Summary of Study ST002785

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 PR001736. The data can be accessed directly via it's Project DOI: 10.21228/M89Q7K This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002785
Study TitleMetabolic changes of the human kidney during isolated normothermic perfusion with red blood cell based perfusate - perfusate
Study TypeExperimental
Study SummaryThis study investigates how glucose, lactate and 20 amino acids in the perfusate of normothermically perfused human kidneys that were not suitable for transplantation changes over time.
Institute
KU Leuven
DepartmentMicrobiology, Immunology and Transplantation
LaboratoryLab of Abdominal Transplantation
Last NameJochmans
First NameIna
AddressHerestraat 49, Leuven, 3000, Belgium
Emailina.jochmans@kuleuven.be
PhoneNone
Submit Date2023-07-17
Num Groups2
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-08-07
Release Version1
Ina Jochmans Ina Jochmans
https://dx.doi.org/10.21228/M89Q7K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001736
Project DOI:doi: 10.21228/M89Q7K
Project Title:Metabolic changes during normothermic isolated kidney perfusion
Project Type:Experimental
Project Summary:Normothermic isolated kidney perfusion is being developed as a method to preserve donor kidneys and to assess their future function before they are transplanted. Donor kidneys can be exposed to different types and degrees of ischemic injury before they are preserved. This project studies how the metabolome changes in relation to different types and degrees of ischemia.
Institute:KU Leuven
Department:Microbiology, Immunology and Transplantation
Laboratory:Lab of Abdominal Transplantation
Last Name:Jochmans
First Name:Ina
Address:Herestraat 49, Leuven, 3000, Belgium
Email:ina.jochmans@kuleuven.be
Phone:None
Funding Source:FTBO, KOOR, FWO
Contributors:Julie De Beule, Bart Ghesquière, Ina Jochmans

Subject:

Subject ID:SU002892
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Group Timepoint
SA298891H02L_T0DBD 0
SA298892H05_T0DBD 0
SA298893H05_T2DBD 120
SA298894H02L_T2DBD 120
SA298895H05_T0.25DBD 15
SA298896H02L_T0.25DBD 15
SA298897H05_T3DBD 180
SA298898H02L_T3DBD 180
SA298899H02L_T4DBD 240
SA298900H05_T4DBD 240
SA298901H05_T0.50DBD 30
SA298902H02L_T0.50DBD 30
SA298903H02L_T0.75DBD 45
SA298904H05_T0.75DBD 45
SA298905H05_T1DBD 60
SA298906H02L_T1DBD 60
SA298907H04_T0DCD 0
SA298908H01_T0DCD 0
SA298909H03_T0DCD 0
SA298910H02_T0DCD 0
SA298911H03_T2DCD 120
SA298912H04_T2DCD 120
SA298913H01_T2DCD 120
SA298914H02_T2DCD 120
SA298915H01_T0.25DCD 15
SA298916H04_T0.25DCD 15
SA298917H02_T0.25DCD 15
SA298918H03_T0.25DCD 15
SA298919H02_T3DCD 180
SA298920H04_T3DCD 180
SA298921H01_T3DCD 180
SA298922H03_T3DCD 180
SA298923H04_T4DCD 240
SA298924H01_T4DCD 240
SA298925H02_T4DCD 240
SA298926H03_T4DCD 240
SA298927H01_T0.50DCD 30
SA298928H04_T0.50DCD 30
SA298929H02_T0.50DCD 30
SA298930H03_T0.50DCD 30
SA298931H01_T0.75DCD 45
SA298932H02_T0.75DCD 45
SA298933H03_T0.75DCD 45
SA298934H04_T0.75DCD 45
SA298935H02_T1DCD 60
SA298936H03_T1DCD 60
SA298937H01_T1DCD 60
SA298938H04_T1DCD 60
Showing results 1 to 48 of 48

Collection:

Collection ID:CO002885
Collection Summary:Perfusate samples were collected in ethylenediaminetetraacetic acid (EDTA) tubes, at baseline (before the kidney was mounted on the normothermic perfusion device), every 15 minutes during the first hour and hourly thereafter. One milliliter perfusate aliquots (centrifuged 1000g, 10 minutes, 4°C) were snap frozen in liquid nitrogen and stored at -80°C until analysis.
Sample Type:Perfusate
Collection Frequency:Baseline (T0) and during perfusion at 15 min (T0.25), 30 min (T0.50), 45 min (T0.75), 1 hour (T1), 2 hours (T2), 3 hours (T3), 4 hours (T4)
Storage Conditions:-80℃
Additives:EDTA

