Summary of Study ST003783

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002360. The data can be accessed directly via it's Project DOI: 10.21228/M8KG1C This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST003783
Study TitleBiomonitoring of (pseudo)pregnancy in giant panda urine using steroidomics
Study SummaryThe physiological processes during (pseudo)pregnancy in giant pandas are poorly understood and diagnosis of actual pregnancy is only possible in the final 2-3 weeks of the cycle. Therefore, in this study, urine samples from different phases of the reproductive cycle of giant pandas were analyzed using a steroidomics approach. In total, six pregnant and seven pseudopregnant cycles were included. Each cycle was subdivided in six reproductive phases and three samples were selected per phase. The steroidomics approach was used to investigate differences in hormonal changes during the (pseudo)pregnant cycle to gain more information of underlying endocrinological processes and look for potential (early) pregnancy biomarkers. Additionally, current widely used immunoassay targets were examined and validated. The most abundant progestogen, glucocorticoid, and prostaglandin metabolites were identified and were significantly higher during the final stages of the cycle in pregnant females. Several detected androgens, on the other hand, were significantly higher in pregnant females around the timing of corpus luteum reactivation and embryo implantation.
Institute
Ghent University
DepartmentTranslational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine
LaboratoryLaboratory of Integrative Metabolomics (LIMET)
Last NameCools
First NameTom
AddressSalisburylaan 133 9820 Merelbeke
Emailtom.cools@ugent.be; lynn.vanhaecke@ugent.be; jella.wauters@ugent.be
Phone+32 (0)9 264 74 51
Submit Date2025-02-16
Raw Data AvailableYes
Raw Data File Type(s)mzXML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-08-01
Release Version1
Tom Cools Tom Cools
https://dx.doi.org/10.21228/M8KG1C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002360
Project DOI:doi: 10.21228/M8KG1C
Project Title:Giant panda pregnancy metabolomics studies
Project Summary:Monitoring and detection of pregnancy in giant pandas is hampered by phenomena such as delayed implantation and obligatory pseudopregnancy. Urine samples from different phases of the reproductive cycle of pregnant and pseudopregnant giant pandas were therefore analyzed with two UHPLC-HRMS-based methods: polar metabolomics and steroidomics. Discriminative differences were investigated to comprehense physiological differences and enable early discrimination between the two states.
Institute:Ghent University
Department:Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine
Laboratory:Laboratory of Integrative Metabolomics
Last Name:Cools
First Name:Tom
Address:Salisburylaan 133 9820 Merelbeke
Email:tom.cools@ugent.be; lynn.vanhaecke@ugent.be; jella.wauters@ugent.be
Phone:+32 (0)9 264 74 51

Subject:

Subject ID:SU003917
Subject Type:Mammal
Subject Species:Giant panda (Ailuropoda melanoleuca)
Taxonomy ID:9646
Gender:Female

Factors:

