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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000236 |
| Study Title | Quick Comparison of Urine Metabolites in Human and SD Rats of Different Sex by Untargeted UPLC-TOFMS and In-house Software Platform |
| Study Type | Biomarker Discovery |
| Study Summary | 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. All urine samples were frozen at -80°C prior to analysis. |
| 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 |
| liangqiande@yeah.net | |
| Submit Date | 2015-08-09 |
| Num Groups | 4 |
| Total Subjects | 43 |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-09-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA011030 | woman10 | Female |
| SA011031 | woman11 | Female |
| SA011032 | woman12 | Female |
| SA011033 | woman9 | Female |
| SA011034 | woman7 | Female |
| SA011035 | woman5 | Female |
| SA011036 | woman6 | Female |
| SA011037 | woman13 | Female |
| SA011038 | FemaleRat1 | Female |
| SA011039 | FemaleRat6 | Female |
| SA011040 | FemaleRat7 | Female |
| SA011041 | FemaleRat8 | Female |
| SA011042 | FemaleRat5 | Female |
| SA011043 | FemaleRat4 | Female |
| SA011044 | FemaleRat2 | Female |
| SA011045 | FemaleRat3 | Female |
| SA011046 | woman4 | Female |
| SA011047 | woman8 | Female |
| SA011048 | woman3 | Female |
| SA011049 | woman1 | Female |
| SA011050 | woman2 | Female |
| SA011051 | man8 | Male |
| SA011052 | man9 | Male |
| SA011053 | MaleRat7 | Male |
| SA011054 | man7 | Male |
| SA011055 | MaleRat8 | Male |
| SA011056 | man5 | Male |
| SA011057 | man2 | Male |
| SA011058 | man3 | Male |
| SA011059 | man4 | Male |
| SA011060 | MaleRat6 | Male |
| SA011061 | man6 | Male |
| SA011062 | MaleRat4 | Male |
| SA011063 | man12 | Male |
| SA011064 | man13 | Male |
| SA011065 | man14 | Male |
| SA011066 | man1 | Male |
| SA011067 | man11 | Male |
| SA011068 | man10 | Male |
| SA011069 | MaleRat3 | Male |
| SA011070 | MaleRat2 | Male |
| SA011071 | MaleRat1 | Male |
| SA011072 | MaleRat5 | Male |
| 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: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 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 |
