Summary of study ST001711

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 PR001095. The data can be accessed directly via it's Project DOI: 10.21228/M85976 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.

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Study IDST001711
Study TitleMetabolic signatures of NAFLD - Polar metabolomics data (part II)
Study SummaryAnalysis of polar metabolites Serum samples were randomized and sample preparation was carried out as described previously (Castilloet al. 2011). In summary, 400 μL of MeOH containing ISTDs (heptadecanoic acid, deuterium-labeled DL-valine, deuterium-labeled succinic acid, and deuterium-labeled glutamic acid, c = 1 µg/mL) was added to 30 µl of the serum samples which were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min) and 350 μL of the supernatant was collected after centrifugation. The solvent was evaporated to dryness and 25 μL of MOX reagent was added and the sample was incubated for 60 min at 45 °C. 25 μL of MSTFA was added and after 60 min incubation at 45 °C 25 μL of the retention index standard mixture (n-alkanes, c=10 µg/mL) was added. The analyses were carried out on an Agilent 7890B GC coupled to 7200 QTOF MS. Injection volume was 1 µL with 100:1 cold solvent split on PTV at 70 °C, heating to 300 °C at 120 °C/minute. Column: Zebron ZB-SemiVolatiles. Length: 20m, I.D. 0.18mm, film thickness: 0.18 µm. With initial Helium flow 1.2 mL/min, increasing to 2.4 mL/min after 16 mins. Oven temperature program: 50 °C (5 min), then to 270°C at 20 °C/min and then to 300 °C at 40 °C/min (5 min). EI source: 250 °C, 70 eV electron energy, 35µA emission, solvent delay 3 min. Mass range 55 to 650 amu, acquisition rate 5 spectra/s, acquisition time 200 ms/spectrum. Quad at 150 °C, 1.5 mL/min N2 collision flow, aux-2 temperature: 280 °C. Calibration curves were constructed using alanine, citric acid, fumaric acid, glutamic acid, glycine, lactic acid, malic acid, 2-hydroxybutyric acid, 3-hydroxybutyric acid, linoleic acid, oleic acid, palmitic acid, stearic acid, cholesterol, fructose, glutamine, indole-3-propionic acid, isoleucine, leucine, proline, succinic acid, valine, asparagine, aspartic acid, arachidonic acid, glycerol-3-phosphate, lysine, methionine, ornithine, phenylalanine, serine and threonine purchased from Sigma-Aldrich (St. Louis, MO, USA) at concentration range of 0.1 to 80 μg/mL. An aliquot of each sample was collected and pooled and used as quality control samples, together with a NIST SRM 1950 serum sample and an in-house pooled serum sample. Relative standard deviations (% RSDs) of the metabolite concentrations in control serum samples showed % RSDs within accepted analytical limits at averages of 27.2% and 29.2% for in-house QC abd pooled QC samples.
Institute
Örebro University
Last NameMcGlinchey
First NameAidan
AddressSchool of Medical Sciences, Örebro, Örebro, 70281, Sweden
Emailaidan.mcglinchey@oru.se
Phone+46736485638
Submit Date2021-02-17
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailGC-MS
Release Date2021-05-01
Release Version1
Aidan McGlinchey Aidan McGlinchey
https://dx.doi.org/10.21228/M85976
