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For: Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S. Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics 2016;12:14. [PMID: 26612985 PMCID: PMC4648992 DOI: 10.1007/s11306-015-0879-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
1
Bosco A, Arru F, Abis A, Fanos V, Dessì A. Application of Multiomics in Perinatology: A Metabolomics Integration-Focused Review. Int J Mol Sci 2025;26:4164. [PMID: 40362403 PMCID: PMC12071719 DOI: 10.3390/ijms26094164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 03/13/2025] [Accepted: 04/22/2025] [Indexed: 05/15/2025]  Open
2
Garcia-Aloy M, Rainer J, Franceschi P. Data Treatment for LC-MS Untargeted Analysis. Methods Mol Biol 2025;2891:91-108. [PMID: 39812978 DOI: 10.1007/978-1-0716-4334-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
3
Toral PG, Hervás G, Frutos P. Invited review: Research on ruminal biohydrogenation-Achievements, gaps in knowledge, and future approaches from the perspective of dairy science. J Dairy Sci 2024;107:10115-10140. [PMID: 39154717 DOI: 10.3168/jds.2023-24591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/18/2024] [Indexed: 08/20/2024]
4
Dabbousy R, Rima M, Roufayel R, Rahal M, Legros C, Sabatier JM, Fajloun Z. Plant Metabolomics: The Future of Anticancer Drug Discovery. Pharmaceuticals (Basel) 2024;17:1307. [PMID: 39458949 PMCID: PMC11510165 DOI: 10.3390/ph17101307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 09/19/2024] [Accepted: 09/25/2024] [Indexed: 10/28/2024]  Open
5
Samanipour S, Barron LP, van Herwerden D, Praetorius A, Thomas KV, O’Brien JW. Exploring the Chemical Space of the Exposome: How Far Have We Gone? JACS AU 2024;4:2412-2425. [PMID: 39055136 PMCID: PMC11267556 DOI: 10.1021/jacsau.4c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024]
6
McKay RT. Metabolomics and NMR. Handb Exp Pharmacol 2023;277:73-116. [PMID: 36355220 DOI: 10.1007/164_2022_616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
7
Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022;12:584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022]  Open
8
Morgan EW, Perdew GH, Patterson AD. Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. Toxicol Sci 2022;187:189-213. [PMID: 35285497 PMCID: PMC9154275 DOI: 10.1093/toxsci/kfac029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
9
Woods HB, Pinfield S. Incentivising research data sharing: a scoping review. Wellcome Open Res 2022;6:355. [PMID: 35169638 PMCID: PMC8808319 DOI: 10.12688/wellcomeopenres.17286.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 11/20/2022]  Open
10
Krämer J, Kang R, Grimm LM, De Cola L, Picchetti P, Biedermann F. Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chem Rev 2022;122:3459-3636. [PMID: 34995461 PMCID: PMC8832467 DOI: 10.1021/acs.chemrev.1c00746] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 02/08/2023]
11
Du X, Aristizabal-Henao JJ, Garrett TJ, Brochhausen M, Hogan WR, Lemas DJ. A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research. Metabolites 2022;12:87. [PMID: 35050209 PMCID: PMC8779534 DOI: 10.3390/metabo12010087] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/25/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]  Open
12
Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022;414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
13
Woods HB, Pinfield S. Incentivising research data sharing: a scoping review. Wellcome Open Res 2021;6:355. [DOI: 10.12688/wellcomeopenres.17286.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 11/20/2022]  Open
14
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. Metabolites 2021;11:metabo11030163. [PMID: 33808985 PMCID: PMC8000456 DOI: 10.3390/metabo11030163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/20/2022]  Open
15
Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021;40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
16
Lian N, Shi LQ, Hao ZM, Chen M. Research progress and perspective in metabolism and metabolomics of psoriasis. Chin Med J (Engl) 2020;133:2976-2986. [PMID: 33237698 PMCID: PMC7752687 DOI: 10.1097/cm9.0000000000001242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 12/28/2022]  Open
17
Opialla T, Kempa S, Pietzke M. Towards a More Reliable Identification of Isomeric Metabolites Using Pattern Guided Retention Validation. Metabolites 2020;10:457. [PMID: 33198249 PMCID: PMC7696895 DOI: 10.3390/metabo10110457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023]  Open
18
Letertre MPM, Dervilly G, Giraudeau P. Combined Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry Approaches for Metabolomics. Anal Chem 2020;93:500-518. [PMID: 33155816 DOI: 10.1021/acs.analchem.0c04371] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
19