Subject type: Mammal; Subject species: Giant panda (Ailuropoda melanoleuca) (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Reproductive cycle Reproductive phase
SA410606Blank27Acetonitrile Blank Blank
SA410607Blank21Acetonitrile Blank Blank
SA410608Blank22Acetonitrile Blank Blank
SA410609Blank23Acetonitrile Blank Blank
SA410610Blank24Acetonitrile Blank Blank
SA410611Blank25Acetonitrile Blank Blank
SA410612Blank26Acetonitrile Blank Blank
SA410613Blank28Acetonitrile Blank Blank
SA410614Blank19Acetonitrile Blank Blank
SA410615Blank29Acetonitrile Blank Blank
SA410616Blank30Acetonitrile Blank Blank
SA410617Blank31Acetonitrile Blank Blank
SA410618Blank32Acetonitrile Blank Blank
SA410619Blank34Acetonitrile Blank Blank
SA410620Blank35Acetonitrile Blank Blank
SA410621Blank36Acetonitrile Blank Blank
SA410622Blank20Acetonitrile Blank Blank
SA410623Blank18Acetonitrile Blank Blank
SA410624Blank38Acetonitrile Blank Blank
SA410625Blank8Acetonitrile Blank Blank
SA410626Blank1Acetonitrile Blank Blank
SA410627Blank2Acetonitrile Blank Blank
SA410628Blank3Acetonitrile Blank Blank
SA410629Blank4Acetonitrile Blank Blank
SA410630Blank5Acetonitrile Blank Blank
SA410631Blank6Acetonitrile Blank Blank
SA410632Blank7Acetonitrile Blank Blank
SA410633Blank9Acetonitrile Blank Blank
SA410634Blank17Acetonitrile Blank Blank
SA410635Blank10Acetonitrile Blank Blank
SA410636Blank11Acetonitrile Blank Blank
SA410637Blank12Acetonitrile Blank Blank
SA410638Blank13Acetonitrile Blank Blank
SA410639Blank14Acetonitrile Blank Blank
SA410640Blank15Acetonitrile Blank Blank
SA410641Blank16Acetonitrile Blank Blank
SA410642Blank37Acetonitrile Blank Blank
SA410643Blank33Acetonitrile Blank Blank
SA410644Blank39Acetonitrile Blank Blank
SA410645Blank67Acetonitrile Blank Blank
SA410646Blank60Acetonitrile Blank Blank
SA410647Blank61Acetonitrile Blank Blank
SA410648Blank40Acetonitrile Blank Blank
SA410649Blank63Acetonitrile Blank Blank
SA410650Blank64Acetonitrile Blank Blank
SA410651Blank65Acetonitrile Blank Blank
SA410652Blank66Acetonitrile Blank Blank
SA410653Blank68Acetonitrile Blank Blank
SA410654Blank58Acetonitrile Blank Blank
SA410655Blank69Acetonitrile Blank Blank
SA410656Blank70Acetonitrile Blank Blank
SA410657Blank71Acetonitrile Blank Blank
SA410658Blank72Acetonitrile Blank Blank
SA410659Blank73Acetonitrile Blank Blank
SA410660Blank74Acetonitrile Blank Blank
SA410661Blank75Acetonitrile Blank Blank
SA410662Blank59Acetonitrile Blank Blank
SA410663Blank62Acetonitrile Blank Blank
SA410664Blank57Acetonitrile Blank Blank
SA410665Blank47Acetonitrile Blank Blank
SA410666Blank41Acetonitrile Blank Blank
SA410667Blank42Acetonitrile Blank Blank
SA410668Blank43Acetonitrile Blank Blank
SA410669Blank56Acetonitrile Blank Blank
SA410670Blank44Acetonitrile Blank Blank
SA410671Blank46Acetonitrile Blank Blank
SA410672Blank45Acetonitrile Blank Blank
SA410673Blank48Acetonitrile Blank Blank
SA410674Blank49Acetonitrile Blank Blank
SA410675Blank50Acetonitrile Blank Blank
SA410676Blank51Acetonitrile Blank Blank
SA410677Blank52Acetonitrile Blank Blank
SA410678Blank53Acetonitrile Blank Blank
SA410679Blank54Acetonitrile Blank Blank
SA410680Blank55Acetonitrile Blank Blank
SA410681FFR200121Urine Fragmentation Fragmentation
SA410682TT190822Urine Fragmentation Fragmentation
SA410683JB220315Urine Fragmentation Fragmentation
SA410684JB220815Urine Fragmentation Fragmentation
SA410685JB220812Urine Fragmentation Fragmentation
SA410686FFr170114Urine Pregnancy Anestrus
SA410687MM190315Urine Pregnancy Anestrus
SA410688MM190114Urine Pregnancy Anestrus
SA410689WW191101Urine Pregnancy Anestrus
SA410690WW191130Urine Pregnancy Anestrus
SA410691WW191223Urine Pregnancy Anestrus
SA410692MM190215Urine Pregnancy Anestrus
SA410693FFr170101Urine Pregnancy Anestrus
SA410694HH150309Urine Pregnancy Anestrus
SA410695FFr170130Urine Pregnancy Anestrus
SA410696FFr210301Urine Pregnancy Anestrus
SA410697FFr210203Urine Pregnancy Anestrus
SA410698FFr210102Urine Pregnancy Anestrus
SA410699HH190301Urine Pregnancy Anestrus
SA410700HH190201Urine Pregnancy Anestrus
SA410701HH190101Urine Pregnancy Anestrus
SA410702HH150130Urine Pregnancy Anestrus
SA410703HH150215Urine Pregnancy Anestrus
SA410704WW200131_1Urine Pregnancy CLD1
SA410705FFr210409Urine Pregnancy CLD1
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Collection:

