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Chilling Truth: The Effects of Storage Temperature on the Metabolic Profiles of Food

ABSTRACT: Food is a chemically complex matrix comprised of macronutrients, micronutrients, and thousands of small, bioactive metabolites. Emerging omics technologies have revealed that these metabolites influence flavor, nutritional quality, and human health. Yet, many bioactive small molecules associated with beneficial health outcomes are chemically labile, making appropriate sample preservation critical. Following existing standards from clinical research, storage at -80 C is widely used in foodomics to minimize enzymatic activity and metabolite degradation. Yet, the viability of these conditions to the biological and chemical diversity of food has yet to be rigorously evaluated. This study investigates how storage temperature affects the stability of metabolites in eleven different foods: cocoa powder, milk chocolate, ground beef, apple, carrot, beet leaf, beet root, potato, and both uncooked and cooked rice. Prepared food samples were divided for storage at 25 C, 4 C, and -20 C, with -80 C samples serving as a baseline. Samples were collected at three and six months from each storage condition to assess metabolite stability over time. Analysis of all samples was performed by nontargeted metabolomics and targeted LC-PDA analysis of carotenoids. Our results showed that metabolite stability was matrix dependent, with some foods (i.e. provide food names) showing significant variation in global metabolome profiles while others (i.e. provide food names) had no observable differences. Collectively, these findings suggest that sample preservation is essential for maintaining metabolite integrity in food matrices and must be carefully considered to ensure accurate characterization of food metabolic profiles.

INSTRUMENT(S): Xevo G2-XS QTof

ORGANISM(S): Bos Taurus (ncbitaxon:9913) Daucus Carota (ncbitaxon:4039) Solanum Tuberosum (ncbitaxon:4113) Oryza Sativa (ncbitaxon:4530) Solanum Lycopersicum (ncbitaxon:4081) Theobroma Cacao Beta Vulgaris Subsp. Vulgaris (ncbitaxon:3555)

SUBMITTER: Jessica Prenni

PROVIDER: MSV000100777 | MassIVE | Mon Feb 09 12:28:00 GMT 2026

REPOSITORIES: MassIVE

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Project description:The Biospecimen Pre-analytical Variables (BPV) Program is a National Cancer Institute-sponsored study to systematically assess the effects of pre-analytical factors on the molecular profile of biospecimens. A robust biospecimen collection infrastructure was established to prospectively collect biospecimens using rigorous standard operating procedures to control for most variables while introducing experimental conditions to study specific biospecimen handling issues, including the cold ischemic time (delay to formalin fixation), time in formalin, freezing methods, and storage temperatures and durations. RNA and DNA from biospecimens collected under these conditions was analyzed on multiple molecular platforms. The potential effects of these pre-analytical conditions on protein integrity and detection of metabolites were also examined. 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The study includes 240 plasma samples collected from 40 donors.</li> <li>Investigate the effect of the delay to fixation on the proteome and phosphoproteome -FFPE (MassSpec by Caprion). The study is to do proteome and phosphoproteome analysis on Delay to fixation was carried out using FFPE tumor samples from colon and ovarian cancer patients comparing 2, 3, and 12hr delay to fixation to the 1hr time point. The study includes 100 samples 20 donors.</li> <li>Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling- Frozen tissue and plasma (MassSpec by Caprion). The study was to evaluate the effects of storage conditions on tumor specimens. Plasma samples from 40 cancer patients stored at two different temperatures (-80°C and LN2) for a given period (0-2, 6-8, and 12-14 months) were evaluated. Frozen kidney tumor samples from 20 patients were compared for effects of different snap frozen (dry ice vs. LN2) and storage temperatures (-80°C and LN2). The study includes 100 tissue and 240 plasma samples from 60 donors.</li> <li>Preanalytical Impacts on Genomic Sequencing by Next Generation Sequencing (NGS) technology (mRNA/miRNA and WES by Expression Analysis). The goal of the study is to determine the effects of cold ischemic delay-to-fixation (4 time points) and formalin preservation (FFPE) on the nature and quality of genomic profiles using the matched freshly frozen sample as the gold standard, which including WES, RNAseq. The study includes 395 samples from 37 donors.</li> <li>Preanalytical Impacts on Copy Number Variation (CNV) Detection by aCGH technology (aCGH by Georgetown University). This study was to use aCGH to evaluate the effect of variation in cold ischemia time and time in formalin fixation on CNV in DNA extracted from kidney cancer specimens. 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Chilling Truth: The Effects of Storage Temperature on the Metabolic Profiles of Food

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