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Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples.
Broeckling CD, Beger RD, Cheng LL, Cumeras R, Cuthbertson DJ, Dasari S, Davis WC, Dunn WB, Evans AM, Fernández-Ochoa A, Gika H, Goodacre R, Goodman KD, Gouveia GJ, Hsu PC, Kirwan JA, Kodra D, Kuligowski J, Lan RS, Monge ME, Moussa LW, Nair SG, Reisdorph N, Sherrod SD, Ulmer Holland C, Vuckovic D, Yu LR, Zhang B, Theodoridis G, Mosley JD. Broeckling CD, et al. Anal Chem. 2023 Dec 26;95(51):18645-18654. doi: 10.1021/acs.analchem.3c02924. Epub 2023 Dec 6. Anal Chem. 2023. PMID: 38055671 Free PMC article. Review.
Recent advances in mass spectrometry-based computational metabolomics.
Ebbels TMD, van der Hooft JJJ, Chatelaine H, Broeckling C, Zamboni N, Hassoun S, Mathé EA. Ebbels TMD, et al. Curr Opin Chem Biol. 2023 Jun;74:102288. doi: 10.1016/j.cbpa.2023.102288. Epub 2023 Mar 24. Curr Opin Chem Biol. 2023. PMID: 36966702 Free PMC article. Review.
The metaRbolomics Toolbox in Bioconductor and beyond.
Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. Stanstrup J, et al. Metabolites. 2019 Sep 23;9(10):200. doi: 10.3390/metabo9100200. Metabolites. 2019. PMID: 31548506 Free PMC article. Review.
A Practical Guide to Metabolomics Software Development.
Chang HY, Colby SM, Du X, Gomez JD, Helf MJ, Kechris K, Kirkpatrick CR, Li S, Patti GJ, Renslow RS, Subramaniam S, Verma M, Xia J, Young JD. Chang HY, et al. Anal Chem. 2021 Feb 2;93(4):1912-1923. doi: 10.1021/acs.analchem.0c03581. Epub 2021 Jan 19. Anal Chem. 2021. PMID: 33467846 Free PMC article.
Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.
Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL 2nd, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Aksenov AA, et al. Nat Biotechnol. 2021 Feb;39(2):169-173. doi: 10.1038/s41587-020-0700-3. Epub 2020 Nov 9. Nat Biotechnol. 2021. PMID: 33169034 Free PMC article.