{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST004264","ANALYSIS_ID":"AN007096","PROJECT_ID":"PR002691","VERSION":"1","CREATED_ON":"October 8, 2025, 11:07 am"},

"PROJECT":{"PROJECT_TITLE":"Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus","PROJECT_TYPE":"MS quantitative analysis","PROJECT_SUMMARY":"Eurasian common shrews (Sorex araneus) maintain exceptionally high metabolic rates year-round, posing a significant energetic challenge during winter when food availability declines. To investigate seasonal metabolic regulation, we performed metabolomic profiling of blood—central to energy homeostasis—across seasons, using a bottom-up/shotgun DDA LC-MSMS metabolomics analytical strategy. This approach reveals molecular adaptations that support metabolic resilience and highlights key regulatory shifts in response to environmental stress.","INSTITUTE":"Aalborg University","DEPARTMENT":"Health Science and Technology","LABORATORY":"Molecular Pharmacology","LAST_NAME":"Zeng","FIRST_NAME":"Yuanyuan","ADDRESS":"Thulevej 34 Aalborg SØ, Aalborg, Aalborg, 9210, Denmark","EMAIL":"yuanyzeng@outlook.com","PHONE":"55204123"},

"STUDY":{"STUDY_TITLE":"Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus","STUDY_TYPE":"MS quantitative analysis","STUDY_SUMMARY":"To meet the challenge of wintering in place many high-latitude small mammals reduce energy demands through hibernation. In contrast, short-lived Eurasian common shrews, Sorex araneus, remain active and shrink, including energy-intensive organs in winter, regrowing in spring in an evolved strategy called Dehnel’s phenomenon. How this size change is linked to metabolic and regulatory changes to sustain their high metabolism is unknown. We analyzed metabolic, proteomic, and gene expression profiles spanning the entirety of Dehnel’s seasonal cycle in wild shrews. We show regulatory changes to oxidative phosphorylation and increased fatty acid metabolism during autumn-to-winter shrinkage, as previously found in hibernating species. But in shrews we also found upregulated winter expression of genes involved in gluconeogenesis: the biosynthesis of glucose from non-carbohydrate substrates. Co-expression models revealed changes in size and metabolic gene expression interconnect via FOXO signaling, whose overexpression reduces size and extends lifespan in many model organisms. We propose that while shifts in gluconeogenesis meet the challenge posed by high metabolic rate and active winter lifestyle, FOXO signaling is central to Dehnel’s phenomenon, with spring downregulation limiting lifespan in these shrews.","INSTITUTE":"Aalborg University","DEPARTMENT":"Health Science and Technology","LABORATORY":"Molecular Pharmacology","LAST_NAME":"Zeng","FIRST_NAME":"Yuanyuan","ADDRESS":"Thulevej 34 Aalborg SØ, Aalborg, Aalborg, 9210, Denmark","EMAIL":"yuanyzeng@outlook.com","PHONE":"+4555204123"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Sorex araneus","TAXONOMY_ID":"42254","GENDER":"Not applicable","ANIMAL_ANIMAL_SUPPLIER":"Max Plank Institute of Animal Behavior","ANIMAL_INCLUSION_CRITERIA":"wild types across different seasons"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SUMJUV20_1",
"Factors":{"Sample source":"Blood","Group":"SummerJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-013-CS30423.mzML","RAW_FILE_NAME_POS":"211122-POS-013-CS30423.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMJUV20_2",
"Factors":{"Sample source":"Blood","Group":"SummerJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-029-CS30424.mzML","RAW_FILE_NAME_POS":"211122-POS-029-CS30424.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMJUV20_3",
"Factors":{"Sample source":"Blood","Group":"SummerJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-028-CS30425.mzML","RAW_FILE_NAME_POS":"211122-POS-028-CS30425.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMJUV20_4",
"Factors":{"Sample source":"Blood","Group":"SummerJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-026-CS30426.mzML","RAW_FILE_NAME_POS":"211122-POS-026-CS30426.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMJUV20_5",
"Factors":{"Sample source":"Blood","Group":"SummerJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-038-CS30427.mzML","RAW_FILE_NAME_POS":"211122-POS-038-CS30427.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"FALLJUV20_1",
"Factors":{"Sample source":"Blood","Group":"FallJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-036-CS30433.mzML","RAW_FILE_NAME_POS":"211122-POS-036-CS30433.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"FALLJUV20_2",
