Raw LC-MS/MS data files in Thermo .raw format were processed using MS-DIAL software (version 4.9.221218). The processing workflow included feature detection, chromatographic alignment, feature filtering, gap filling, normalization, and metabolite annotation. Features not detected in more than 50% of the pooled quality control samples were excluded before metabolite annotation.
Metabolite annotation was performed by matching precursor-ion mass and MS/MS fragmentation spectra against the PerSonalbio Next-Generation Metabolomics Database (PSNGM). The PSNGM database integrates an in-house spectral library generated from authentic standards, mzCloud, LIPID MAPS, the Human Metabolome Database (HMDB), MassBank of North America (MoNA), the NIST 2020 MS/MS spectral library, and AI-predicted MS/MS spectral libraries.
The main feature-detection and library-search parameters were an MS1 mass tolerance of 0.01 Da, an MS2 mass tolerance of 0.05 Da, a smoothing level of 3, a minimum peak height of 10,000, a minimum peak width of 5, a mass slice width of 0.05 Da, and a metabolite identification score cutoff of 70. Metabolite annotation outputs included feature ID, metabolite name, molecular formula, measured m/z, retention time, InChIKey, spectral matching score, HMDB identifier, KEGG identifier, chemical classification, reference ion or adduct, normalized peak area, and QC-based relative standard deviation.
Metabolites detected in positive- and negative-ionization modes were annotated using the same processing and library-search workflow. Because individual confirmation with authentic chemical standards was not documented for every metabolite, the reported compounds were treated as annotated metabolites based on accurate-mass and MS/MS spectral-library matching rather than as universally confirmed identifications.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Chromatographic separation was performed using a Vanquish Flex ultra-high-performance liquid chromatography system (Thermo Fisher Scientific, Waltham, MA, USA). Metabolites were separated on an ACQUITY UPLC HSS T3 column (100 Å, 1.8 μm, 2.1 × 100 mm; Waters Corporation, Milford, MA, USA). The column temperature was maintained at 40°C, and the autosampler temperature was set to 8°C. The flow rate was 0.4 mL/min, and the injection volume was 2 μL.
Mobile phase A consisted of water containing 0.1% formic acid, and mobile phase B consisted of acetonitrile containing 0.1% formic acid. The same mobile phases and chromatographic conditions were used for positive- and negative-ionization analyses. The total chromatographic run time was 8.5 min. The gradient elution program was as follows: 0–1.0 min, 5% B; 1.0–4.7 min, a linear increase from 5% to 95% B; 4.7–6.0 min, 95% B; 6.0–6.1 min, a linear decrease from 95% to 5% B; and 6.1–8.5 min, 5% B for column re-equilibration.
"],"publication":["Metabolomics reveals stage-specific internal quality deterioration and distinct metabolic changes in egg albumen and yolk during storage."],"submitter_name":["haoqian zhang"],"submitter_affiliation":["China Agricultural University"],"organism_part":["egg yolk","egg white"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Frozen albumen and yolk samples were thawed on ice before extraction. For each sample, 50 μL of albumen or yolk was mixed with 100 μL of precooled water and homogenized with two steel beads using a high-throughput tissue homogenizer at 55 Hz for 60 s; this homogenization step was repeated twice. Subsequently, 400 μL of precooled methanol/acetonitrile solution (1:1, v/v) was added. The mixture was ultrasonicated for 30 min, incubated at 20°C for 45 min, and centrifuged at 12,000 rpm for 20 min at 4°C. A 450-μL aliquot of the supernatant was collected, vacuum-dried, and reconstituted in 150 μL of 50% methanol containing 5 ppm L-2-chlorophenylalanine as an internal standard. After centrifugation, the reconstituted extract was filtered through a 0.22-μm membrane and transferred to an autosampler vial for LC-MS/MS analysis.
Separate pooled quality control (QC) samples were prepared for albumen and yolk by combining equal 10-μL aliquots from each corresponding processed sample. These pooled QC samples were used to evaluate analytical reproducibility and data quality. Albumen and yolk QC samples were prepared and analyzed separately to account for differences between the two egg compartments. No biological samples from different eggs were pooled for the main metabolomic analysis. The analytical controls described for this study consisted of the compartment-specific pooled QC samples and L-2-chlorophenylalanine internal standard; no separate solvent blank or external standard sample was included in the current experimental record.
"],"organism":["Gallus gallus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15068"],"author":["Ling Lian. College of Animal Science and Technology, China Agricultural University. llian@cau.edu.cn.","Haoqian Zhang. China Agricultural University College of Animal Science and Technology. qianzi0223@163.com."],"data_transformation_protocol":["Native Thermo LC-MS/MS data files in .raw format were imported directly into MS-DIAL software (version 4.9.221218) for data processing. No intermediate conversion to mzML or mzXML format was documented. Raw files acquired in positive- and negative-ionization modes were processed using the same workflow. Data processing included peak detection, chromatographic alignment, feature filtering, gap filling, normalization, and metabolite annotation. Features not detected in more than 50% of the pooled quality control samples were excluded during the initial processing stage. Missing signals were filled using the Gap Filling algorithm implemented in MS-DIAL, followed by normalization.
