Spectrometric Data Processing and Analysis

The RECETOX Spectrometric Data Processing & Analysis Research Infrastructure develop high-throughput processing pipelines and tools dedicated to the processing of high-resolution mass spectrometry (HRMS) data. We focus on tools for functional metabolomics and exposomics and the detection of low abundant compounds in human biospecimen.

The developed pipelines and tools are distributed and made available via the Galaxy platform (UMSA instance) to provide user-friendly access and a graphical user interface. They can also be used as packages and containers using Bioconda and Biocontainers. All developments are open-source and open to contributions on GitHub. The developments are contributing to the newly established EIRENE RI coordinated by RECETOX.

Services

The facility provides the following services:

Access

All tools are available on UMSA - users can login via the LifeScience RI or newly register. The source code for all tools & Galaxy wrappers is hosted on GitHub and distributed under open-source licenses.

Team

Helge Hecht
Helge leads the group since 2022 and is currently a PhD Student with Elliott James Price at RECETOX. His main interest is in software quality, testing and development best practices. He studied Computer Science at TUM (Germany), focusing on medical image analysis, scientific computing, and artificial intelligence – only switching to mass spectrometry data processing and workflow engines in late 2020.

Matej Troják
Matej joined the group in 2021 as a software developer, focusing on the development of Galaxy tools and pipelines and Galaxy administration. He studied computer science with a focus on bioinformatics and systems biology and is currently a PhD Student at the Faculty of Informatics, Masaryk University. He is interested in the application of computational formal methods to natural sciences.

Wudmir Rojas
Wudmir’s interest focuses on the atomistic simulations of mass spectrometry for exposome studies and developing scientific computational applications for mass spectrometry. He has BSc in Engineering Physics (Peru), MSc in Nanoscience and Advanced Materials (Brazil), a PhD in Electronic Engineering (UK) and he was a visiting scholar at TAMU (USA). He applied ab-initio methods to predict x-ray absorption spectra and electron-transport properties of nanoscopic devices. As a postdoc in the Institute of Physics of the Czech Academy of Sciences in Prague, he developed and implemented approaches for molecular quantum transport.

Zargham Ahmad
Zargham joined the team in 2022 and is currently a Master's Student at the Faculty of Informatics, Masaryk University, focusing on cybersecurity management. His main interest is in Cybersecurity, software quality, and development. He studied Computer Science focusing on computer vision, and machine learning at Superior University (Pakistan).

Former Members

Maksym Skoryk
Max has been a group member since late 2020. He is a Chemical Engineering master's student at the Faculty of Chemistry, Brno University of Technology, focusing on bio and medicinal chemistry applications. He is interested in Data Science and is keen on combining his programming and chemistry expertise to solve life sciences and healthcare problems.

Martin Čech
Martin, an alumnus of the Faculty of Informatics, Masaryk University, joined the project in 2020 with a background in scientific software development and experience with the Galaxy platform. He helps to steer the technical aspects of the pipelines towards reproducibility, reusability, and open science. He is a proponent of free open source software and FAIR data.

Contact

For more or specific information, please, contact:

References

Posters

Metabolomics 2021 - Developing Modular Galaxy Workflows for High-Resolution Mass Spectrometry Exposomics Data Processing

Metabolomics 2022 - Quantum chemistry EI Mass Spectrometry database for exposome research