A dual QTOF–QTrap analytical platform for comprehensive tracking of Doxycycline and its degradation byproducts in biological and nanoparticle-based delivery systems

Doxycycline (DOX) is a second-generation tetracycline antibiotic extensively used in clinical practice, not only for its antimicrobial activity but also for its emerging therapeutic potential in modulating extracellular matrix (ECM) in remodeling processes. Increasing evidence supports its role in attenuating pathological conditions associated with ECM degradation by targeting matrix metalloproteinases type 2 (MMP-2), including cancer progression and abdominal aortic aneurysm (AAA). However, DOX exhibits limited stability in aqueous and semi-physiological environments, undergoing hydrolysis and oxidative reactions that lead to the generation of multiple degradation byproducts, thereby compromising its efficacy and safety profile. In this study, we systematically mapped the degradation pathways of DOX under rigorously controlled physicochemical and biological conditions. High-resolution QTOF mass spectrometry operating in SWATH data-independent acquisition mode enabled unbiased identification of multiple, structurally distinct degradation byproducts, as well as the DOX parent compound, using curated metabolite libraries from SCIEX platform. Building on this annotation step, we established a complementary QTrap-based targeted workflow to quantify low-abundance metabolites intra- and extracellular through isotope-specific transitions derived from the QTOF analysis and to monitor their temporal kinetics with high sensitivity. Together, this integrated analytical strategy provides refined insight into the intrinsic instability of DOX and its potential biological consequences. To translate degradation mapping into a biologically relevant context, OM-PLGA NPs were incorporated as a controlled delivery platform that modulates DOX exposure, slows spontaneous degradation, and creates the matrix conditions required to validate the sensitivity of the QTRAP workflow in complex cellular environments. This validation demonstrated that OM-PLGA nanoparticles not only preserve DOX in its bioactive form through microenvironmental shielding, but also results in enhanced pharmacological activity, particularly sustained inhibition of MMP-2, a central enzyme in AAA-associated ECM remodeling. Together, these results highlight the dual value of the advanced analytical workflow and the nanocarrier strategy, demonstrating how integrating high-resolution mass spectrometry with nanoparticle engineering overcomes the intrinsic instability of DOX and provides deeper mechanistic insight across both analytical and biological dimensions. • A dual platform that maps doxycycline and its low-level degradation products. • High-resolution profiling reveals multiple parallel degradation pathways. • PLGA nanoparticles protect doxycycline and increase its activity.