Metabolites were annotated using the PerSonalbio Next-Generation Metabolomics Database (PSNGM). This database integrates an in-house spectral library generated from authentic standards, mzCloud, LIPID MAPS, the Human Metabolome Database (HMDB), MassBank of North America (MoNA), the NIST 2020 MS/MS spectral library, and AI-predicted MS/MS spectral libraries. The main MS-DIAL processing and library-search parameters were an MS1 tolerance of 0.01, an MS2 tolerance of 0.05, a smoothing level of 3, a minimum peak height of 10,000, a minimum peak width of 5, a mass slice width of 0.05, and an identification score cutoff of 70.
After export from MS-DIAL, residual missing values in the metabolite abundance matrix were imputed with one-fifth of the minimum nonzero abundance observed for the corresponding metabolite. The coefficient of variation was calculated for each metabolite across the pooled QC samples, and metabolites with a QC coefficient of variation greater than 30% were excluded. The resulting metabolite abundance matrices were mean-centered and scaled to unit variance before multivariate statistical analysis. Subsequent statistical analyses were performed using R-based workflows on the PerSonalbio GenesCloud platform.
"],"study_factor":["Group"],"submitter_email":["qianzi0223@163.com"],"sample_collection_protocol":["Fresh shell eggs were collected within 24 h after laying from individually caged hens at the experimental farm of China Agricultural University, Beijing, China. Eggs were stored at 25.0–25.5°C and 18–20% relative humidity and sampled at 0, 7, 14, 21, and 28 days. Twenty eggs were used per time point for metabolomic analysis. Albumen and yolk from each egg were separated aseptically as paired samples, immediately frozen in liquid nitrogen, and stored at 80°C until analysis.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","Internal egg quality","Albumen","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","egg yolk","Vanquish Flex","egg white","Egg storage","Yolk","Gallus gallus"],"curator_keywords":["Metabolomics","Internal egg quality","Albumen","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","egg yolk","Vanquish Flex","egg white","Egg storage","Yolk","Gallus gallus"],"mass_spectrometry_protocol":["Mass spectrometric data were acquired using an Orbitrap Exploris 120 high-resolution mass spectrometer equipped with a heated electrospray ionization (HESI) source (Thermo Fisher Scientific, Waltham, MA, USA). The instrument was controlled using Xcalibur software, version 4.7 (Thermo Fisher Scientific). Data-dependent acquisition (DDA) was performed separately in positive- and negative-ionization modes. The spray voltage was set to 3.5 kV in positive-ion mode and 3.0 kV in negative-ion mode. The sheath gas and auxiliary gas flow rates were set to 40 and 10 arbitrary units, respectively. The ion-transfer capillary temperature was maintained at 320°C, and the auxiliary gas heater temperature was set to 300°C.
Full-scan MS spectra were acquired over an m/z range of 70–1,000 at a resolution of 60,000. The automatic gain control target was set to Standard, and the maximum ion injection time was 100 ms. The four most intense precursor ions were selected for data-dependent MS/MS fragmentation in each acquisition cycle. A dynamic exclusion time of 4 s was applied. MS/MS spectra were acquired at a resolution of 15,000 using higher-energy collisional dissociation with a normalized collision energy of 30%. For MS/MS acquisition, the automatic gain control target was set to Standard, and the maximum ion injection time was set to Auto.
"],"additional_accession":[]},"is_claimable":false,"name":"Metabolomics reveals stage-specific internal quality deterioration and distinct metabolic changes in egg albumen and yolk during storage","description":"Internal quality of chicken eggs deteriorates during storage, but the biochemical changes occurring in albumen and yolk over storage time remain insufficiently characterized. This study investigated changes in internal quality traits and specific metabolite profiles in albumen and yolk of chicken eggs at 25.0 to 25.5°C stored for 0, 7, 14, 21, and 28 days. A total of 216 eggs were used, including 116 eggs for internal quality measurements at 0, 7, 14, 21, and 28 days (n = 24, 22, 20, 23, and 27, respectively) and 100 eggs for metabolomic analysis (n = 20 per time point). Paired albumen and yolk samples were collected from each egg and subjected to untargeted liquid chromatography–tandem mass spectrometry (LC-MS/MS) metabolomics. The results showed that albumen height and Haugh unit decreased markedly by day 7 and further declined by day 21, whereas yolk color changed mainly at day 21 and day 28. After data preprocessing and quality control (QC)-based filtering, 919 and 1104 annotated metabolites were retained in albumen and yolk, respectively. Based on multigroup comparisons across the five storage time points, 267 and 286 differential metabolites were identified in albumen and yolk, respectively. In albumen, deterioration at day 7 was associated with changes in nucleotide- and cofactor-related metabolites, including UMP, adenosine, NAD+, and FAD. By day 21, aggravated albumen deterioration was characterized by glycation- and nitrogen-related metabolites, including N-(1-deoxy-1-fructosyl)phenylalanine, N-(1-deoxy-1-fructosyl)tyrosine, pyroglutamic acid, and cadaverine. In yolk, deterioration at day 21 was mainly associated with lipid oxidation and membrane lipid remodeling, as indicated by changes in arachidonic acid, linoleic acid, 15-oxoETE, D-sphingosine, and sphinganine. These results indicate that albumen and yolk show distinct time-dependent metabolic changes during storage. The representative metabolites identified in this study may serve as candidate indicators for stage-specific evaluation of egg quality deterioration during storage.
","dates":{"publication":"2026-07-17","submission":"2026-07-17"},"accession":"MTBLS15068","cross_references":{}}