Collection ID:CO003910
Collection Summary:All urine samples were collected either via aspiration from the concrete floor with a clean syringe in the absence of the animal or by direct urination in a small container (trained animals). After collection, the samples were transferred to a collection vial and stored at -20°C until shipment to the Laboratory of Integrative Metabolomics (LIMET) at Ghent University (Belgium). Before analysis, urinary specific gravity (USpG) was measured using a handheld digital refractometer designed for cat (PAL-USG (Cat), range 1.000-1.080, Atago™, Fukaya, Japan) or human urine (Pal-10S (Human), range 1.000-1.060, Atago™, Fukaya, Japan). The urine samples were collected during 6 phases of the reproductive cycle: anestrus (start of observations until cross-over between progestogens and estrogens, which marks the start of the pro-estrus), early corpus luteum dormancy phase (CLD1, following ovulation, variable length), middle corpus luteum dormancy phase (CLD2, starting ± 80 days prior to birth/end of the cycle), late corpus luteum dormancy phase (CLD3, starting ± 60 days prior to birth/end of the cycle), early active luteal phase (EAL, from start of secondary, more increased progesterone peak ± 42 days prior to birth/end of the cycle until PGFM peak), and late active luteal phase (LAL, post PGFM peak until birth/end of the cycle).
Sample Type:Urine
Storage Conditions:-20℃

Treatment:

Treatment ID:TR003926
Treatment Summary:No treatment. All samples were filtered by being transferred to a 15 mL Nunc® tube (Thermo Fisher Scientific, San José, California, USA) inserted with a small-sized disposable plastic funnel with a cotton-wool filter plug.

Sample Preparation:

Sampleprep ID:SP003923
Sampleprep Summary:10 µL of an internal standard solution was added to 200 µL or urine. Then 1 mL of EtOAc was added to the urine sample, followed by vortexing for 30 seconds, and then shaking for 5 min at 1 g and 22.5°C in a New Brunswick Innova 42 incubator (Eppendorf, Hamburg, Germany). Subsequently, the sample was centrifuged for 10 min at 10,000 g and 4°C. 950 µL of the supernatant was transferred into a 1.5 mL Eppendorf and evaporated to dryness under a gentle stream of nitrogen at 40°C. The residue was then reconstituted by first adding 40 µL MeOH and vortexing rigorously. Subsequently, 60 µL urine was added which was aspirated from the urine fraction that remained after yielding the EtOAc supernatant. The extract was then vortexed and centrifuged again for 10 min at 10,000 g and 4°C. Finally, 90 µL of the extract was transferred into a glass HPLC vial with insert for analysis.
Extract Storage:4℃

Combined analysis:

Analysis ID AN006213 AN006214 AN006215 AN006216
Chromatography ID CH004712 CH004712 CH004713 CH004713
MS ID MS005917 MS005918 MS005919 MS005920
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Thermo Vanquish Horizon Thermo Vanquish Horizon Thermo Dionex Ultimate 3000 XRS Thermo Dionex Ultimate 3000 XRS
Column Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Orbitrap Exploris 120 Thermo Orbitrap Exploris 120 Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units AUC AUC Not applicable AUC

Chromatography:

