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Açaí and juçara processing generates substantial seed residues, creating environmental and logistical challenges while offering opportunities for value addition within a circular food bioeconomy. This study investigated the chemical diversity of Euterpe oleracea, Euterpe precatoria and Euterpe edulis seed residues to support their valorization as potential functional food ingredients. Dried seeds were ball-milled and extracted by ultrasound-assisted maceration with ethanol/water (70:30, v/v) over three consecutive 1-h cycles. Three independent extracts per species were analyzed in triplicate by liquid chromatography–tandem mass spectrometry (LC–MS/MS), combining electrospray ionization (ESI) and atmospheric-pressure chemical ionization (APCI) in positive and negative modes. The dataset comprised 120 acquisitions (108 sample analyses and 12 pooled quality-control injections). Features were processed using MZmine 4.10 and evaluated by principal component analysis (PCA) and exploratory partial least-squares discriminant analysis (PLS-DA) for each ionization mode. The four modes provided complementary chemical coverage and species-associated discrimination. The first two principal components explained 57% of variance in APCI(+), 58% in APCI(−), 45% in ESI(+) and 58% in ESI(−). In ESI(−), features near m/z 877 and 885 were associated with E. oleracea, whereas m/z 431 and 377 contributed to the separation of E. edulis and E. precatoria, respectively. Signals around m/z 452, 485 and 523 were observed in representative ESI(+) chromatograms from all three species, indicating shared chemical features despite their distinct fingerprints. APCI(+) also showed recurring signals near m/z 403 and 663 across the three species. MS1 data and fragment-ion patterns guided proposed annotations of catechin/epicatechin-related constituents (m/z 289) and A- and B-type procyanidin oligomers (m/z 575, 577 and 865), prioritized for E. oleracea. For E. edulis, candidate phenolic acids included 4-hydroxybenzoic (m/z 137), protocatechuic (m/z 153), p-coumaric (m/z 163), gallic (m/z 169) and ferulic (m/z 193) acids, in agreement with seed-specific literature. For E. precatoria, screening considered protocatechuic- (m/z 153), vanillic- (m/z 167), ferulic- (m/z 193), and ellagic-acid-related (m/z 301) candidates, alongside a feature near m/z 341 potentially attributable to a caffeic-acid glycoside or carbohydrate-related isobar. Caffeic- (m/z 179) and caffeoylquinic-acid-related (m/z 353) candidates were also considered across the dataset. These chemically distinct yet partially overlapping profiles are relevant because flavan-3-ols, procyanidins and phenolic acids have documented antioxidant potential, and açaí seed procyanidin-rich extracts have shown anti-inflammatory effects in experimental models. Thus, compositional differences could guide species-specific selection and processing, while common mass-spectral signals suggest complementary opportunities across the three residues. Integrating these fingerprints with proximate composition, dietary fiber, total phenolics and antioxidant capacity will strengthen the assessment of their suitability as functional food ingredients. Species-guided utilization could reduce disposal impacts, add value to local supply chains and promote the sustainability of Amazonian and Atlantic Forest fruit production. Acknowledgments: FAPESP, FAPERJ and CNPq.
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