Establishing accurate, sensitive, and high-throughput pesticide residue detection technologies is crucial for ensuring food safety. In this study, we developed a quartz plate cover to level the liquid surface and maintain consistent laser focus during SERS acquisition. This design significantly improved signal uniformity and reproducibility across multiple wells. By leveraging the sharp Raman peak at 2155 cm−1, one-step synthesized gold@Prussian blue nanoparticles (Au@PB NPs) were employed to eliminate spectral interference from complex food matrices and target. In the competitive immunoassay, thiamethoxam (TXM) in the sample competed with TXM antigen-conjugated magnetic beads for binding to the probes. Higher TXM concentrations resulted in reduced binding of SERS probes to the capture substrate and a subsequent decrease in Raman intensity at 2155 cm−1. Uder optimized conditions, the platform achieved a linear detection range of 1-100 ng/mL and a detection limit of 0.19 ng/mL. The method was validated in pear, leek, and celery samples, showing high accuracy and consistency with HPLC-MS/MS results. This automated SERS platform combines strong anti-interference capability and signal stability with scalable high-throughput performance, providing a robust solution for the trace-level detection of pesticide residues in complex matrices.

Understanding the residue behavior of spirodiclofen (SPI) and chlorfenapyr (CHL) is crucial for ensuring food safety and safeguarding human health. This study systematically investigated the degradation patterns, residue accumulation, and dietary risk assessment in the pear orchard environment. The experimental results indicate that the average recovery rate of SPI and CHL in pear ranged from 80.9% to 110.6%, with a RSD of 0.2% to 5.3%. The degradation half-lives of SPI and CHL in pears were 6.3 days and 10.3 days, respectively. Following repeated pesticide applications, both compounds exhibited a certain degree of residue accumulation in pears. The results of the dietary risk assessment indicate that the intake of CHL in pears does not pose significant health risks and remains within acceptable limits. However, the dietary exposure levels of SPI suggest a potential chronic dietary intake risk for children. For SPI, it is recommended to apply a single spray at the maximum recommended dose. The interval to harvest is 28 days. For CHL, it is recommended to use it at the maximum recommended dose, spraying twice with an interval of 7 days. The interval to harvest is 7 days. This study offers a critical foundation for the development of pesticide application guidelines and Maximum Residue Limit (MRL) values for SPI and CHL on pears.

Nucleic acid aptamers are short oligonucleotide sequences selected in vitro by Systematic Evolution of Ligands by EXponential enrichment (SELEX). Often described as “chemical antibodies”, they can recognize diverse targets with high affinity and specificity through structure-dependent interactions and offer multiple attractive features. Although riboswitches contain natural aptamer domains, SELEX has remained the dominant strategy for aptamer generation for over 35 years, with ongoing methodological development. These advances have expanded the application potential of aptamers in food safety, disease diagnosis, and drug delivery. Nevertheless, their reliable translation into practical applications remains challenging, largely due to complex matrix effects in real samples, which may interfere with aptamer folding, stability, and target recognition. In response to this challenge, increasing efforts have focused on matrix-integrated SELEX strategies that incorporate representative sample environments into the selection process. This review systematically summarizes recent progress in this developing field and discusses its potential as an upstream strategy for improving aptamer robustness and applicability. We first outline the biological basis of aptamers and the evolution of SELEX, followed by a brief overview of post-SELEX optimization approaches. We then provide an integrated analysis of matrix-integrated SELEX strategies, with emphasis on matrix-spiked selection, matrix-based negative selection, and holistic matrix selection, together with their underlying mechanisms, performance outcomes, and representative applications in environmental adaptation, interference suppression, and biomarker discovery. Finally, we discuss the remaining technical and conceptual challenges and highlight future directions for developing more robust, efficient, and application-oriented aptamer screening platforms.

