ArticleMass spectrometry (Tokyo, Japan)2014
Rethinking Mass Spectrometry-Based Small Molecule Identification Strategies in Metabolomics.
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 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts.Phenomics (Cham, Switzerland) · 2025Review
- Data Processing of Product Ion Spectra: Methods to Control False Discovery Rate in Compound Search Results for Untargeted Metabolomics.Mass spectrometry (Tokyo, Japan) · 2024Article
- Data Processing of Product Ion Spectra: Redundancy of Product Ion Spectra of Small Molecules in Data-Dependent Acquisition Dataset.Mass spectrometry (Tokyo, Japan) · 2023Article
- Comparative metabolomics analysis reveals alkaloid repertoires in young and mature Mitragyna speciosa (Korth.) Havil. Leaves.PloS one · 2023Article
- Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules.Mass spectrometry (Tokyo, Japan) · 2022Article
- A Perspective and Framework for Developing Sample Type Specific Databases for LC/MS-Based Clinical Metabolomics.Metabolites · 2019Article
- Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification.Journal of proteome research · 2018Article
- Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data.BMC bioinformatics · 2018Article
- Untargeted Metabolomics Strategies-Challenges and Emerging Directions.Journal of the American Society for Mass Spectrometry · 2016Review
- Technical Challenges in Mass Spectrometry-Based Metabolomics.Mass spectrometry (Tokyo, Japan) · 2016Article
- MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.Journal of cheminformatics · 2015Article
- 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
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The CASMI 2013 (Critical Assessment of Small Molecule Identification 2013, http://casmi-contest.org/) contest was held to systematically evaluate strategies used for mass spectrometry-based identification of small molecules. The results of the contest highlight that, because of the extensive efforts made towards the construction of databases and search tools, database-assisted small molecule identification can now automatically annotate some metabolite signals found in the metabolome data. In this commentary, the current state of metabolite annotation is compared with that of transcriptomics and proteomics. The comparison suggested that certain limitations in the metabolite annotation process need to be addressed, such as (i) the completeness of the database, (ii) the conversion between raw data and structure, (iii) the one-to-one correspondence between measured data and correct search results, and (iv) the false discovery rate in database search results.
Indexed as
Identifiers
What OpenQuestion holds
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.