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Marine sinking particles transport carbon from the surface and bury it in deep-sea sediments, where it can be sequestered on geologic time scales. The combination of the surface ocean food web that produces these particles and the particle-associated microbial community that degrades them creates a complex set of variables that control organic matter cycling. We use targeted metabolomics to characterize a suite of small biomolecules, or metabolites, in sinking particles and compare their metabolite composition to that of the suspended particles in the euphotic zone from which they are likely derived. These samples were collected in the South Atlantic subtropical gyre, as well as in the equatorial Atlantic region and the Amazon River plume. The composition of targeted metabolites in the sinking particles was relatively similar throughout the transect, despite the distinct oceanic regions in which they were generated. Metabolites possibly derived from the degradation of nucleic acids and lipids, such as xanthine and glycine betaine, were an increased mole fraction of the targeted metabolites in the sinking particles relative to surface suspended particles, while algal-derived metabolites like the osmolyte dimethylsulfoniopropionate were a smaller fraction of the observed metabolites on the sinking particles. These compositional changes are shaped both by the removal of metabolites associated with detritus delivered from the surface ocean and by production of metabolites by the sinking particle-associated microbial communities. Furthermore, they provide a basis for examining the types and quantities of metabolites that may be delivered to the deep sea by sinking particles. Sinking particles in the ocean are composed of a complex and varying mixture of dead or dying phytoplankton, zooplankton fecal pellets, aggregates held together by exopolysaccharides, and the microbes degrading this organic matter (Alldredge and Gotschalk 1989; Azam and Long 2001; Jackson 2001; Kiørboe and Jackson 2001; Roman et al. 2002; Durkin et al. 2016). These particles are responsible for delivering organic and inorganic carbon to deep-ocean sediments where the carbon is buried on geologic time scales. Estimates from satellite data and models place the total global flux of carbon out of the euphotic zone at around 6 Pg C yr (Siegel et al. 2014). However, the variables that control the magnitude of this flux in different ocean regions are still not fully understood. An important variable is the source and composition of particle-associated organic matter and the mechanisms by which it is transformed and remineralized by particle-associated microbial communities (reviewed by Boyd and Trull 2007). Marine particles are known hotspots of microbial activity. Microbes actively colonize these particles to exploit the *Correspondence: [email protected] This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. Additional Supporting Information may be found in the online version of this article. Present address: Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, District of Columbia