Chromatography ID:CH004712
Chromatography Summary:Chromatographic separation of samples with sample_id starting with "230925"
Methods Filename:Steroidomics_GP_Protocols.pdf
Instrument Name:Thermo Vanquish Horizon
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:0.45mL/min: 0-5.8 min: 40-65% B, 5.8-9.0 min: 65-100% B; 9.0-10.5 min: 100% B, 10.5-10.6 min: 100-40% B, 10.6-12.5 min: 40% B
Flow Rate:0.45mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% Methanol; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH004713
Chromatography Summary:Chromatographic separation of samples with sample_id starting with "240504". NOTE: For the fragmentation data, we did not process any results (targeted or untargeted) as we just matched the fragmentation spectra.
Methods Filename:Steroidomics_GP_Protocols.pdf
Instrument Name:Thermo Dionex Ultimate 3000 XRS
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:0.55mL/min: 0-5.0 min: 40-65% B, 5.0-8.5 min: 65-100% B; 8.5-10.5 min: 100% B, 10.5-10.6 min: 100-40% B, 10.6-12.5 min: 40% B
Flow Rate:0.55mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% Methanol; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005917
Analysis ID:AN006213
Instrument Name:Thermo Orbitrap Exploris 120
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The ionization source was positioned according to the values 0/L-M/1.5. Gas flow rates of the sheath, auxiliary and sweep gas were 50, 10, and 2 arbitrary units (a.u.) respectively. A vaporizer and capillary temperature of 500 and 325 °C were applied combined with an S-lens RF level of 80%, a spray voltage of ± 4.0 kV, an m/z scan range from 60 to 900 Da, and an automatic gain control (AGC) target of 1e5 ions at a maximum injection time of 50 ms. The resolution was 60,000 FWHM (full at half maximum).
Ion Mode:POSITIVE
Analysis Protocol File:Steroidomics_GP_Protocols.pdf
  
MS ID:MS005918
Analysis ID:AN006214
Instrument Name:Thermo Orbitrap Exploris 120
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The ionization source was positioned according to the values 0/L-M/1.5. Gas flow rates of the sheath, auxiliary and sweep gas were 50, 10, and 2 arbitrary units (a.u.) respectively. A vaporizer and capillary temperature of 500 and 325 °C were applied combined with an S-lens RF level of 80%, a spray voltage of ± 4.0 kV, an m/z scan range from 60 to 900 Da, and an automatic gain control (AGC) target of 1e5 ions at a maximum injection time of 50 ms. The resolution was 60,000 FWHM (full at half maximum).
Ion Mode:NEGATIVE
Analysis Protocol File:Steroidomics_GP_Protocols.pdf
  
MS ID:MS005919
Analysis ID:AN006215
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Fragmentation data: NOTE - For the fragmentation data, we did not process any results (targeted or untargeted) as we just matched the fragmentation spectra. The ionization source was positioned according to the values 0/B/1. Gas flow rates of the sheath, auxiliary and sweep gas were 50, 10, and 2 arbitrary units (a.u.) respectively. A vaporizer and capillary temperature of 500 and 325 °C were applied combined with an S-lens RF level of 80%, a spray voltage of ± 4.0 kV, an m/z scan range from 60 to 900 Da, and an automatic gain control (AGC) target of 2e5 ions at a maximum injection time of 100 ms. The resolution was 17,500 FWHM (full at half maximum). The AGC target was adjusted to 2e5 ions at a maximum injection time of 100 ms. Parallel reaction monitoring was applied with an isolation window of 1.0 Da and 3 collision energies: 15, 30, and 50 eV.
Ion Mode:POSITIVE
Analysis Protocol File:Steroidomics_GP_Protocols.pdf
  
MS ID:MS005920
Analysis ID:AN006216
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Fragmentation data: NOTE - For the fragmentation data, we did not process any results (targeted or untargeted) as we just matched the fragmentation spectra. The ionization source was positioned according to the values 0/B/1. Gas flow rates of the sheath, auxiliary and sweep gas were 50, 10, and 2 arbitrary units (a.u.) respectively. A vaporizer and capillary temperature of 500 and 325 °C were applied combined with an S-lens RF level of 80%, a spray voltage of ± 4.0 kV, an m/z scan range from 60 to 900 Da, and an automatic gain control (AGC) target of 2e5 ions at a maximum injection time of 100 ms. The resolution was 17,500 FWHM (full at half maximum). The AGC target was adjusted to 2e5 ions at a maximum injection time of 100 ms. Parallel reaction monitoring was applied with an isolation window of 1.0 Da and 3 collision energies: 15, 30, and 50 eV.
Ion Mode:NEGATIVE
Analysis Protocol File:Steroidomics_GP_Protocols.pdf
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