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001095
Project DOI:doi: 10.21228/M85976
Project Title:Metabolomic signatures of NAFLD
Project Summary:Background and Aims: Nonalcoholic fatty liver disease (NAFLD) is a progressive liver disease that is strongly associated with type 2 diabetes. Accurate, non-invasive diagnostic tests to delineate the different stages: degree of steatosis, grade of nonalcoholic steatohepatitis (NASH) and stage fibrosis represent an unmet medical need. In our previous studies, we successfully identified specific serum molecular lipid signatures which associate with the amount of liver fat as well as with NASH. Here we report underlying associations between clinical data, lipidomic profiles, metabolic profiles and clinical outcomes, including downstream identification of potential biomarkers for various stages of the disease. Method: We leverage several statistical and machine-learning approaches to analyse clinical, lipidomic and metabolomic profiles of individuals from the European Horizon 2020 project: Elucidating Pathways of Steatohepatitis (EPoS). We interrogate data on patients representing the full spectrum of NAFLD/NASH derived from the EPoS European NAFLD Registry (n = 627). We condense the EPoS lipidomic data into lipid clusters and subsequently apply non-rejection-rate-pruned partial correlation network techniques to facilitate network analysis between the datasets of lipidomic, metabolomic and clinical data. For biomarker identification, a random forest ensemble classification approach was used to both search for valid disease biomarkers and to compare classification performance of lipids, metabolites and clinical factors in combination. Results: We found that steatosis and fibrosis grades were strongly associated with (1) an increase of triglycerides with low carbon number and double bond count as well as (2) a decrease of specific phospholipids, including lysophosphatidylcholines. In addition to the network topology as a result itself, we also present lipid clusters (LCs) of interest to the derived network of proposed interactions in our NAFLD data from the EPoS cohort, along with preliminary metabolite and lipid biomarkers to classify NAFLD fibrosis. Conclusions: Our findings suggest that dysregulation of lipid metabolism in progressive stages of NAFLD is reflected in circulation and may thus hold diagnostic value as well as offer new insights about NAFLD pathogenesis. Using this cohort as a proof-of-concept, we demonstrate current progress in tuning the accuracy random forest approaches with a view to predicting various subtypes of NAFLD patient using a minimal set of lipidomic and metabolic markers. For the first time, a detailed network-based picture emerges between lipids, polar metabolites and clinical variables. Lipidomic / metabolomic markers may provide an alternative method of NAFLD patient classification and risk stratification to guide therapy.
Institute:Örebro University
Last Name:McGlinchey
First Name:Aidan
Address:School of Medical Sciences, Örebro, Örebro, 70281, Sweden
Email:aidan.mcglinchey@oru.se
Phone:+46736485638

