Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F25%3A00141838" target="_blank" >RIV/00216224:14310/25:00141838 - isvavai.cz</a>
Result on the web
<a href="https://gigabytejournal.com/articles/160" target="_blank" >https://gigabytejournal.com/articles/160</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.46471/gigabyte.160" target="_blank" >10.46471/gigabyte.160</a>

Result language
angličtina
Original language name
Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction
Original language description
High-performance computing (HPC) environments are crucial for computational research, including quantum chemistry (QC), but pose challenges for non-expert users. Researchers with limited computational knowledge struggle to utilise domain-specific software and access mass spectra prediction for in silico annotation. Here, we provide a robust workflow that leverages interoperable file formats for molecular structures to ensure integration across various QC tools. The quantum chemistry package for mass spectral predictions after electron ionization or collision-induced dissociation has been integrated into the Galaxy platform, enabling automated analysis of fragmentation mechanisms. The extended tight binding quantum chemistry package, chosen for its balance between accuracy and computational efficiency, provides molecular geometry optimisation. A Docker image encapsulates the necessary software stack. We demonstrated the workflow for four molecules, highlighting the scalability and efficiency of our solution via runtime performance analysis. This work shows how non-HPC users can make these predictions effortlessly, using advanced computational tools without needing in-depth expertise.
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
10700 - Other natural 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
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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