Progressive peak clustering in GC-MS Metabolomic experiments applied to Leishmania parasites

Souza, D. P. D., Saunders, E. C., McConville, M. J., & Likić, V. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl085 · Cited by 68 · see citing works

NanoLC‐FT‐ICR MS improves proteome coverage attainable for ∼3000 laser‐microdissected breast carcinoma cells

Umar, A., Luider, T. M., Foekens, J. A., & Paša‐Tolić, L. (2006) · PROTEOMICS · doi:10.1002/pmic.200600293 · Cited by 67 · see citing works

Algorithm for locating analytes of interest based on mass spectral similarity in GC × GC–TOF-MS data: analysis of metabolites in human infant urine

SINHA, A., Hope, J. L., Prazen, B. J., et al. (2004) · Journal of Chromatography A · doi:10.1016/s0021-9673(04)01418-9 · Cited by 65 · see citing works

Toxicological evaluation of complex mixtures by pattern recognition: correlating chemical fingerprints to mutagenicity.

Eide, I., Neverdal, G., Thorvaldsen, B., Grung, B., & Kvalheim, O. M. (2002) · Environmental Health Perspectives · doi:10.1289/ehp.02110s6985 · Cited by 59 · see citing works

Mass Spectrometry Reveals Specific and Global Molecular Transformations during Viral Infection

Go, E. P., Wikoff, W. R., Shen, Z., O’Maille, G., Morita, H., Conrads, T. P., Nordstrom, A., Trauger, S. A., Uritboonthai, W., Lucas, D. A., et al. (2006) · Journal of Proteome Research · doi:10.1021/pr060215t · Cited by 46 · see citing works

A methodology for automated comparative analysis of metabolite profiling data

Frenzel, T., Miller, A., & Engel, K. (2003) · European Food Research and Technology · doi:10.1007/s00217-002-0659-y · Cited by 44 · see citing works

MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics

Spasić, ‪., Dunn, W. B., Velarde, G., Tseng, A., JENKINS, H. A., Hardy, N. W., Oliver, S. G., & Kell, D. B. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-281 · Cited by 44 · see citing works

HiRes—a tool for comprehensive assessment and interpretation of metabolomic data

Zhao, Q., Stoyanova, R. S., Du, S., Sajda, P., & Brown, T. R. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl428 · Cited by 43 · see citing works

Metabolomics as a diagnostic tool for hepatology: validation in a naturally occurring canine model

Whitfield, P. D., Noble, P. M., Major, H. J., Beynon, R. J., Burrow, R., Freeman, A., & German, A. J. (2005) · Metabolomics · doi:10.1007/s11306-005-0001-3 · Cited by 35 · see citing works

Correlation of pyrolysis-gas chromatography mass spectra and nuclear magnetic resonance spectra of pitch fractions separated by planar chromatography

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A new technique (COMSPARI) to facilitate the identification of minor compounds in complex mixtures by GC/MS and LC/MS: tools for the visualization of matched datasets

Katz, J. E., Dumlao, D. S., Clarke, S. D., & Hau, J. (2004) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2003.12.011 · Cited by 27 · see citing works

Phospholipid capture combined with non-linear chromatographic correction for improved serum metabolite profiling

Want, E. J., Smith, C. A., Qin, C., Horne, K. C. V., & Siuzdak, G. E. (2006) · Metabolomics · doi:10.1007/s11306-006-0028-0 · Cited by 24 · see citing works

Technical problems and practical operations in plant metabolomics

Bamba, T., & Fukusaki, E. (2006) · Journal of Pesticide Science · doi:10.1584/jpestics.31.300 · Cited by 19 · see citing works

3-Isopropylmalate Is the Major Endogenous Substrate of the Saccharomyces cerevisiae trans-Aconitate Methyltransferase

Katz, J. E., Dumlao, D. S., Wasserman, J. I., Lansdown, M. G., Jung, M. E., Faull, K. F., & Clarke, S. G. (2004) · Biochemistry · doi:10.1021/bi049784+ · Cited by 16 · see citing works

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

Pluskal, T., Castillo, S., Villar‐Briones, A., & Orešič, M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-395 · Cited by 3,852 · see citing works

Global metabolic profiling of animal and human tissues via UPLC-MS

Want, E. J., Masson, P., Michopoulos, F., Wilson, I. D., Theodoridis, G. A., Plumb, R. S., Shockcor, J. P., Loftus, N. J., Holmes, E. C., & Nicholson, J. K. (2012) · Nature Protocols · doi:10.1038/nprot.2012.135 · Cited by 1,626 · see citing works

Integrated, Nontargeted Ultrahigh Performance Liquid Chromatography/Electrospray Ionization Tandem Mass Spectrometry Platform for the Identification and Relative Quantification of the Small-Molecule Complement of Biological Systems

Evans, A. M., DeHaven, C. D., Barrett, T., Mitchell, M. W., & Milgram, K. E. (2009) · Analytical Chemistry · doi:10.1021/ac901536h · Cited by 1,315 · see citing works

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T. R., & Neumann, S. (2011) · Analytical Chemistry · doi:10.1021/ac202450g · Cited by 1,208 · see citing works

Highly sensitive feature detection for high resolution LC/MS

Tautenhahn, R., Böttcher, C., & Neumann, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-504 · Cited by 1,175 · see citing works

Global metabolic profiling procedures for urine using UPLC–MS

Want, E. J., Wilson, I. D., Gika, H., Theodoridis, G. A., Plumb, R. S., Shockcor, J. P., Holmes, E. C., & Nicholson, J. K. (2010) · Nature Protocols · doi:10.1038/nprot.2010.50 · Cited by 1,180 · see citing works

Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

Dunn, W. B., Broadhurst, D., Atherton, H. J., Goodacre, R., & Griffin, J. L. (2010) · Chemical Society Reviews · doi:10.1039/b906712b · Cited by 870 · see citing works

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

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