Subject:

Subject ID:SU001788
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sex NAFLD.Category T2DM Kleiner.Steatosis Inflammation
SA1597131022385746F 1 NA 1 -
SA1597141022385747F 1 NA 1 1
SA1597151022385761F 1 NA 1 1
SA1597161022385792F 1 NA 1 3
SA1597171022385834F 1 NA 2 1
SA1597181022385816F 1 NA 2 1
SA1597191022385771F 1 NA 2 2
SA1597201022385802F 1 NA 3 1
SA1597211022385801F 1 NA 3 1
SA1597221022385768F 1 NA 3 1
SA1597231022385786F 1 NA 3 2
SA1597241022385784F 1 NA 3 2
SA1597251022385755F 1 NA 3 2
SA1597261022385754F 1 NA 3 2
SA1597271022385832F 1 NA 3 2
SA1597281022385865F 1 N 1 -
SA1597291022386491F 1 N 1 -
SA1597301028971690F 1 N 1 -
SA1597311028940127F 1 N 1 -
SA1597321022386174F 1 N 1 -
SA1597331026694081F 1 N 1 -
SA1597341022385897F 1 N 1 1
SA1597351022386559F 1 N 1 1
SA1597361022385762F 1 N 1 1
SA1597371022385836F 1 N 1 1
SA1597381022386512F 1 N 1 1
SA1597391022386514F 1 N 1 1
SA1597401022386602F 1 N 1 1
SA1597411022385872F 1 N 1 1
SA1597421022385880F 1 N 1 1
SA1597431028939921F 1 N 1 1
SA1597441022385912F 1 N 1 1
SA1597451022385905F 1 N 1 1
SA1597461022386990F 1 N 1 1
SA1597471022386190F 1 N 1 1
SA1597481022386422F 1 N 1 1
SA1597491028938105F 1 N 1 2
SA1597501022386925F 1 N 2 -
SA1597511022386548F 1 N 2 -
SA1597521022386196F 1 N 2 -
SA1597531022386594F 1 N 2 -
SA1597541026694239F 1 N 2 1
SA1597551022386943F 1 N 2 1
SA1597561022386572F 1 N 2 1
SA1597571022385839F 1 N 2 2
SA1597581028938200F 1 N 2 2
SA1597591022386199F 1 N 2 2
SA1597601022386586F 1 N 2 3
SA1597611022385777F 1 N 3 1
SA1597621026698295F 1 N 3 1
SA1597631022386494F 1 N 3 2
SA1597641022385780F 1 N 3 2
SA1597651026697459F 1 N 3 2
SA1597661022386537F 1 N 3 2
SA1597671022386517F 1 N NA 1
SA1597681028938307F 1 N NA NA
SA1597701022386450F 1 Y 1 -
SA1597711028971722F 1 Y 1 -
SA1597721028938157F 1 Y 1 1
SA1597731022386593F 1 Y 1 1
SA1597741022386206F 1 Y 1 1
SA1597751022386493F 1 Y 1 1
SA1597761028939905F 1 Y 1 1
SA1597771022385758F 1 Y 3 -
SA1597781022386466F 1 Y 3 -
SA1597791022386583F 1 Y 3 1
SA1597801022385807F 1 Y 3 1
SA1597691022386482F 1 Y - 2
SA1597811022385803F 2 NA 2 2
SA1597821022385810F 2 NA 2 2
SA1597831022385745F 2 NA 3 1
SA1597841022385770F 2 NA 3 3
SA1597851028939780F 2 N 1 -
SA1597861022386150F 2 N 1 -
SA1597871022386903F 2 N 1 1
SA1597881022386454F 2 N 1 1
SA1597891028938244F 2 N 1 1
SA1597901022386991F 2 N 1 1
SA1597911022387178F 2 N 1 1
SA1597921028939875F 2 N 1 1
SA1597931022386576F 2 N 1 1
SA1597941028938158F 2 N 1 1
SA1597951022386498F 2 N 1 2
SA1597961022385924F 2 N 1 2
SA1597971022385859F 2 N 1 2
SA1597981022386131F 2 N 1 2
SA1597991022386478F 2 N 2 -
SA1598001022387102F 2 N 2 1
SA1598011028971662F 2 N 2 1
SA1598021022386561F 2 N 2 1
SA1598031022387123F 2 N 2 1
SA1598041022385845F 2 N 2 1
SA1598051022386912F 2 N 2 1
SA1598061028971709F 2 N 2 1
SA1598071022385892F 2 N 2 1
SA1598081022386181F 2 N 2 1
SA1598091022387151F 2 N 2 2
SA1598101022386557F 2 N 2 2
SA1598111022387205F 2 N 2 2
SA1598121022386163F 2 N 2 2
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Collection:

