Denice van Herwerden wins poster prize at ISEAC-41

Presenting a toolbox for processing HRMS data in Non Targeted Analysis

1 December 2023

During the 41st International Conference on Environmental & Food Monitoring (ISEAC-41) held last week in Amsterdam, PhD student Denice van Herwerden presented a poster describing the open-access, open-source and modular jHRMS toolbox for the processing of HRMS data. It earned her the prize for best poster in the environmental category.

Denice van Herwerden at ISEAC-41. Photo: HIMS.

The toolbox is aimed at non-target analysis (NTA) of biological or environmental samples analyzed with chromatography coupled with high-resolution mass spectrometry (HRMS). Such analysis generally yields complex data. While there are a variety of tools and software available for the processing of these complex datasets, not all programs are open-source or open-access, provide sufficient freedom to tailor all data processing needs, or are fully suited for the processing of NTA data. Therefore, as part of her PhD research, Van Herwerden developed a modular open-source and open-access framework for the processing of HRMS data. She cooperated with colleagues at the research group Environmental Modeling & Computational Mass Spectrometry (EMCMS) led by Dr Saer Samanipour, researchers at the Center for Analytical Sciences Amsterdam (CASA) and the Queensland Alliance for Environmental Health Sciences (QAEHS, Australia).

Modular open-access and open-source Julia HRMS toolbox

The HRMS toolbox allows the user to perform a variety of different workflows, containing steps from feature detection to trend analysis. The steps related to processing the raw data, which can be performed on variety of analysis methods (e.g., data independent analysis and data dependent analysis), are feature detection (SAFD), componentization (CompCreate), and suspect screening. Then, for the interpretation of the extracted information, library searching (ULSA), alignment of features or components, and statistical analysis (i.e., PLS-R, PLS-DA, HCA, SVD, and k-means) could be performed. The library search algorithm comes with a built-in database that contains spectra from MassBank EU, MassBank of North America, and the Global Natural Products Social Molecular Networking (GNPS). Alternatively, the user can provide their own database given that it is formatted correctly. Moreover, the HRMS toolbox allows significant modularity, which enables users to perform steps within a workflow using different algorithms or programs and use this output within the HRMS toolbox. For example, the output of Patroon can be easily converted to that of the HRMS toolbox and vice-versa. Additionally, the toolbox comes with a set of built-in visualization tools that enable the user to evaluate their raw data and the results from the different algorithms. Finally, the toolbox also allows users to perform a variety of statistical analysis approaches for initial screening to evaluate if these could provide useful insight or trends in a dataset.

Overall, the HRMS toolbox is an open-access and open-source program developed for the analysis of HRMS data, which can be used in a highly modular way as well as being tailored to user specific needs. To showcase the toolbox, a set of wastewater and biological samples has been processed.

Denice van Herwerden^1,2, E. Kant¹, L. M. O’Brien³, V. Turkina^1,2, A. Nikolopoulos¹, J. Hu¹, J. W. O’Brien^1,3, K. V. Thomas³, S. Samanipour^1,2,3

¹ Van ’t Hoff Institute for Molecular Sciences (HIMS), Amsterdam, the Netherlands; ² Center for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands; ³ Queensland Alliance for Environmental Health Sciences (QAEHS), Queensland, Australia.

Denice van Herwerden wins poster prize at ISEAC-41

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