Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction
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 s...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
GigaScience Press
2025-07-01
|
| Series: | GigaByte |
| Online Access: | https://gigabytejournal.com/articles/160 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849708394399662080 |
|---|---|
| author | Wudmir Y. Rojas Zargham Ahmad Julia Jakiela Helge Hecht Jana Klánová Elliott J. Price |
| author_facet | Wudmir Y. Rojas Zargham Ahmad Julia Jakiela Helge Hecht Jana Klánová Elliott J. Price |
| author_sort | Wudmir Y. Rojas |
| collection | DOAJ |
| 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.
|
| format | Article |
| id | doaj-art-a2b84464c3914bc1a339f709d412c6bf |
| institution | DOAJ |
| issn | 2709-4715 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | GigaScience Press |
| record_format | Article |
| series | GigaByte |
| spelling | doaj-art-a2b84464c3914bc1a339f709d412c6bf2025-08-20T03:15:39ZengGigaScience PressGigaByte2709-47152025-07-0110.46471/gigabyte.160Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS predictionWudmir Y. Rojas 0https://orcid.org/0000-0001-7036-9987Zargham Ahmad 1https://orcid.org/0000-0002-6096-224XJulia Jakiela 2https://orcid.org/0009-0001-2017-8805Helge Hecht 3https://orcid.org/0000-0001-6744-996XJana Klánová 4https://orcid.org/0000-0002-8818-5307Elliott J. Price 5https://orcid.org/0000-0001-5691-7000Faculty of Science, https://ror.org/02j46qs45Masaryk University, RECETOX, Kotlářská 2, 60200, Brno, Czech RepublicFaculty of Science, https://ror.org/02j46qs45Masaryk University, RECETOX, Kotlářská 2, 60200, Brno, Czech RepublicSchool of Chemistry, https://ror.org/01nrxwf90University of Edinburgh, Edinburgh, UKFaculty of Science, https://ror.org/02j46qs45Masaryk University, RECETOX, Kotlářská 2, 60200, Brno, Czech RepublicFaculty of Science, https://ror.org/02j46qs45Masaryk University, RECETOX, Kotlářská 2, 60200, Brno, Czech RepublicFaculty of Science, https://ror.org/02j46qs45Masaryk University, RECETOX, Kotlářská 2, 60200, Brno, Czech Republic 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. https://gigabytejournal.com/articles/160 |
| spellingShingle | Wudmir Y. Rojas Zargham Ahmad Julia Jakiela Helge Hecht Jana Klánová Elliott J. Price Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction GigaByte |
| title | Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction |
| title_full | Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction |
| title_fullStr | Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction |
| title_full_unstemmed | Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction |
| title_short | Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction |
| title_sort | galaxy qcxms for straightforward semi empirical quantum mechanical ei ms prediction |
| url | https://gigabytejournal.com/articles/160 |
| work_keys_str_mv | AT wudmiryrojas galaxyqcxmsforstraightforwardsemiempiricalquantummechanicaleimsprediction AT zarghamahmad galaxyqcxmsforstraightforwardsemiempiricalquantummechanicaleimsprediction AT juliajakiela galaxyqcxmsforstraightforwardsemiempiricalquantummechanicaleimsprediction AT helgehecht galaxyqcxmsforstraightforwardsemiempiricalquantummechanicaleimsprediction AT janaklanova galaxyqcxmsforstraightforwardsemiempiricalquantummechanicaleimsprediction AT elliottjprice galaxyqcxmsforstraightforwardsemiempiricalquantummechanicaleimsprediction |