Collection ID:CO001781
Collection Summary:Serum samples were randomized and sample preparation was carried out as described previously (Castilloet al. 2011). In summary, 400 μL of MeOH containing ISTDs (heptadecanoic acid, deuterium-labeled DL-valine, deuterium-labeled succinic acid, and deuterium-labeled glutamic acid, c = 1 µg/mL) was added to 30 µl of the serum samples which were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min) and 350 μL of the supernatant was collected after centrifugation. The solvent was evaporated to dryness and 25 μL of MOX reagent was added and the sample was incubated for 60 min at 45 °C. 25 μL of MSTFA was added and after 60 min incubation at 45 °C 25 μL of the retention index standard mixture (n-alkanes, c=10 µg/mL) was added. The analyses were carried out on an Agilent 7890B GC coupled to 7200 QTOF MS. Injection volume was 1 µL with 100:1 cold solvent split on PTV at 70 °C, heating to 300 °C at 120 °C/minute. Column: Zebron ZB-SemiVolatiles. Length: 20m, I.D. 0.18mm, film thickness: 0.18 µm. With initial Helium flow 1.2 mL/min, increasing to 2.4 mL/min after 16 mins. Oven temperature program: 50 °C (5 min), then to 270°C at 20 °C/min and then to 300 °C at 40 °C/min (5 min). EI source: 250 °C, 70 eV electron energy, 35µA emission, solvent delay 3 min. Mass range 55 to 650 amu, acquisition rate 5 spectra/s, acquisition time 200 ms/spectrum. Quad at 150 °C, 1.5 mL/min N2 collision flow, aux-2 temperature: 280 °C. Calibration curves were constructed using alanine, citric acid, fumaric acid, glutamic acid, glycine, lactic acid, malic acid, 2-hydroxybutyric acid, 3-hydroxybutyric acid, linoleic acid, oleic acid, palmitic acid, stearic acid, cholesterol, fructose, glutamine, indole-3-propionic acid, isoleucine, leucine, proline, succinic acid, valine, asparagine, aspartic acid, arachidonic acid, glycerol-3-phosphate, lysine, methionine, ornithine, phenylalanine, serine and threonine purchased from Sigma-Aldrich (St. Louis, MO, USA) at concentration range of 0.1 to 80 μg/mL. An aliquot of each sample was collected and pooled and used as quality control samples, together with a NIST SRM 1950 serum sample and an in-house pooled serum sample. Relative standard deviations (% RSDs) of the metabolite concentrations in control serum samples showed % RSDs within accepted analytical limits at averages of 27.2% and 29.2% for in-house QC abd pooled QC samples.
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001801
Treatment Summary:No treatment applied.

Sample Preparation:

Sampleprep ID:SP001794
Sampleprep Summary:Serum samples were randomized and sample preparation was carried out as described previously (Castilloet al. 2011). In summary, 400 μL of MeOH containing ISTDs (heptadecanoic acid, deuterium-labeled DL-valine, deuterium-labeled succinic acid, and deuterium-labeled glutamic acid, c = 1 µg/mL) was added to 30 µl of the serum samples which were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min) and 350 μL of the supernatant was collected after centrifugation. The solvent was evaporated to dryness and 25 μL of MOX reagent was added and the sample was incubated for 60 min at 45 °C. 25 μL of MSTFA was added and after 60 min incubation at 45 °C 25 μL of the retention index standard mixture (n-alkanes, c=10 µg/mL) was added. The analyses were carried out on an Agilent 7890B GC coupled to 7200 QTOF MS. Injection volume was 1 µL with 100:1 cold solvent split on PTV at 70 °C, heating to 300 °C at 120 °C/minute. Column: Zebron ZB-SemiVolatiles. Length: 20m, I.D. 0.18mm, film thickness: 0.18 µm. With initial Helium flow 1.2 mL/min, increasing to 2.4 mL/min after 16 mins. Oven temperature program: 50 °C (5 min), then to 270°C at 20 °C/min and then to 300 °C at 40 °C/min (5 min). EI source: 250 °C, 70 eV electron energy, 35µA emission, solvent delay 3 min. Mass range 55 to 650 amu, acquisition rate 5 spectra/s, acquisition time 200 ms/spectrum. Quad at 150 °C, 1.5 mL/min N2 collision flow, aux-2 temperature: 280 °C. Calibration curves were constructed using alanine, citric acid, fumaric acid, glutamic acid, glycine, lactic acid, malic acid, 2-hydroxybutyric acid, 3-hydroxybutyric acid, linoleic acid, oleic acid, palmitic acid, stearic acid, cholesterol, fructose, glutamine, indole-3-propionic acid, isoleucine, leucine, proline, succinic acid, valine, asparagine, aspartic acid, arachidonic acid, glycerol-3-phosphate, lysine, methionine, ornithine, phenylalanine, serine and threonine purchased from Sigma-Aldrich (St. Louis, MO, USA) at concentration range of 0.1 to 80 μg/mL. An aliquot of each sample was collected and pooled and used as quality control samples, together with a NIST SRM 1950 serum sample and an in-house pooled serum sample. Relative standard deviations (% RSDs) of the metabolite concentrations in control serum samples showed % RSDs within accepted analytical limits at averages of 27.2% and 29.2% for in-house QC abd pooled QC samples.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002786
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Zebron ZB-SemiVolatiles (20m x 0.18mm, 0.18µm)
MS Type EI
MS instrument type GC QTOF MS
MS instrument name Agilent 7200 QTOF
Ion Mode UNSPECIFIED
Units log2-transformed

