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Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics.

van der Hooft JJJ, Wandy J, Young F, Padmanabhan S, Gerasimidis K, Burgess KEV, Barrett MP, Rogers S.

Anal Chem. 2017 Jul 18;89(14):7569-7577. doi: 10.1021/acs.analchem.7b01391. Epub 2017 Jul 5.


Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra.

Rogers S, Ong CW, Wandy J, Ernst M, Ridder L, van der Hooft JJJ.

Faraday Discuss. 2019 May 23. doi: 10.1039/c8fd00235e. [Epub ahead of print]


Topic modeling for untargeted substructure exploration in metabolomics.

van der Hooft JJ, Wandy J, Barrett MP, Burgess KE, Rogers S.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13738-13743. Epub 2016 Nov 16.


Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification.

Wolahan SM, Hirt D, Glenn TC.

In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25.

5. web-based topic modelling for substructure discovery in mass spectrometry.

Wandy J, Zhu Y, van der Hooft JJJ, Daly R, Barrett MP, Rogers S.

Bioinformatics. 2017 Sep 14. doi: 10.1093/bioinformatics/btx582. [Epub ahead of print]


MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools.

Ernst M, Kang KB, Caraballo-Rodríguez AM, Nothias LF, Wandy J, Chen C, Wang M, Rogers S, Medema MH, Dorrestein PC, van der Hooft JJJ.

Metabolites. 2019 Jul 16;9(7). pii: E144. doi: 10.3390/metabo9070144.


Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry.

Ranninger C, Schmidt LE, Rurik M, Limonciel A, Jennings P, Kohlbacher O, Huber CG.

Anal Chim Acta. 2016 Aug 3;930:13-22. doi: 10.1016/j.aca.2016.05.017. Epub 2016 May 25.


Untargeted metabolomics.

Vinayavekhin N, Saghatelian A.

Curr Protoc Mol Biol. 2010 Apr;Chapter 30:Unit 30.1.1-24. doi: 10.1002/0471142727.mb3001s90.


Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics.

Domingo-Almenara X, Montenegro-Burke JR, Guijas C, Majumder EL, Benton HP, Siuzdak G.

Anal Chem. 2019 Mar 5;91(5):3246-3253. doi: 10.1021/acs.analchem.8b03126. Epub 2019 Feb 11.


Development of high-performance chemical isotope labeling LC-MS for profiling the human fecal metabolome.

Xu W, Chen D, Wang N, Zhang T, Zhou R, Huan T, Lu Y, Su X, Xie Q, Li L, Li L.

Anal Chem. 2015 Jan 20;87(2):829-36. doi: 10.1021/ac503619q. Epub 2014 Dec 25.


The application of a novel high-resolution mass spectrometry-based analytical strategy to rapid metabolite profiling of a dual drug combination in humans.

Xing J, Zang M, Liu H.

Anal Chim Acta. 2017 Nov 15;993:38-46. doi: 10.1016/j.aca.2017.08.047. Epub 2017 Sep 13.


Sample preparation optimization in fecal metabolic profiling.

Deda O, Chatziioannou AC, Fasoula S, Palachanis D, Raikos Ν, Theodoridis GA, Gika HG.

J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Mar 15;1047:115-123. doi: 10.1016/j.jchromb.2016.06.047. Epub 2016 Jun 28.


Enhanced acylcarnitine annotation in high-resolution mass spectrometry data: fragmentation analysis for the classification and annotation of acylcarnitines.

van der Hooft JJ, Ridder L, Barrett MP, Burgess KE.

Front Bioeng Biotechnol. 2015 Mar 9;3:26. doi: 10.3389/fbioe.2015.00026. eCollection 2015.


Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

Treutler H, Tsugawa H, Porzel A, Gorzolka K, Tissier A, Neumann S, Balcke GU.

Anal Chem. 2016 Aug 16;88(16):8082-90. doi: 10.1021/acs.analchem.6b01569. Epub 2016 Aug 2.


Dansylation isotope labeling liquid chromatography mass spectrometry for parallel profiling of human urinary and fecal submetabolomes.

Su X, Wang N, Chen D, Li Y, Lu Y, Huan T, Xu W, Li L, Li L.

Anal Chim Acta. 2016 Jan 15;903:100-9. doi: 10.1016/j.aca.2015.11.027. Epub 2015 Nov 25.


Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics.

Neumann NK, Lehner SM, Kluger B, Bueschl C, Sedelmaier K, Lemmens M, Krska R, Schuhmacher R.

Anal Chem. 2014 Aug 5;86(15):7320-7. doi: 10.1021/ac501358z. Epub 2014 Jul 14.


compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets.

Edmands WM, Petrick L, Barupal DK, Scalbert A, Wilson MJ, Wickliffe JK, Rappaport SM.

Anal Chem. 2017 Apr 4;89(7):3919-3928. doi: 10.1021/acs.analchem.6b02394. Epub 2017 Mar 27.


Enhanced MS/MS coverage for metabolite identification in LC-MS-based untargeted metabolomics by target-directed data dependent acquisition with time-staggered precursor ion list.

Wang Y, Feng R, Wang R, Yang F, Li P, Wan JB.

Anal Chim Acta. 2017 Nov 1;992:67-75. doi: 10.1016/j.aca.2017.08.044. Epub 2017 Sep 13.


Rat Fecal Metabolomics-Based Analysis.

Deda O, Gika HG, Theodoridis GA.

Methods Mol Biol. 2018;1738:149-157. doi: 10.1007/978-1-4939-7643-0_10.


Automated pathway and reaction prediction facilitates in silico identification of unknown metabolites in human cohort studies.

Quell JD, Römisch-Margl W, Colombo M, Krumsiek J, Evans AM, Mohney R, Salomaa V, de Faire U, Groop LC, Agakov F, Looker HC, McKeigue P, Colhoun HM, Kastenmüller G.

J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Dec 15;1071:58-67. doi: 10.1016/j.jchromb.2017.04.002. Epub 2017 Apr 4.

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