ArticleMass spectrometry (Tokyo, Japan)2014
Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS.
Article in Mass spectrometry (Tokyo, Japan), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- The DNA adenine methylase ofFrontiers in microbiology · 2023Article
- Custom-made design of metabolite composition in N. benthamiana leaves using CRISPR activators.Plant biotechnology journal · 2022Article
- patRoon: open source software platform for environmental mass spectrometry based non-target screening.Journal of cheminformatics · 2021Article
- Metabolic Signatures in Response to Abscisic Acid (ABA) Treatment in Brassica napus Guard Cells Revealed by Metabolomics.Scientific reports · 2017Article
- CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry.Phytochemistry letters · 2017Article
- Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.Journal of cheminformatics · 2017Article
- Integrated Framework for Identifying Toxic Transformation Products in Complex Environmental Mixtures.Environmental science & technology letters · 2017Article
- Epimetabolites: discovering metabolism beyond building and burning.Current opinion in chemical biology · 2017Review
- Winners of CASMI2013: Automated Tools and Challenge Data.Mass spectrometry (Tokyo, Japan) · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The second Critical Assessment of Small Molecule Identification (CASMI) contest took place in 2013. A joint team from the Swiss Federal Institute of Aquatic Science and Technology (Eawag) and Leibniz Institute of Plant Biochemistry (IPB) participated in CASMI 2013 with an automatic workflow-style entry. MOLGEN-MS/MS was used for Category 1, molecular formula calculation, restricted by the information given for each challenge. MetFrag and MetFusion were used for Category 2, structure identification, retrieving candidates from the compound databases KEGG, PubChem and ChemSpider and joining these lists pre-submission. The results from Category 1 were used to guide whether formula or exact mass searches were performed for Category 2. The Category 2 results were impressive considering the database size and automated regime used, although these could not compete with the manual approach of the contest winner. The Category 1 results were affected by large m/z and ppm values in the challenge data, where strategies beyond pure enumeration from other participants were more successful. However, the combination used for the CASMI 2013 entries was extremely useful for developing decision-making criteria for automatic, high throughput general unknown (non-target) identification and for future contests.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.