The nPYc-Toolbox, a Python module for the pre-processing, quality-control, and analysis of metabolic profiling datasets.

Sands CJ, Wolfer AM, Correia GD, Sadawi N, Ahmed A, Jiménez B, Lewis MR, Glen RC, Nicholson JK, Pearce JT.

Bioinformatics. 2019 Jul 26. pii: btz566. doi: 10.1093/bioinformatics/btz566

Systematic Isolation and Structure Elucidation of Urinary Metabolites Optimized for the Analytical-Scale Molecular Profiling Laboratory.

Whiley L, Chekmeneva E, Berry DJ, Jiménez B, Yuen AHY, Salam A, Hussain H, Witt M, Takats Z, Nicholson J, Lewis MR.

Anal Chem. 2019 Jul 16;91(14):8873-8882. doi: 10.1021/acs.analchem.9b00241

Application of novel solid phase extraction-NMR protocols for metabolic profiling of human urine.

McGill D, Chekmeneva E, Lindon JC, Takats Z, Nicholson JK.

Faraday Discuss. 2019 May 22. doi: 10.1039/c8fd00220g

pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra.

Rodriguez-Martinez A, Ayala R, Posma JM, Harvey N, Jiménez B, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME.

Bioinformatics. 2019 Jun 1;35(11):1916-1922. doi: 10.1093/bioinformatics/bty837

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR.

Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149

Quantitative Lipoprotein Subclass and Low Molecular Weight Metabolite Analysis in Human Serum and Plasma by 1H NMR Spectroscopy in a Multilaboratory Trial.

Jiménez B, Holmes E, Heude C, Tolson RF, Harvey N, Lodge SL, Chetwynd AJ, Cannet C, Fang F, Pearce JTM, Lewis MR, Viant MR, Lindon JC, Spraul M, Schäfer H, Nicholson JK.

Anal Chem. 2018 Oct 16;90(20):11962-11971. doi: 10.1021/acs.analchem.8b02412

Ultra-Performance Liquid Chromatography-High-Resolution Mass Spectrometry and Direct Infusion-High-Resolution Mass Spectrometry for Combined Exploratory and Targeted Metabolic Profiling of Human Urine.

Chekmeneva E, Dos Santos Correia G, Gómez-Romero M, Stamler J, Chan Q, Elliott P, Nicholson JK, Holmes E.

J Proteome Res. 2018 Oct 5;17(10):3492-3502. doi: 10.1021/acs.jproteome.8b00413

XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules.

Domingo-Almenara X, Montenegro-Burke JR, Ivanisevic J, Thomas A, Sidibé J, Teav T, Guijas C, Aisporna AE, Rinehart D, Hoang L, Nordström A, Gómez-Romero M, Whiley L, Lewis MR, Nicholson JK, Benton HP, Siuzdak G.

Nat Methods. 2018 Sep;15(9):681-684. doi: 10.1038/s41592-018-0110-3

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies.

Broadhurst D, Goodacre R, Reinke SN, Kuligowski J, Wilson ID, Lewis MR, Dunn WB.

Metabolomics. 2018;14(6):72. doi: 10.1007/s11306-018-1367-3

J-Resolved 1H NMR 1D-Projections for Large-Scale Metabolic Phenotyping Studies: Application to Blood Plasma Analysis.

Rodriguez-Martinez A, Posma JM, Ayala R, Harvey N, Jimenez B, Neves AL, Lindon JC, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME.

Anal Chem. 2017 Nov 7;89(21):11405-11412. doi: 10.1021/acs.analchem.7b02374

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling.

Castagné R, Boulangé CL, Karaman I, Campanella G, Santos Ferreira DL, Kaluarachchi MR, Lehne B, Moayyeri A, Lewis MR, Spagou K, Dona AC, Evangelos V, Tracy R, Greenland P, Lindon JC, Herrington D, Ebbels TMD, Elliott P, Tzoulaki I, Chadeau-Hyam M.

J Proteome Res. 2017 Oct 6;16(10):3623-3633. doi: 10.1021/acs.jproteome.7b00344

Development and Application of Ultra-Performance Liquid Chromatography-TOF MS for Precision Large Scale Urinary Metabolic Phenotyping.

Lewis MR, Pearce JT, Spagou K, Green M, Dona AC, Yuen AH, David M, Berry DJ, Chappell K, Horneffer-van der Sluis V, Shaw R, Lovestone S, Elliott P, Shockcor J, Lindon JC, Cloarec O, Takats Z, Holmes E, Nicholson JK.

Anal Chem. 2016 Sep 20;88(18):9004-13. doi: 10.1021/acs.analchem.6b01481

Analysis of polar urinary metabolites for metabolic phenotyping using supercritical fluid chromatography and mass spectrometry.

Sen A, Knappy C, Lewis MR, Plumb RS, Wilson ID, Nicholson JK, Smith NW.

J Chromatogr A. 2016 Jun 3;1449:141-55. doi: 10.1016/j.chroma.2016.04.040

Bile acid profiling and quantification in biofluids using ultra-performance liquid chromatography tandem mass spectrometry.

Sarafian MH, Lewis MR, Pechlivanis A, Ralphs S, McPhail MJ, Patel VC, Dumas ME, Holmes E, Nicholson JK.

Anal Chem. 2015 Oct 6;87(19):9662-70. doi: 10.1021/acs.analchem.5b01556

High-Throughput Microbore UPLC-MS Metabolic Phenotyping of Urine for Large-Scale Epidemiology Studies.

Gray N, Lewis MR, Plumb RS, Wilson ID, Nicholson JK.

J Proteome Res. 2015 Jun 5;14(6):2714-21. doi: 10.1021/acs.jproteome.5b00203

Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping.

Dona AC, Jiménez B, Schäfer H, Humpfer E, Spraul M, Lewis MR, Pearce JT, Holmes E, Lindon JC, Nicholson JK.

Anal Chem. 2014 Oct 7;86(19):9887-94. doi: 10.1021/ac5025039

Objective set of criteria for optimization of sample preparation procedures for ultra-high throughput untargeted blood plasma lipid profiling by ultra performance liquid chromatography-mass spectrometry.

Sarafian MH, Gaudin M, Lewis MR, Martin FP, Holmes E, Nicholson JK, Dumas ME.

Anal Chem. 2014 Jun 17;86(12):5766-74. doi: 10.1021/ac500317c

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