Summary of Study ST000236

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 PR000189. The data can be accessed directly via it's Project DOI: 10.21228/M8TS3D This work is supported by NIH grant, U2C- DK119886.

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Study IDST000236
Study TitleQuick Comparison of Urine Metabolites in Human and SD Rats of Different Sex by Untargeted UPLC-TOFMS and In-house Software Platform
Study TypeBiomarker Discovery
Study SummaryHuman urine samples were collected before breakfast from 14 male and 13 female Chinese post-graduate students, age from 23 to 29, on the morning of sample collection day. Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. All urine samples were frozen at -80°C prior to analysis.
Institute
Beijing Institute of Radiation Medicine
DepartmentDepartment of Pharmacology and Toxicology
Last NameLiang
First NameQiande
Address27 Taiping Road, Beijing, P.R.China
Emailliangqiande@yeah.net
Submit Date2015-08-09
Num Groups4
Total Subjects43
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2015-09-09
Release Version1
Qiande Liang Qiande Liang
https://dx.doi.org/10.21228/M8TS3D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000189
Project DOI:doi: 10.21228/M8TS3D
Project Title:Quick Comparison of Metabolites in Human and Rats of Different Sex by Untargeted UPLC-TOFMS and In-house Software Platform
Project Type:Biomarker Discovery
Project Summary:Metabolite difference between sexes has rarely been observed in global manner. In this study, untargeted UPLC-TOFMS and an in-house software platform were used for quick comparison of sex difference of urinary metabolites in human, and of urinary and serum metabolites in SD rats. In addition, as a convenient opportunity, the species difference of urinary metabolites between human and SD rats were also observed. Human urine samples were collected before breakfast from 14 male and 13 female Chinese post-graduate students, age from 23 to 29, on the morning of sample collection day. Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. Then a blood sample (3-5ml) was collected from the aorta of the rat under anesthesia and centrifuged to obtain serum. All urine and serum samples were frozen at -80°C prior to analysis. The study of sex differences is important for finding the best course of treatment of disease as well as for developing novel targets of therapy. A more complete understanding of the metabolic differences across sex-based subgroups is helpful to improve the mechanistic understanding of sex differences.
Institute:Beijing Institute of Radiation Medicine
Department:Department of Pharmacology and Toxicology
Last Name:Liang
First Name:Qiande
Address:27 Taiping Road, Beijing, P.R.China
Email:liangqiande@yeah.net

Subject:

Subject ID:SU000256
Subject Type:Human/animal
Subject Species:Homo sapiens;Rattus norvegicus
Taxonomy ID:9606;10116
Genotype Strain:Sprague-Dawley (Rat)
Age Or Age Range:23-29 (Human)
Weight Or Weight Range:220-250g (Rat)
Gender:Male/Female (Human and Rat)
Human Race:Yellow Race (Human)
Human Inclusion Criteria:Post-graduate students (Human)
Animal Housing:pathogen-free animal facility (Rat)
Animal Light Cycle:12h light/dark cycle (Rat)
Animal Feed:free access to standard food (Rat)
Animal Water:free access to water (Rat)
Species Group:Mammal

Factors:

Subject type: Human/animal; Subject species: Homo sapiens;Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Gender
SA011030woman10Female
SA011031woman11Female
SA011032woman12Female
SA011033woman9Female
SA011034woman7Female
SA011035woman5Female
SA011036woman6Female
SA011037woman13Female
SA011038FemaleRat1Female
SA011039FemaleRat6Female
SA011040FemaleRat7Female
SA011041FemaleRat8Female
SA011042FemaleRat5Female
SA011043FemaleRat4Female
SA011044FemaleRat2Female
SA011045FemaleRat3Female
SA011046woman4Female
SA011047woman8Female
SA011048woman3Female
SA011049woman1Female
SA011050woman2Female
SA011051man8Male
SA011052man9Male
SA011053MaleRat7Male
SA011054man7Male
SA011055MaleRat8Male
SA011056man5Male
SA011057man2Male
SA011058man3Male
SA011059man4Male
SA011060MaleRat6Male
SA011061man6Male
SA011062MaleRat4Male
SA011063man12Male
SA011064man13Male
SA011065man14Male
SA011066man1Male
SA011067man11Male
SA011068man10Male
SA011069MaleRat3Male
SA011070MaleRat2Male
SA011071MaleRat1Male
SA011072MaleRat5Male
Showing results 1 to 43 of 43

