Proteomic Meta-Study Harmonization, Mechanotyping and Drug Repurposing Candidate Prediction with ProHarMeD

• DOI: 10.14293/gof.23.35
• Publication Date: 2023-10-10T10:45:40Z
• Authors: Klaudia Adamowicz; Lis Arend; Andreas Maier; Johannes Schmidt; Bernhard Kuster; Olga Tsoy; Olga Zolotareva; Jan Baumbach; Tanja Laske
• Keywords: Repurposing; Drug repositioning; Harmonization

<p class="first" dir="auto" id="d14843789e169">Mass spectrometry-based proteomics plays a vital role in biomarker identification and understanding disease mechanisms through mechanotyping. However, utilizing publicly available data for these purposes poses challenges due to diversity involving various sources, model organisms, assay systems. Furthermore, the lack of identifier standardization hinders effective integration across publications. To tackle issues, we introduce ProHarMeD, versatile solution as web tool, Python library, R package. It harmonizes biomarkers from multiple studies, facilitating ID name conversions between protein gene levels organisms ortholog mapping. The tool identifies shared IDs among proposes mechanisms, interactively suggests potential drug repurposing candidates. ProHarMeD's efficacy is demonstrated using four bone regeneration studies. For those, intersection size was increased by 50 % harmonization compared non-harmonized lists. also reveals mechanism with corresponding targets, including Fondaparinux, licensed candidate treat thrombosis. it known improve healing, which provides validation our approach. With researchers have one-stop suite meta-analyses on data, conversion remapping evaluation, bridging gaps proteomics, exploration, repurposing. accessible at https://apps.cosy.bio/proharmed/.