Through field trials, this study comprehensively investigated the dissipation, metabolism, processing factors (PFs), and risk assessment of dinotefuran, imidacloprid, pyraclostrobin, thiamethoxam, and their metabolites in shiitake mushrooms from cultivation to postharvest processing. In the laboratory, common postharvest industrial and household processing methods were simulated, including washing, boiling, pickling, stir-frying, sauce processing, hot-air processing, and crisp processing. Understanding the fate of residues is crucial for ensuring food safety and safeguarding human health. The limit of quantification (LOQ) for 6-chloronicotinic acid, thiamethoxam and clothianidin was 10 μg/kg, while the LOQs for other analytes were 2 μg/kg. Field trials showed that the degradation of the four pesticides followed first-order kinetics, with half-lives ranging from 1.1 to 1.8 days. After washing, boiling, pickling, stir-frying, and sauce processing, the concentrations of all pesticides-except for a metabolite of pyraclostrobin (BF-500-3)-were reduced to varying degrees (PF < 1). Hot air processing led to 4.3- and 4.6-fold increases in the concentrations of dinotefuran and 6-chloronicotinic acid, respectively, while the concentrations of all other pesticides decreased (PF < 1). Crisp processing increased the concentration of all pesticide residues by a factor of 2.0 to 4.0. Additionally, the content of BF-500-3 increased significantly by 2.9-4.9 times after washing, boiling, pickling, and stir-frying. However, it decreased after hot air processing and sauce processing. The risk quotient values of all pesticides were below 1, indicating that both chronic and acute dietary risks were acceptable. This study provides valuable data for the control of pesticide residues in processed products, which has both theoretical and practical significance in ensuring the quality and safety of shiitake mushrooms and protecting human health.

Arsenic (As) contamination threatens ecosystems and human health, and iron (hydr)oxides-mediated formation of Fe-As composites is a key strategy for arsenic immobilization, while the long-term stability of these composites under complex environmental conditions remains a critical concern. This study systematically investigated the interactive effects of environmental factors (temperature: 5–35 °C, pH: 4–8, competing ions: phosphate and citrate) and material intrinsic properties (ferrihydrite aging: 0–60 days, Fe/As molar ratio: 1.875 and 5.66, adsorption time) on Fe-As composite stability using multiscale characterization techniques and theoretical modeling. Results showed that temperature was the dominant controlling factor, with arsenic release increasing by 4.25% per 1 °C rise (178% higher at 35 °C vs. 20 °C) and an exponential relationship model established (R2 = 0.96). Ferrihydrite aging enhanced stability, as 60-day aged composites (Fh60d-As) exhibited minimal arsenic release (18.83%) at pH 4/20 °C, attributed to increase As(V)-O-Fe binding energy (1.2 eV) and -OH group enhancement (12.5%). Phosphate induced 2.4-fold higher arsenic release than citrate, and lower pH (4–6) reduced release via enhanced protonation. A stability prediction model was developed (R2 = 0.91), and practical remediation strategies were proposed: maintaining temperatures below 25 °C in arsenic-containing waste repositories and using pre-aged iron-based materials. This work provides quantitative benchmarks and mechanistic insights for contaminated site rehabilitation.

Malathion is a commonly used organophosphorus pesticide with low acute toxicity, but overuse leads to residue accumulation and potential health risks. In this study, we introduced an integrated strategy combining magnetic nanoparticle-assisted capture-SELEX with a pattern recognition-based colorimetric aptasensor array for matrixaware identification of malathion in fruits and vegetables. Four malathion-specific aptamers were first obtained via capture-SELEX, exhibiting distinct apparent binding affinities ranging from 0.61 to 0.75 mu g/mL. Rather than functioning as quantitative probes, these aptamers were deliberately implemented as an ensemble of identification elements to generate distinct gold nanoparticles (AuNPs) colorimetric fingerprints. These response variations arise not only from aptamer-target binding, but also from matrix interference with aptamer-AuNP interactions and potential cross-reactivity between the matrix and both aptamers and AuNPs. By supervised linear discriminant analysis (LDA), eighteen fruit and vegetable matrices spiked with malathion (0.3, 0.5, 0.7 mu g/ mL) enabled complete classification across all response profiles (four aptamers & times; eighteen matrices & times; five replicates). Additionally, 36 unknown samples were consistently and accurately assigned to their corresponding matrix categories, demonstrating the capability to detect malathion while accounting for matrix effects. This pattern aptasensor represents an alternative to conventional lock-and-key biosensors, providing a robust strategy for reliable malathion identification in complex food matrices.

To investigate the impact of brassinolide (BR) and sodium nitrophenolate (CNS) applied during the growth period on the aroma profile of stored Huangguan pear, this study utilized headspace solid-phase microextraction (HS-SPME) in combination with two-dimensional gas chromatography/time-of-flight mass spectrometry (GC×GC-TOFMS) technology to obtain the aroma fingerprint of Huangguan pear. The results revealed that both BR and CNS inhibited the formation of volatile substances; the inhibition produced by CNS was weaker than that by BR prior to the mid-storage period; the accumulation brought by BR was stronger than that by CNS in the later storage stage. BR and CNS significantly modified the aroma characteristics, and were not beneficial for enhancing the flavor quality of Huangguan pear. This research elaborated in detail on the effects of BR and CNS on the flavor characteristics of pear fruits during storage, providing significant theoretical support for the applicability of plant growth regulators in production.