"Factors":{"Sample source":"Blood","Group":"FallJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-011-CS30434.mzML","RAW_FILE_NAME_POS":"211122-POS-011-CS30434.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"FALLJUV20_3",
"Factors":{"Sample source":"Blood","Group":"FallJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-031-CS30435.mzML","RAW_FILE_NAME_POS":"211122-POS-031-CS30435.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"FALLJUV20_4",
"Factors":{"Sample source":"Blood","Group":"FallJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-012-CS30436.mzML","RAW_FILE_NAME_POS":"211122-POS-012-CS30436.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WINTERJUV21_1",
"Factors":{"Sample source":"Blood","Group":"WinterJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-010-CS30437.mzML","RAW_FILE_NAME_POS":"211122-POS-010-CS30437.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WINTERJUV21_2",
"Factors":{"Sample source":"Blood","Group":"WinterJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-042-CS30438.mzML","RAW_FILE_NAME_POS":"211122-POS-042-CS30438.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WINTERJUV21_3",
"Factors":{"Sample source":"Blood","Group":"WinterJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-032-CS30439.mzML","RAW_FILE_NAME_POS":"211122-POS-031-CS30435.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WINTERJUV21_4",
"Factors":{"Sample source":"Blood","Group":"WinterJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-027-CS30440.mzML","RAW_FILE_NAME_POS":"211122-POS-027-CS30440.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WINTERJUV21_5",
"Factors":{"Sample source":"Blood","Group":"WinterJuveniles"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-014-CS30441.mzML","RAW_FILE_NAME_POS":"211122-POS-014-CS30441.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SPRINGAD21_1",
"Factors":{"Sample source":"Blood","Group":"SpringAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-025-CS30442.mzML","RAW_FILE_NAME_POS":"211122-POS-025-CS30442.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SPRINGAD21_2",
"Factors":{"Sample source":"Blood","Group":"SpringAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-040-CS30443.mzML","RAW_FILE_NAME_POS":"211122-POS-040-CS30443.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SPRINGAD21_3",
"Factors":{"Sample source":"Blood","Group":"SpringAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-022-CS30444.mzML","RAW_FILE_NAME_POS":"211122-POS-022-CS30444.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SPRINGAD21_4",
"Factors":{"Sample source":"Blood","Group":"SpringAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-035-CS32290.mzML","RAW_FILE_NAME_POS":"211122-POS-035-CS32290.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SPRINGAD21_5",
"Factors":{"Sample source":"Blood","Group":"SpringAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-019-CS32291.mzML","RAW_FILE_NAME_POS":"211122-POS-019-CS32291.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMAD21_1",
"Factors":{"Sample source":"Blood","Group":"SummerAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-024-CS32292.mzML","RAW_FILE_NAME_POS":"211122-POS-024-CS32292.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMAD21_2",
"Factors":{"Sample source":"Blood","Group":"SummerAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-017-CS32293.mzML","RAW_FILE_NAME_POS":"211122-POS-017-CS32293.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMAD21_3",
"Factors":{"Sample source":"Blood","Group":"SummerAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-021-CS32294.mzML","RAW_FILE_NAME_POS":"211122-POS-021-CS32294.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMAD21_4",
"Factors":{"Sample source":"Blood","Group":"SummerAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-034-CS32295.mzML","RAW_FILE_NAME_POS":"211122-POS-034-CS32295.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"SUMAD21_5",
"Factors":{"Sample source":"Blood","Group":"SummerAdults"},
