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MetFrag relaunched: incorporating strategies beyond in silico fragmentation

Christoph Ruttkies, Emma L. Schymanski, Sebastian Wolf, Juliane Hollender, Steffen Neumann
2016 Journal of Cheminformatics  
The in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass  ...  The changes to MetFrag were evaluated on the original dataset as well as a dataset of 473 merged high resolution tandem mass spectra (HR-MS/MS) and compared with another open source in silico fragmenter  ...  Michael Stravs, Birgit Beck and other members of the Environmental Chemistry Department at Eawag; Tobias Schulze, Martin Krauss and others at the Helmholtz Centre for Environmental Research (UFZ) involved in  ... 
doi:10.1186/s13321-016-0115-9 pmid:26834843 pmcid:PMC4732001 fatcat:3owseprkrrawtem5qq54bpezom

Retrospective non-target analysis to support regulatory water monitoring: from masses of interest to recommendations via in silico workflows

Adelene Lai, Randolph R. Singh, Lubomira Kovalova, Oliver Jaeggi, Todor Kondić, Emma L. Schymanski
2021 Environmental Sciences Europe  
This regulator-supplied information was incorporated into MetFrag, an in silico identification tool replete with "post-relaunch" features used here.  ...  This work aimed to establish an open in silico workflow to identify environmental chemical unknowns via retrospective NTA within the scope of a pre-existing Swiss environmental monitoring campaign focusing  ...  Contributors to CompTox, MetFrag, the suspect lists on the NORMAN Suspect List Exchange, the Open software used here, and Open Science in general are gratefully appreciated.  ... 
doi:10.1186/s12302-021-00475-1 fatcat:wwgk7kjnlbebvfglzvoydmf4ze

Expanding the Coverage of the Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches [article]

Xuetong Li, Hongxia Zhou, Ning Xiao, Xueting Wu, Yuanhong Shan, Longxian Chen, Cuiting Wang, Zixuan Wang, Jirong Huang, Aihong Li, Xuan Li
2020 bioRxiv   pre-print
The experimental reference spectra, and in silico reference spectra were adopted to facilitate the structural annotation.  ...  To further characterize the structure of metabolites, two approaches, structural motif search combined with neutral loss scanning, and metabolite association network were incorporated into our strategy  ...  MetFrag relaunched: incorporating 6 2 4 strategies beyond in silico fragmentation. J Cheminform 2016;8:3. 6 2 5 [20] Shen X, Wang R, Xiong X, Yin Y, Cai Y, Ma Z, et al.  ... 
doi:10.1101/2020.03.04.976266 fatcat:6vzeuktrhnavjeaopamurnb7ny

Untargeted high-resolution plasma metabolomic profiling predicts outcomes in patients with coronary artery disease

Anurag Mehta, Chang Liu, Aditi Nayak, Ayman S. Tahhan, Yi-An Ko, Devinder S. Dhindsa, Jeong Hwan Kim, Salim S. Hayek, Laurence S. Sperling, Puja K. Mehta, Yan V. Sun, Karan Uppal (+3 others)
2020 PLoS ONE  
Differential regulation of six metabolic pathways involved in myocardial energetics and systemic inflammation is independently associated with mortality in patients with CAD.  ...  Metabolic features and pathways associated with mortality were identified in 454 subjects using metabolome-wide association studies and Mummichog, respectively, and validated in 322 subjects.  ...  MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform. 2016; 8:3. https://doi.org/10.1186/s13321-016-0115-9 PMID: 26834843 23.  ... 
doi:10.1371/journal.pone.0237579 pmid:32810196 fatcat:xngxqttwz5hy7e7sywyx2lxv2y

Automated fragment identification for electron ionisation mass spectrometry: application to atmospheric measurements of halocarbons [article]

Myriam Guillevic
2021 arXiv   pre-print
Results: Based on co-eluting mass/charge fragments, we developed an innovative data analysis method to reliably reconstruct the chemical formulae of the fragments, using efficient combinatorics and graph  ...  In this work, we present data analysis tools to enable automated identification of unknown compounds measured by GC-EI-HRMS.  ...  Ruttkies, C., Schymanski, E.L., Wolf, S., Hollender, J., Neumann, S.: MetFrag relaunched: incorporating strategies beyond in silico fragmentation.  ... 
arXiv:2103.13807v1 fatcat:issqxu3yojfw7po5bhtps2nshe

Phenomenal Biannual Progress Report - D1.4.1

Steinbeck, Namrata Kale, Kenneth Haug, Pablo Moreno, David Johnson, Et.Al
2015 Zenodo  
"MetFrag relaunched: incorporating strategies beyond in silico fragmentation."  ...  continue beyond the initial 3-year funding period of PhenoMeNal.  ...  PhenoMeNal Scientific Advisory Board meeting: As an outcome of the suggestions made during the kick-off meeting, a PhenoMeNal SAB representing experts in the field of metabolomics, bioinformatics, clinical  ... 
doi:10.5281/zenodo.832241 fatcat:q6go7nieyzbo7na5cu6wwp2mty

Disentangling metabolic functions of bacteria in the honey bee gut

Lucie Kešnerová, Ruben A. T. Mars, Kirsten M. Ellegaard, Michaël Troilo, Uwe Sauer, Philipp Engel, David Relman
2017 PLoS Biology  
We then determined the contribution of individual community members in mono-colonized bees and recapitulated our findings using in vitro cultures.  ...  In turn, multiple species were responsible for the accumulation of organic acids and aromatic compound degradation intermediates.  ...  Emma Schymanski for excellent help with the interpretation of MS/MS fragmentation spectra, Guillermo Garcia Osuna for help with the preparation of culture media, and Fabienne Wichmann for editing the manuscript  ... 
doi:10.1371/journal.pbio.2003467 pmid:29232373 pmcid:PMC5726620 fatcat:x5nxyw2mhzbw5izi53x4q3drga

MOESM1 of The RiBaTox web tool: selecting methods to assess and manage the diverse problem of chemical pollution in surface waters

Kees Kramer, Frank Sleeuwaert, Guy Engelen, Christin MĂźller, Werner Brack, Leo Posthuma
2019 Figshare  
The model is used by companies to assess the effect of ingredients in different products.  ...  Within SOLUTIONS project, both receptor mediated model predictions have been used by partners involved in Chemical Analytical tools.  ...  MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J. Cheminform. 8: 1- 16.; https://doi.org/10.1186/s13321-016-0115-9 5.  ... 
doi:10.6084/m9.figshare.9923471 fatcat:4qjsdqautbhhbd7jxzh7osx3hi