Background The β-Lactoglobulin (β-LG), a major milk allergen, contributes to rising health concerns, especially in infants and children. Although rapid detection methods have been reported, the complex matrix effects in food samples pose a crucial challenge to their practical application, demanding more available and effective β-LG detection strategies. Results In this study, we introduced a novel strategy of aptamer-based sensing array coupled with multiple pattern recognition algorithms for accurate β-LG detection by circumventing the challenge of the complex matrix effects. Four aptamers were selected as the recognition probes, while fifteen samples were chosen as the pattern recognition model, with the color change of AuNPs serving as the response signal. In the AuNP colorimetric array, β-LG-spiked sample matrices induced red-to-blue color transitions by modulating salt-induced AuNP aggregation, due to variable protective effects from aptamers and potential cross-reactivity with matrix. The difference in colorimetric responses between spiked and unspiked samples was considered as the unique fingerprint pattern for β-LG in each matrix, followed by multiple pattern recognition algorithms, for better orthogonality to complete β-LG identification and prediction of the unknown samples. Based on 1500 responses (4 aptamers × 15 matrices × 5 replicates × 5 concentrations), the three algorithms collectively achieved over 95% classification accuracy and established a minimum discriminable concentration of 20 nM for reliable pattern-recognition-based differentiation of β-LG across diverse food matrices. Linear discriminant analysis achieved 95.3% accuracy in blind testing of 150 samples. Significance and novelty In contrast to conventional single “lock-and-key” aptasensors, the proposed strategy offers a platform with high sensitivity and robust anti-interference performance, enabling reliable allergen detection in complex food matrices.

Abstract Ganzhou City in Jiangxi Province is a core production area for navel oranges in China and represents a typical selenium-rich specialty agricultural region. However, the selenium-rich red soils in southern Jiangxi are strongly acidic with high iron-manganese oxide content, which strongly immobilizes soil selenium, severely restricting the development of the local selenium-enriched navel orange industry. Low-molecular-weight organic acids (LMWOAs), as root exudates and microbial metabolites, can activate soil selenium and synergistically promote plant growth. However, the regulatory mechanisms of LMWOAs on soil selenium speciation remain unclear. This study investigated how low-molecular-weight organic acids (LMWOAs) affect selenium transformation and availability in selenium-enriched red soils. Six LMWOAs at concentrations of 0.1–100 mmol kg⁻¹ were tested to examine their influence on selenium speciation and dissolved organic matter (DOM) composition. Soil selenium speciation and DOM fluorescent components were analyzed following LMWOAs application to assess the relationship between DOM changes and selenium transformation. LMWOAs significantly increased soluble selenium (SOL-Se) content, especially under 100 mmol kg⁻¹ citric acid (CA). Low-concentration treatments (≤10 mmol kg⁻¹) promoted the release of exchangeable (EXC-Se) and Fe-Mn oxide-bound (FMO-Se) selenium, while high-concentration treatments (100 mmol kg⁻¹) of CA, acetic acid (AA), and n-butyric acid (N-BA) inhibited their release. Only oxalic acid (OA) increased organically bound selenium (OM-Se). DOM components were negatively correlated with bioavailable selenium under CA treatment, but positively correlated with bound selenium under 10 mmol kg⁻¹ OA. LMWOAs notably alter soil selenium speciation. Short-term application enhances selenium bioavailability, promoting plant uptake. Prolonged use may increase humification, immobilizing selenium and reducing its availability. In contaminated areas, long-term LMWOAs application can mitigate selenium toxicity through immobilization. As natural rhizosphere exudates, LMWOAs are biodegradable and environmentally safe, posing minimal risk to soil ecosystems.