Sielemann K, Hafner A, Pucker B. The reuse of public datasets in the life sciences: potential risks and rewards. PeerJ 2020;8:e9954. [PMID: 33024631 PMCID: PMC7518187 DOI: 10.7717/peerj.9954] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]  Open
20
Liu P, Wang L, Du Q, Du H. Chemotype classification and biomarker screening of male Eucommia ulmoides Oliv. flower core collections using UPLC-QTOF/MS-based non-targeted metabolomics. PeerJ 2020;8:e9786. [PMID: 32884862 PMCID: PMC7444510 DOI: 10.7717/peerj.9786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/31/2020] [Indexed: 01/27/2023]  Open
21
López-Moreno A, Suárez A, Avanzi C, Monteoliva-Sánchez M, Aguilera M. Probiotic Strains and Intervention Total Doses for Modulating Obesity-Related Microbiota Dysbiosis: A Systematic Review and Meta-analysis. Nutrients 2020;12:E1921. [PMID: 32610476 PMCID: PMC7400323 DOI: 10.3390/nu12071921] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]  Open
22
Palermo A, Huan T, Rinehart D, Rinschen MM, Li S, O'Donnell VB, Fahy E, Xue J, Subramaniam S, Benton HP, Siuzdak G. Cloud-based archived metabolomics data: A resource for in-source fragmentation/annotation, meta-analysis and systems biology. ANALYTICAL SCIENCE ADVANCES 2020;1:70-80. [PMID: 35190800 PMCID: PMC8858440 DOI: 10.1002/ansa.202000042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
23
Pourchet M, Debrauwer L, Klanova J, Price EJ, Covaci A, Caballero-Casero N, Oberacher H, Lamoree M, Damont A, Fenaille F, Vlaanderen J, Meijer J, Krauss M, Sarigiannis D, Barouki R, Le Bizec B, Antignac JP. Suspect and non-targeted screening of chemicals of emerging concern for human biomonitoring, environmental health studies and support to risk assessment: From promises to challenges and harmonisation issues. ENVIRONMENT INTERNATIONAL 2020;139:105545. [PMID: 32361063 DOI: 10.1016/j.envint.2020.105545] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 05/07/2023]
24
Eicher T, Kinnebrew G, Patt A, Spencer K, Ying K, Ma Q, Machiraju R, Mathé EA. Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. Metabolites 2020;10:E202. [PMID: 32429287 PMCID: PMC7281435 DOI: 10.3390/metabo10050202] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]  Open
25
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Res 2020;9:136. [PMID: 32308977 PMCID: PMC7141167 DOI: 10.12688/f1000research.18236.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 01/08/2023]  Open
26
Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC. Mass spectrometry searches using MASST. Nat Biotechnol 2020;38:23-26. [PMID: 31894142 PMCID: PMC7236533 DOI: 10.1038/s41587-019-0375-9] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
27
Rodrigues AM, Ribeiro-Barros AI, António C. Experimental Design and Sample Preparation in Forest Tree Metabolomics. Metabolites 2019;9:E285. [PMID: 31766588 PMCID: PMC6950530 DOI: 10.3390/metabo9120285] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]  Open
28
Manzi M, Riquelme G, Zabalegui N, Monge ME. Improving diagnosis of genitourinary cancers: Biomarker discovery strategies through mass spectrometry-based metabolomics. J Pharm Biomed Anal 2019;178:112905. [PMID: 31707200 DOI: 10.1016/j.jpba.2019.112905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
29
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinformatics 2019;35:3752-3760. [PMID: 30851093 PMCID: PMC6761976 DOI: 10.1093/bioinformatics/btz160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]  Open
30
Goodacre R. The blind men and the elephant: challenges in the analysis of complex natural mixtures. Faraday Discuss 2019;218:524-539. [PMID: 31309965 DOI: 10.1039/c9fd00074g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
31
Schmitz-Spanke S. Toxicogenomics - What added Value Do These Approaches Provide for Carcinogen Risk Assessment? ENVIRONMENTAL RESEARCH 2019;173:157-164. [PMID: 30909101 DOI: 10.1016/j.envres.2019.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
32
Beyß M, Azzouzi S, Weitzel M, Wiechert W, Nöh K. The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis. Front Microbiol 2019;10:1022. [PMID: 31178829 PMCID: PMC6543931 DOI: 10.3389/fmicb.2019.01022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022]  Open
33
Barba I, Andrés M, Garcia-Dorado D. Metabolomics and Heart Diseases: From Basic to Clinical Approach. Curr Med Chem 2019;26:46-59. [PMID: 28990507 DOI: 10.2174/0929867324666171006151408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 03/15/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022]
34
Chibli LA, Rosa AL, Nonato MC, Da Costa FB. Untargeted LC-MS metabolomic studies of Asteraceae species to discover inhibitors of Leishmania major dihydroorotate dehydrogenase. Metabolomics 2019;15:59. [PMID: 30949823 DOI: 10.1007/s11306-019-1520-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/25/2019] [Indexed: 12/18/2022]
35