Treatment:

Treatment ID:TR002901
Treatment Summary:Human kidneys retrieved to be transplanted but finally deemed not suitable for transplantation by all Eurotransplant kidney transplant centers were brought to the lab. The kidneys were retrieved following national protocols and stored in IGL-1 on ice. Kidneys were donated after brain death (DBD) or after circulatory death (DCD). All kidneys were flushed with 200 ml of Ringer’s solution before mounting them on the ex situ circuit to wash out IGL-1.

Sample Preparation:

Sampleprep ID:SP002898
Sampleprep Summary:Samples were extracted in an 80% methanol (80:20 methanol:water) (Methanol ≥99.9%, HiPerSolv CHROMANORM®, ULTRA for LC-MS, suitable for UPLC/UHPLC-MS instruments, VWR, Belgium) extraction buffer containing 1 µM of deuterated D27 myristic acid, 5 µM D12 glucose, 3 µM 13C5-D5-15N Glutamic acid and 3 µM D7-15N4-Arginine as internal standards. 10 µl of sample was added to 990 µl of the extraction buffer and stored overnight at -80 °C. Insolubilities and precipitated proteins were removed by centrifugation at 20.000 g, for 15 min at 4 °C. 200 µL of the supernatant was transferred to an appropriate mass-spectrometry vial. 10 µl of sample was added to 990 µl of the extraction buffer and stored overnight at -80 °C.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004532
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1290 Infinity
Column Agilent InfinityLab Poroshell 120 (2.1 x 150 mm, 2.7 um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Focus
Ion Mode NEGATIVE
Units Peak area

Chromatography:

Chromatography ID:CH003405
Chromatography Summary:10 µl was loaded onto an Ultra Performance Liquid Chromatograph (UPLC) equipped with a Hydrophilic Interaction Liquid Chromatography (HILIC) column (InfinityLab Poroshell 120 HILIC-Z PEEK-lined 2.1 x 150 mm, 2.7 µm column; Agilent, Santa Clara, USA)) and connected in-line to a Q-exactive Orbitrap Focus (Thermo Fisher Scientific, Massachusetts, USA) mass spectrometer. A linear gradient was built up starting with 90% solvent A (LC-MS grade acetonitrile, Acetonitrile hypergrade for LC-MS LiChrosolv, Supelco (Merck), Germany) and 10% solvent B (10 mM ammonium acetate (LiChropur™, eluent additive for LC-MS, (Merck), Germany), pH 9.3). At 2 min the gradient increased to 60% of solvent B and maintained at 60% until 15 min. The gradient returned to 10% solvent B at 16 min and remained until 25 min. The flow rate was 250 µl/min and the column was kept at 25°C throughout the analysis. The MS operated in negative ion mode, with a spray voltage of 2.9 kV and a temperature of the capillary of 325 °C. Gas settings were as follows: sheath gas 40 and auxiliary gas 15. The vaporizer temperature was set at 300 °C. A full scan (resolution of 70.000 and scan range of m/z 70-1050) was applied. XCalibur version to operate the LC-MS was 4.2.47.
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent InfinityLab Poroshell 120 (2.1 x 150 mm, 2.7 um)
Column Temperature:25°C
Flow Gradient:A linear gradient was built up starting with 90% solvent A and 10% solvent B. At 2 min the gradient increased to 60% of solvent B and maintained at 60% until 15 min.
Flow Rate:250 µl/min
Solvent A:100% acetonitrile
Solvent B:100% water; 10 mM ammonium acetate, pH 9.3
Chromatography Type:HILIC

MS:

MS ID:MS004279
Analysis ID:AN004532
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw MS data were converted into mzML using the MSConvert tool of Proteowizard (version 3.0.20247). Peak picking was performed with El_Maven (El_Maven, Elucidata, Massachusetts, USA, version 0.12.0). Metabolites were identified using an in-house library containing exact mass and retention time. The mass accuracy during data processing in El Maven was set at 10 ppm. Calculation of abundances was done in the LC-MS Workflow of El_Maven. Raw abundances (peak area values) for each metabolite were corrected for internal standard (Myristic acid d27).
Ion Mode:NEGATIVE
  logo