Lactoferrin (Lf) is closely associated with the growth of infants and children, and its recognition is imperative due to its rising application as a prevalent nutritional fortification in infant formula. In this study, an ssDNA aptamer was screened out that enabled sandwich recognition of Lf by forming an aptamer pair with another available aptamer. During the process, the reported aptamer (SeqT1.1) was selected as the substrateto be linked onto pre- blocked microplates for capturing Lf, followed by the addition of the ssDNA library, resulting in the formation of the sandwich complex of the "SeqT1.1/Lf/ssDNA library" that was subsequently collected for screening. After seven rounds, we discovered a new ssDNA aptamer (Seq6T) through a comprehensive analysis involving sequence frequency, secondary structures, homology, and sequence truncation, which helped address the binding interference between aptamer pairs with each other's binding. The Seq6T demonstrated good specificity and lownanomolar affinity by ELONA (KD, 12.59 nM) and CE-LIF (KD, 22.44 nM) assays, which illustrated the potential of applying that in both homogeneous and non-homogeneous environments. The sandwich recognition of "SeqT1.1/Lf/Seq6T" was further verified by molecular docking and ELONA, with a good detection limit of 18.35 nM. The aptamer pairs provided a considerable basis for accelerating the sandwich recognition applications towards Lf.

Chlorothalonil and its toxic metabolite, 4-hydroxy-chlorothalonil, pose significant environmental and health risks. However, their simultaneous and accurate detection remains challenging due to their differing ionization efficiencies in mass spectrometry and the interference caused by enzymatic reactions in sulfur-rich vegetables. This study developed a UHPLC-MS/MS method for simultaneous detection of chlorothalonil and 4-hydroxy-chlorothalonil, using an atmospheric pressure chemical ionization (APCI) source, optimizing the probe temperature to 600 °C and a set of optimal chromatography parameters. A low-temperature and acidification synergistic enzyme inhibition strategy was developed, involving refrigerating samples and extraction reagents, acidifying with citric acid before sample homogenization, and extracting with formic acid/acetonitrile, significantly improving chlorothalonil recovery. Method validation demonstrated limits of detection (LOD) and quantification (LOQ) of 0.003 mg/kg and 0.01 mg/kg, respectively, with recoveries of 76.5–91.1% for chlorothalonil and 87.6–96.7% for 4-hydroxy-chlorothalonil. The method was successfully applied in monitoring the residue risks in sulfur-rich vegetables.

Lateral flow immunochromatography (LFIA) combined with surface enhanced Raman scattering (SERS) offers significant potential for highly sensitive point-of-care (POC) diagnostics. Using probes with strong SERS signals in the silent region (1800-2800 cm(-1)) avoids interference from complex fingerprint region spectra (<1800 cm(-1)), thus improving the accuracy of surface-enhanced Raman scattering-based lateral flow immunoassay (SERS-LFIA) strips. However, the scarcity of strong, non-overlapping silent region spectra and the signal reproducibility restricted by stringent preparation conditions limit practical application of SERS-LFIA based on silent region probes. To address these challenges, we combined two enhancement substrates (gold and silver) with three Prussian blue-like signal substances (Fe-4[Fe(CN)(6)](3), Cu-2[Fe(CN)(6)], and Pb-2[Fe(CN)(6)]) in a one-pot process, creating six SERS probes with highly reproducible and non-overlapping signals in the silent region. Notably, the use of different enhancement substrates enabled more non-overlapping spectra, improving the applicability of silent region probes in multiplex analysis. Additionally, the one-pot preparation and antibody coupling process improved signal reproducibility across different batches, crucial for quantitative analysis. In a proof-of-concept demonstration for detecting five aminoglycoside antibiotics, six SERS probes were combined with competitive immune reactions to develop a SERS-LFIA strip with robust analytical performance. This study advances the rational design of instant multiplex analysis system and can be applied to a wide range of POC analyses, including food safety and environmental monitoring.

Surface-Enhanced Raman Scattering-Lateral Flow Immunoassay (SERS-LFIA) inherits the advantages of simplicity, rapidness, and stability from Lateral Flow Immunoassay (LFIA), while integrating the sensitivity and accuracy of SERS, thereby attracting extensive attention in the field of food safety monitoring. This paper delves into the design strategies and principles underlying SERS-LFIA, introducing the detection formats based on SERS and contrasting the differences between traditional Raman molecules and those located in the Raman-silent region. It analyzes two immunoassay methods, namely sandwich and competitive, along with their respective applications. Importantly, by reviewing the applications of SERS-LFIA in food safety monitoring over the past 5 years, this paper summarizes the challenges faced by SERS-LFIA technology in practical applications and development. Furthermore, it provides a forward-looking perspective on the future development of SERS-LFIA. As a pivotal analytical method in the field of food safety monitoring, SERS-LFIA is demonstrating immense potential. It is hoped that this paper will offer valuable insights for the future development and application of SERS-LFIA.