"Additional sample data":{"RAW_FILE_NAME_NEG":"211122-NEG-039-CS32591.mzML","RAW_FILE_NAME_POS":"211122-POS-039-CS32591.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Eurasian common shrews were trapped using insulated wooden traps in Radolfzell, Germany, at five different stages of development: large-brained summer juveniles (n=5), shrinking autumn juveniles (n=4), small winter juveniles (n=5), regrowing spring adults (n=5), and regrown summer adults (n=5). Blood was collected prior to perfusion through the heart, let stand for 15 minutes, spun down at 1200 rpm, the serum pipetted off and then stored at −80°C. Shrews were perfused under anesthesia via the vascular system with PAXgene Tissue Fixative.","SAMPLE_TYPE":"Blood (plasma)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma was aliquoted and stored at −80 °C until extraction. For metabolite extraction, frozen aliquots were thawed on ice and proteins were precipitated by adding ice-cold organic solvent (methanol), followed by vortex mixing, brief incubation on ice, and centrifugation at high speed (4 °C). The clarified supernatant was transferred to new tubes and reconstituted in the initial LC–MS solvent prior to analysis. Blank and pooled QC extracts were prepared and processed alongside study samples under the same conditions.","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The analysis was carried out using a UPLC system (Vanquish, Thermo Fisher Scientific) coupled with a high-resolution quadrupole-orbitrap mass spectrometer (Q Exactive™ HF Hybrid Quadrupole-Orbitrap, Thermo Fisher Scientific). An electrospray ionization interface was used as ionization source. Analysis was performed in negative and positive ionization mode. A QC sample was analysed in MS/MS mode for identification of compounds. The UPLC was performed using a slightly modified version of the protocol described by Catalin et al. (UPLC/MS Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes, Water Application note 2011, 720004042en).","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)","SOLVENT_A":"100% water; 10 mM ammonium formate; 0.1% formic acid (pH 3.1)","SOLVENT_B":"100% methanol; 10 mM ammonium formate, 0.1% formic acid","FLOW_GRADIENT":"0.0 min 0% B 2.0 min 0% B 12.0 min 35% B 13.0 min 90% B 14.0 min 90% B 15.0 min 0% B","FLOW_RATE":"300 μL/min","COLUMN_TEMPERATURE":"30 °C","METHODS_FILENAME":"Waters_Water_Soluble_Vitamin-Bs.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"MS acquisition Comments: UPLC (Thermo Vanquish) coupled to Q Exactive HF (Orbitrap). ESI in positive and negative modes; QC run in dd-MS2 for identification. Data processing Comments: Thermo .RAW → mzML (ProteoWizard). Peak picking/alignment performed; features annotated by accurate mass (±3 ppm), retention time vs in-house standards, and MS/MS matching. Software/procedures used for feature assignments: Thermo Xcalibur plus in-house workflows; method adapted from Catalin et al., 2011 (Waters app note 720004042en)."},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[{"Metabolite":"1-Methyl 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"Metabolites":[{"metabolite_name":"1-Methyl Adenosine"},{"metabolite_name":"3-Hydroxy-2-methyl-4-pyrone"},{"metabolite_name":"3-Methylhistidine"},{"metabolite_name":"4-Hydroxyproline"},{"metabolite_name":"7-Methylguanine"},{"metabolite_name":"Allantoin"},{"metabolite_name":"Allopurinol"},{"metabolite_name":"Camphor"},{"metabolite_name":"Carnitine"},{"metabolite_name":"Citrulline"},{"metabolite_name":"Cortisone"},{"metabolite_name":"Cotinine"},{"metabolite_name":"Glutathione disulfide"},{"metabolite_name":"Histidine"},{"metabolite_name":"Inosine"},{"metabolite_name":"Isoleucine"},{"metabolite_name":"Leucine"},{"metabolite_name":"Linoleic acid"},{"metabolite_name":"Methionine"},{"metabolite_name":"Myristoylcarnitine"},{"metabolite_name":"N8-Acetylspermidine"},{"metabolite_name":"N-Acetyl-glycine"},{"metabolite_name":"N-Acetyl-ornithine"},{"metabolite_name":"Nicotine amide"},{"metabolite_name":"Nicotinic acid"},{"metabolite_name":"Pantothenic acid"},{"metabolite_name":"Phenylalanine"},{"metabolite_name":"Pipecolinic acid"},{"metabolite_name":"Thiamine"},{"metabolite_name":"Trimethylamine N-Oxide"},{"metabolite_name":"Tyrosine"},{"metabolite_name":"Uridine"},{"metabolite_name":"Urocanic acid"},{"metabolite_name":"Valine"},{"metabolite_name":"Xanthine"},{"metabolite_name":"α-aminobutyric acid"},{"metabolite_name":"12(S)-HETE"},{"metabolite_name":"2''-Deoxyuridine"},{"metabolite_name":"2-Ethylhexyl sulfate"},{"metabolite_name":"2-Ethylhydracrylic/2-(hydroxymethyl)butanoi acid"},{"metabolite_name":"2-Hydroxyphenylacetic acid"},{"metabolite_name":"2-Oxoglutaric acid"},{"metabolite_name":"3-Methyl-2-oxovaleric acid"},{"metabolite_name":"3-Methyladipic/pimelic acid"},{"metabolite_name":"3-Phenyllactic acid"},{"metabolite_name":"3-Ureidopropionic acid"},{"metabolite_name":"5-Hydroxyindole-3-acetic acid"},{"metabolite_name":"5-Methylcytosine"},{"metabolite_name":"8-Aminooctanoic 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}

}