Chromatography:

Chromatography ID:CH002061
Chromatography Comments:Zebron ZB-SemiVolatiles (20m, I.D. 0.18mm, film thickness 0.18µm)
Instrument Name:Agilent 7890B
Column Name:Zebron ZB-SemiVolatiles (20m x 0.18mm, 0.18µm)
Chromatography Type:GC

MS:

MS ID:MS002582
Analysis ID:AN002786
Instrument Name:Agilent 7200 QTOF
Instrument Type:GC QTOF MS
MS Type:EI
MS Comments:In summary, 400 μL of MeOH containing ISTDs (heptadecanoic acid, deuterium-labeled DL-valine, deuterium-labeled succinic acid, and deuterium-labeled glutamic acid, c = 1 µg/mL) was added to 30 µl of the serum samples which were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min) and 350 μL of the supernatant was collected after centrifugation. The solvent was evaporated to dryness and 25 μL of MOX reagent was added and the sample was incubated for 60 min at 45 °C. 25 μL of MSTFA was added and after 60 min incubation at 45 °C 25 μL of the retention index standard mixture (n-alkanes, c=10 µg/mL) was added. The analyses were carried out on an Agilent 7890B GC coupled to 7200 QTOF MS. Injection volume was 1 µL with 100:1 cold solvent split on PTV at 70 °C, heating to 300 °C at 120 °C/minute. Column: Zebron ZB-SemiVolatiles. Length: 20m, I.D. 0.18mm, film thickness: 0.18 µm. With initial Helium flow 1.2 mL/min, increasing to 2.4 mL/min after 16 mins. Oven temperature program: 50 °C (5 min), then to 270°C at 20 °C/min and then to 300 °C at 40 °C/min (5 min). EI source: 250 °C, 70 eV electron energy, 35µA emission, solvent delay 3 min. Mass range 55 to 650 amu, acquisition rate 5 spectra/s, acquisition time 200 ms/spectrum. Quad at 150 °C, 1.5 mL/min N2 collision flow, aux-2 temperature: 280 °C. Calibration curves were constructed using alanine, citric acid, fumaric acid, glutamic acid, glycine, lactic acid, malic acid, 2-hydroxybutyric acid, 3-hydroxybutyric acid, linoleic acid, oleic acid, palmitic acid, stearic acid, cholesterol, fructose, glutamine, indole-3-propionic acid, isoleucine, leucine, proline, succinic acid, valine, asparagine, aspartic acid, arachidonic acid, glycerol-3-phosphate, lysine, methionine, ornithine, phenylalanine, serine and threonine purchased from Sigma-Aldrich (St. Louis, MO, USA) at concentration range of 0.1 to 80 μg/mL. An aliquot of each sample was collected and pooled and used as quality control samples, together with a NIST SRM 1950 serum sample and an in-house pooled serum sample. Relative standard deviations (% RSDs) of the metabolite concentrations in control serum samples showed % RSDs within accepted analytical limits at averages of 27.2% and 29.2% for in-house QC abd pooled QC samples. Data values for final analysis were log2-transformed and scaled to zero mean and unit variance.
Ion Mode:UNSPECIFIED
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