Considine EC, Salek RM. A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics. Metabolites 2019;9:E43. [PMID: 30841575 PMCID: PMC6468746 DOI: 10.3390/metabo9030043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/23/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022]  Open
36
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. PhenoMeNal: processing and analysis of metabolomics data in the cloud. Gigascience 2019;8:giy149. [PMID: 30535405 PMCID: PMC6377398 DOI: 10.1093/gigascience/giy149] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/19/2018] [Accepted: 11/20/2018] [Indexed: 12/02/2022]  Open
37
McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Nat Prod Rep 2019;36:35-107. [PMID: 30003207 PMCID: PMC6350634 DOI: 10.1039/c7np00064b] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/20/2022]
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Allard PM, Bisson J, Azzollini A, Pauli GF, Cordell GA, Wolfender JL. Pharmacognosy in the digital era: shifting to contextualized metabolomics. Curr Opin Biotechnol 2018;54:57-64. [PMID: 29499476 PMCID: PMC6110999 DOI: 10.1016/j.copbio.2018.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/26/2018] [Accepted: 02/13/2018] [Indexed: 01/01/2023]
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Witting M, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis NE, Schirra HJ, Kaleta C, Casanueva O. Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. Front Mol Biosci 2018;5:96. [PMID: 30488036 PMCID: PMC6246695 DOI: 10.3389/fmolb.2018.00096] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/22/2018] [Indexed: 02/05/2023]  Open
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Cui L, Lu H, Lee YH. Challenges and emergent solutions for LC-MS/MS based untargeted metabolomics in diseases. MASS SPECTROMETRY REVIEWS 2018;37:772-792. [PMID: 29486047 DOI: 10.1002/mas.21562] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023]
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Ahmed WM, Brinkman P, Weda H, Knobel HH, Xu Y, Nijsen TM, Goodacre R, Rattray N, Vink TJ, Santonico M, Pennazza G, Montuschi P, Sterk PJ, Fowler SJ. Methodological considerations for large-scale breath analysis studies: lessons from the U-BIOPRED severe asthma project. J Breath Res 2018;13:016001. [PMID: 30272570 DOI: 10.1088/1752-7163/aae557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J Lipid Res 2018;59:2001-2017. [PMID: 30115755 PMCID: PMC6168311 DOI: 10.1194/jlr.s087163] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/11/2018] [Indexed: 12/19/2022]  Open
43
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Best practice data life cycle approaches for the life sciences. F1000Res 2018;6:1618. [PMID: 30109017 DOI: 10.12688/f1000research.12344.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2017] [Indexed: 11/20/2022]  Open
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Cañueto D, Salek RM, Correig X, Cañellas N. Improving sample classification by harnessing the potential of 1H-NMR signal chemical shifts. Sci Rep 2018;8:11886. [PMID: 30089873 PMCID: PMC6082897 DOI: 10.1038/s41598-018-30351-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022]  Open
45
Dervilly-Pinel G, Royer AL, Bozzetta E, Pezzolato M, Herpin L, Prevost S, Le Bizec B. When LC-HRMS metabolomics gets ISO17025 accredited and ready for official controls – application to the screening of forbidden compounds in livestock. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2018;35:1948-1958. [DOI: 10.1080/19440049.2018.1496280] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Mathé E, Hays JL, Stover DG, Chen JL. The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources. Yearb Med Inform 2018;27:211-222. [PMID: 30157526 PMCID: PMC6115204 DOI: 10.1055/s-0038-1667085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
47
Vuckovic D. Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery. Chem Commun (Camb) 2018;54:6728-6749. [PMID: 29888773 DOI: 10.1039/c8cc02592d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Tugizimana F, Mhlongo MI, Piater LA, Dubery IA. Metabolomics in Plant Priming Research: The Way Forward? Int J Mol Sci 2018;19:ijms19061759. [PMID: 29899301 PMCID: PMC6032392 DOI: 10.3390/ijms19061759] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/02/2018] [Accepted: 06/04/2018] [Indexed: 12/26/2022]  Open
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Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. Current Challenges in Plant Eco-Metabolomics. Int J Mol Sci 2018;19:E1385. [PMID: 29734799 PMCID: PMC5983679 DOI: 10.3390/ijms19051385] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022]  Open
50
Data Treatment for LC-MS Untargeted Analysis. Methods Mol Biol 2018. [PMID: 29654581 DOI: 10.1007/978-1-4939-7643-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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