Collection:

Collection ID:CO000246
Collection Summary:Human urine samples were collected before breakfast from 14 male and 13 female Chinese post-graduate students studying in our academy, age from 23 to 29, on the morning of sample collection day. All urine samples were frozen at -80°C prior to analysis. On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. All urine samples were frozen at -80°C prior to analysis.
Collection Protocol Filename:1_COL_PROT.pdf
Sample Type:Urine
Collection Method:Human: Urine samples were collected before breakfast on the morning of sample collection day. Rat: On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection.
Collection Location:Academy | Lab
Collection Frequency:Once
Collection Duration:24h
Volumeoramount Collected:about 10-50 mL
Storage Conditions:-80°C
Collection Vials:50ml Polypropylene tube
Storage Vials:50ml Polypropylene tube
Collection Tube Temp:Room tempreture

Treatment:

Treatment ID:TR000266
Treatment Summary:Human urine samples were collected before breakfast from 14 male and 13 female Chinese post-graduate students studying in our academy, age from 23 to 29, on the morning of sample collection day. All urine samples were frozen at -80°C prior to analysis. On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. All urine samples were frozen at -80°C prior to analysis.
Animal Anesthesia:Anesthesia using Pentobarbital Sodium
Animal Acclimation Duration:>=3 days
Animal Fasting:24h
Animal Endp Euthanasia:Died in anesthesia status
Animal Endp Tissue Coll List:Urine
Animal Endp Clinical Signs:Died
Human Fasting:No fasting but the urine samples were collected before breakfast

Sample Preparation:

Sampleprep ID:SP000260
Sampleprep Summary:Amygdalin was dissolved in acetonitrile-water(1:1) to form 0.1mg/ml solution. Urine samples were unfrozen at room temperature. 600?l of urine sample was mixed with 20?l Amygdalin solution. After centrifugation at about 14000rpm and -4?, the supernatant was injected into UPLC-TOF MS system.
Sampleprep Protocol Filename:2_PRE_PROT.pdf
Processing Method:Centrifugation
Processing Storage Conditions:Centrifugation at -4?
Extraction Method:Centrifugation
Extract Concentration Dilution:600?l of urine/620?l
Extract Storage:4? after centrifugation and during analysis
Sample Spiking:20?l Amygdalin solution/620?l

Combined analysis:

Analysis ID AN000357 AN000358 AN000359 AN000360 AN000361 AN000362
Analysis type MS MS MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column Waters Acquity HSS T3 (100 x 2.1mm, 1.8um) Waters Acquity HSS T3 (100 x 2.1mm, 1.8um) Waters Acquity HSS T3 (100 x 2.1mm, 1.8um) Waters Acquity HSS T3 (100 x 2.1mm, 1.8um) Waters Acquity HSS T3 (100 x 2.1mm, 1.8um) Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)
MS Type ESI ESI ESI ESI ESI ESI
MS instrument type QTOF QTOF QTOF QTOF QTOF QTOF
MS instrument name Waters Synapt-HDMS Waters Synapt-HDMS Waters Synapt-HDMS Waters Synapt-HDMS Waters Synapt-HDMS Waters Synapt-HDMS
Ion Mode POSITIVE POSITIVE POSITIVE NEGATIVE NEGATIVE NEGATIVE
Units Peak Height Peak Height Peak Height Peak Height Peak Height Peak Height

Chromatography:

Chromatography ID:CH000264
Chromatography Summary:Untargeted UPLC-TOFMS
Methods Filename:3_CHR_PROT.pdf
Instrument Name:Waters Acquity
Column Name:Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)
Column Temperature:24?
Flow Gradient:Isocratic 2% B (01 min), linear gradient from 2% to 5% B (12 min), 5% to 12% B (25 min), 12% to 20% B (510 min), 20% to 30% B (1012 min), 30% to 50% B (1213 min), 50% to 100% B (1315 min), isocratic 100% B for 1min, then back to 2% B in 1 min and isocratic 2% B for 3min before next run
Flow Rate:0.5 ml/min
Injection Temperature:24?
Internal Standard:Amygdalin
Sample Injection:8?L
Sampling Cone:40V
Solvent A:Water containing 0.1% formic acid
Solvent B:Acetonitrile containing 0.1% formic acid
Analytical Time:20min
Capillary Voltage:Positive ion mode:3kV; Negative ion mode: 2.9kV
Chromatography Type:Reversed phase

