ArticleJournal of cheminformatics2024
Reproducible MS/MS library cleaning pipeline in matchms.
Article in Journal of cheminformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- From Single Injection to Dual Insights: Integrating EAD and CID Acquisition for Spectral Library Generation and EAD-CID Spectral Matching.Analytical chemistry · 2026Article
- A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.Nature structural & molecular biology · 2026Article
- X-Align: annotation-independent cross-platform alignment of untargeted metabolomics features.Chemical science · 2026Article
- PyCompound: An Open-Source Python Package for Spectral-Library Matching in Mass Spectrometry-Based Metabolomics.Metabolites · 2026Article
- Foundation Models for Liquid Chromatography-High-Resolution Mass Spectrometry: A New Era beyond Labeled Datasets.Analytical chemistry · 2026Article
- Large-scale discovery and annotation of substructure patterns in mass spectrometry profiles.Nature communications · 2026Article
- The MassBank contributions of the mFam collaboration.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- A Two-Layer Structural Key Framework for Linking Compound Identifiers and MS/MS Evidence in Spectral Database Curation.Metabolites · 2026Article
- Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra.ACS omega · 2026Article
- Comprehensive Curation and Harmonization of Small-Molecule MS/MS Libraries in Spectraverse.Analytical chemistry · 2026Article
- Cross ionization mode chemical similarity prediction between tandem mass spectra in metabolomics.Nature communications · 2026Article
- STRIKER: a spectral metadata repairing tool for expanding the comprehensiveness of spectral libraries.Journal of cheminformatics · 2026Article
- Article
- Review
- Creation of an Open-Access High-Resolution Tandem Mass Spectral Library of 1000 Food Toxicants.Analytical chemistry · 2025Article
- Large-scale generation of in silico based spectral libraries to annotate dark chemical space features in non-target analysis.Analytical and bioanalytical chemistry · 2025Article
- An evaluation methodology for machine learning-based tandem mass spectra similarity prediction.BMC bioinformatics · 2025Article
- Simplistic Software for Analyzing Mass Spectra and a Mixed Experimental-Theoretical Database for Identifying Poisonous and Explosive Substances.Journal of computational chemistry · 2025Article
- Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids.Journal of cheminformatics · 2025Article
- Defining the limits of plant chemical space: challenges and estimations.GigaScience · 2025Article
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Authors and funding
6 authors.
Funding
Abstract
Mass spectral libraries have proven to be essential for mass spectrum annotation, both for library matching and training new machine learning algorithms. A key step in training machine learning models is the availability of high-quality training data. Public libraries of mass spectrometry data that are open to user submission often suffer from limited metadata curation and harmonization. The resulting variability in data quality makes training of machine learning models challenging. Here we present a library cleaning pipeline designed for cleaning tandem mass spectrometry library data. The pipeline is designed with ease of use, flexibility, and reproducibility as leading principles.Scientific contributionThis pipeline will result in cleaner public mass spectral libraries that will improve library searching and the quality of machine-learning training datasets in mass spectrometry. This pipeline builds on previous work by adding new functionality for curating and correcting annotated libraries, by validating structure annotations. Due to the high quality of our software, the reproducibility, and improved logging, we think our new pipeline has the potential to become the standard in the field for cleaning tandem mass spectrometry libraries.
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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.