To achieve rapid screening and semi-quantitative analysis of pesticide residues in mobile laboratories and on-site tea testing, a novel method based on thermal-assisted plasma ionization–time-of-flight mass spectrometry (TAPI-TOF/MS) has been developed for the detection of 20 pesticide residues, including insecticides and fungicides, in tea. This method eliminates the need for liquid chromatography, or column connections. Instead, it utilizes the high temperature of the sample inlet and stage to fully volatilize and inject the sample. By integrating TAPI-TOF/MS with an automated pesticide residue pretreatment instrument, the entire sample extraction process can be performed automatically. The analysis time for each sample has been reduced to 1.5 min, allowing for the processing of 60 samples per batch. An accurate mass spectrometry database has been established for screening and confirmation purposes. The software automatically matches the mass spectrometry database by analyzing the measured ion mass deviation, ion abundance ratio, and the relative contribution weight of each ion, generating a qualitative score ranging from 0 to 100. The lowest concentration yielding a qualitative score of ≥75 was defined as the screening limit, which ranged from 0.10 to 5.00 mg/kg for the 20 pesticides. Within their respective linear ranges, the method demonstrated good linearity with correlation coefficients (R2) ranging from 0.983 to 0.999. The average recovery rates (n = 5) of the target pesticides ranged from 70.6% to 117.0% at the set standard concentrations, with relative standard deviations (RSD) ranging from 1.7% to 13.1%. Using this method, 15 tea samples purchased from the Rizhao market in China were analyzed. Ten samples were found to contain residues of metalaxyl or pyraclostrobin, yielding a detection rate of 66.7%. This technology provides technical support for the rapid detection and quality control of multiple pesticide residues in tea, meeting the requirements for high-throughput and on-site analysis.

Through field trials, this study investigated the dissipation, metabolism, processing factors (PFs), and risk assessment of 26 pesticides and their metabolites from field to table. The half-lives of 25 pesticides detected in strawberries ranged from 1.3 to 4.8 days, following first-order dissipation kinetics. During cooking, the concentrations of most pesticide residues increased (PF = 1.13-2.44). Freeze-drying significantly increased residue levels for nearly all pesticides (PF = 4.01-30.02), except for pymetrozine. In contrast, soaking was found to effectively reduce the concentrations of most pesticide residues (PF = 0.04-0.84). Chronic and acute dietary risk assessments conducted across various countries and populations indicate that the health risks associated with the consumption of fresh strawberries, strawberry crisps, and strawberry jam are within acceptable limits. This study provides valuable data for controlling pesticide residues in processed products, offering significant theoretical and practical implications for ensuring the quality and safety of strawberries.

The Newhall navel orange (Citrus sinensis Osbeck cv. Newhall) is one of the most popular citrus varieties globally. Substituting chemical fertilizers with organic fertilizers is regarded as a key agronomic measure to promote the green cultivation of citrus. However, insufficient data on relevant field effects hindered the optimization of the organic substitution model in Newhall navel orange cultivation. Here, based on an 8-year field experiment, we used fermented liquid rapeseed cake fertilizer as the type of organic fertilizer to explore the long-term effects of substituting chemical fertilizers with organic fertilizers of different nitrogen contents on the fruit-soil-bacteria system of Newhall navel oranges, aiming to evaluate the interrelated responses of the rhizosphere microecology and fruit quality of Newhall navel orange to the fertilizer substitution strategy. The results showed that rhizosphere soil properties (pH, available nutrients, organic carbon fractions, and enzyme activities), microbial characteristics (bacterial diversity and richness), and fruit quality (soluble solids, vitamin C, and sugar content) exhibited positive responses to long-term organic substitution. Microbial biomass carbon and dissolved organic carbon showed significant positive effects on fruit soluble solids, vitamin C, and total sugar content. Long-term organic substitution significantly enhanced the activity of rhizosphere carbohydrate-active enzymes, with Proteobacteria played a positive role in regulating carbon metabolism. Comprehensive analysis of all indicators indicated that 50 % organic nitrogen substitution is an appropriate proportion for promotion in Newhall navel orange production. These observations provide a basis for establishing an effective fertilization model for Newhall navel oranges.