MS:

MS ID:MS000303
Analysis ID:AN000357
Instrument Name:Waters Synapt-HDMS
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3kV
Collision Energy:6V (trap)/4V (transfer)
Collision Gas:Ar
Dry Gas Flow:900 L/h
Dry Gas Temp:450C
Ion Source Temperature:100C
Ionization:ESI
Source Temperature:100C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450C
Acquisition Parameters File:Inlet_Method_File_Name:_20100505
_Positive_Ion_Mode_MS_Method_File_Name:_20120221_pos_50-1500
Processing Parameters File:TR_0-18_50-1500_005_020_YES6_YES.mlm
  
MS ID:MS000304
Analysis ID:AN000358
Instrument Name:Waters Synapt-HDMS
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3kV
Collision Energy:6V (trap)/4V (transfer)
Collision Gas:Ar
Dry Gas Flow:900 L/h
Dry Gas Temp:450?
Ion Source Temperature:100?
Ionization:ESI
Source Temperature:100?
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450?
Acquisition Parameters File:Inlet_Method_File_Name:_20100505
_Positive_Ion_Mode_MS_Method_File_Name:_20120221_pos_50-1500
Processing Parameters File:TR_0-18_50-1500_005_020_YES6_YES.mlm
  
MS ID:MS000305
Analysis ID:AN000359
Instrument Name:Waters Synapt-HDMS
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3kV
Collision Energy:6V (trap)/4V (transfer)
Collision Gas:Ar
Dry Gas Flow:900 L/h
Dry Gas Temp:450C
Ion Source Temperature:100C
Ionization:ESI
Source Temperature:100C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450C
Acquisition Parameters File:Inlet_Method_File_Name:_20100505
_Positive_Ion_Mode_MS_Method_File_Name:_20120221_pos_50-1500
Processing Parameters File:TR_0-18_50-1500_005_020_YES6_YES.mlm
  
MS ID:MS000306
Analysis ID:AN000360
Instrument Name:Waters Synapt-HDMS
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:2.9kV
Collision Energy:6V (trap)/4V (transfer)
Collision Gas:Ar
Dry Gas Flow:900 L/h
Dry Gas Temp:450C
Ion Source Temperature:100C
Ionization:ESI
Source Temperature:100C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450C
Acquisition Parameters File:Inlet_Method_File_Name:_20100505
_Negative_Ion_Mode_MS_Mehod_File_Name:_20120221_neg_50-1500
Processing Parameters File:TR_0-18_50-1500_005_020_YES6_YES.mlm
  
MS ID:MS000307
Analysis ID:AN000361
Instrument Name:Waters Synapt-HDMS
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:2.9kV
Collision Energy:6V (trap)/4V (transfer)
Collision Gas:Ar
Dry Gas Flow:900 L/h
Dry Gas Temp:450C
Ion Source Temperature:100C
Ionization:ESI
Source Temperature:100C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450C
Acquisition Parameters File:Inlet_Method_File_Name:_20100505
_Negative_Ion_Mode_MS_Mehod_File_Name:_20120221_neg_50-1500
Processing Parameters File:TR_0-18_50-1500_005_020_YES6_YES.mlm
  
MS ID:MS000308
Analysis ID:AN000362
Instrument Name:Waters Synapt-HDMS
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:2.9kV
Collision Energy:6V (trap)/4V (transfer)
Collision Gas:Ar
Dry Gas Flow:900 L/h
Dry Gas Temp:450C
Ion Source Temperature:100C
Ionization:ESI
Source Temperature:100C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450C
Acquisition Parameters File:Inlet_Method_File_Name:_20100505
_Negative_Ion_Mode_MS_Mehod_File_Name:_20120221_neg_50-1500
Processing Parameters File:TR_0-18_50-1500_005_020_YES6_YES.mlm
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