Reproducible MS/MS library cleaning pipeline in matchms

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F24%3A00137132" target="_blank" >RIV/00216224:14310/24:00137132 - isvavai.cz</a>
Result on the web
<a href="https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00878-1" target="_blank" >https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00878-1</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s13321-024-00878-1" target="_blank" >10.1186/s13321-024-00878-1</a>

Result language
angličtina
Original language name
Reproducible MS/MS library cleaning pipeline in matchms
Original language description
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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10400 - Chemical sciences

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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