Food allergies have become one of the most pressing issues in food safety and public health globally along with their incidence increasing in recent years. The reliable recognition of allergens from different sources, especially food-hidden allergens, is essential for preventing and controlling food allergies. Recently, aptamers, as emerging recognition elements, have gained considerable attention in food allergy, especially in the detection of food allergens. This review systematically summarizes the latest progress in screening, identification, and application of aptamers against food allergens over the past five years. We first introduce a brief overview of food allergy and aptamers, followed by a detailed focus on the aptamers' research against different food allergens broadly based on the major categories of the Big-8 allergens: highlighting the newly screened aptamers and their applied systematic evolution of ligands by exponential enrichment (SELEX) strategies, and emphasizing their practical applications including aptasensors, allergy inhibitors, or affinity adsorptions. Finally, the remaining challenges and future exploitations faced by aptamers in food allergens are comprehensively discussed and depicted. This review holds the promise of inspiring a broader range of researchers to gain an in-depth understanding of food allergy assisted by aptamer recognition and to facilitate improved biochemical analyses and successful application.

Flavor profiles of various Pyrus spp. cultivars exhibit significant variations, yet the underlying flavor-contributing factors remain elusive. In this investigation, a comprehensive approach encompassing metabolomics analysis, volatile fingerprint analysis, and descriptive sensory analysis was employed to elucidate the flavor disparities among Nanguoli, Korla fragrant pear, and Qiuyueli cultivars and uncover potential flavor contributor. The study comprehensively characterized the categories and concentrations of nonvolatile and volatile metabolites, and 925 metabolites were identified. Flavonoids and esters dominated the highest cumulative response, respectively. Utilizing weighted correlation network analysis (WGCNA), seven highly correlated modules were identified, yielding 407 pivotal metabolites. Further correlation analysis of the differential substances provided potential flavor constituents strongly associated with various sensory attributes; taste factors had a certain association with olfactory characteristics. Our findings demonstrated the manifestation of flavor was a result of the synergistic effect of various compounds; evaluation olfactory flavor necessitated a comprehensive consideration of taste substances.

IntroductionThe application of agricultural film mulching technology has significantly contributed to increasing crop yield and income, but the pollution caused by residual film has seriously affected agricultural production and the natural environment. Agricultural film is commonly employed to enhance the yield of peanuts; its use may lead to excessive dibutyl phthalate (DBP) residues in peanut kernels. But, limited investigations have been conducted on the regulatory mechanism of peanut leaves in response to DBP exposure throughout the entire growth period.MethodsTo bridge this knowledge gap, we investigated the differences in transcriptome and metabolome of peanut leaves under DBP stress.ResultsAccording to visual observations, the results of morphological response showed that the growth of peanut plants was significantly inhibited from seedling to pod stage under DBP treatment. Transcriptomic analysis results showed that the genes AH19G05510 (LRR receptor-like serine threonine-protein kinase) and AH20G31870 (disease resistance), belonging to the FAR1 family and bZIP family respectively, may be key genes involved in the resistance to DBP stress throughout its growth stages. Metabolomic analysis results showed that during the initial stage of DBP stress, the key metabolites in peanut leaves response to stress were carboxylic acids and derivatives, as well as fatty acyls. As peanut growth progressed, flavonoids gradually became more prominent in the resistance to DBP stress. By integrating metabolomics and transcriptomics analysis, we have identified that purine metabolism during seedling and flowering stages, as well as the flavone and flavonol biosynthesis pathways during pod and maturity stages, played a crucial role in response to DBP stress.DiscussionThese findings not only provide valuable key gene and metabolic information for studying anti-plasticizer pollution throughout the entire growth period of peanuts, but also offer reference for enhancing crop resistance to plasticizer pollution through genetic modification and metabolic regulation.

The flavor profiles of cherries cultivated in greenhouse and those grown in open fields show significant variations, however, the underlying flavor-contributing factors remain unidentified. Hence, a joint investigation with widely targeted metabolomics analysis, volatile fingerprint analysis, and descriptive sensory analysis for the Russia 8 and Tieton cherry cultivars was conducted using UPLC-MS/MS and GC × GC-TOFMS to clarify the flavor differences of open-air and greenhouse-grown cherries. The study found that open-air cultivation could lead to the accumulation of non-volatile flavor substances and prompted appearance of higher acidity, astringency, plum-like flavor, and fresh herb notes; most of differential metabolites were significantly positively correlated with astringency, plum-like flavor and bitterness. Through correlation analysis and path analysis, potential flavor components and key important pathways contributing to flavor disparities were provided, and light intensity, soil moisture content, temperature and humidity were inferred as the main factors affecting the flavor profiles of open-air and greenhouse-grown cherries.