Summary of Study ST003880
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 PR002434. The data can be accessed directly via it's Project DOI: 10.21228/M81532 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.
| Study ID | ST003880 |
| Study Title | Untargeted metabolome analysis of control and disease intervertebral disc tissue |
| Study Type | UHPLC-MS/MS untargeted Metabolomics |
| Study Summary | Intervertebral disc degeneration (IVDD) is a multifactorial disease which causes structural and biochemical changes that leads to disability. Identifying the molecular signatures in the intervertebral disc (IVD) during degeneration is crucial to understand the disease pathogenesis. The study aims to identify the metabolic alterations during IVD degeneration. Control and disease IVD tissues were collected and the metabolites were extracted from nucleus pulposus tissue (NP) using triple solvent mixture (Methanol: Acetonitrile: Methanol with 2:2:1 ratio) and profiled using UHPLC-ESI-MS/MS. Untargeted metabolomics identified 832 metabolites from control and disease samples. Differential analysis revealed alterations in amino acids and lipids predominantly. Pathway analysis showed altered metabolites are associated to amino acids category and Phenylalanine and proline are the top upregulated metabolites. Phenylalanine metabolism is the enriched pathway for the upregulated metabolites. In case of lipids, fatty acyl, sphingolipids, glycerophospholipids, prenol lipids were altered during disease. Further large scale analysis are necessary to validate the findings. |
| Institute | Ganga Orthopaedic Research and Education Foundation |
| Department | Proteomics |
| Laboratory | Proteomics |
| Last Name | Tangavel |
| First Name | Dr. Chitraa |
| Address | Ganga Research Centre, 442, Vattamalaipalayam, NGGO Colony, Coimbatore-641022, Coimbatore, Tamil Nadu, 641022, India |
| cthangavel@gmail.com | |
| Phone | +91 8870009209 |
| Submit Date | 2025-03-30 |
| Num Groups | 2 |
| Total Subjects | 61 |
| Num Males | 46 |
| Num Females | 15 |
| Study Comments | NIL |
| Publications | In Progress |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-05-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002434 |
| Project DOI: | doi: 10.21228/M81532 |
| Project Title: | Untargeted metabolome analysis of intervertebral disc tissue |
| Project Type: | UHPLC-MS/MS untargeted Metabolomics |
| Project Summary: | Intervertebral disc degeneration (IVDD) is a multifactorial disease which causes structural and biochemical changes that leads to disability. Identifying the molecular signatures in the intervertebral disc (IVD) during degeneration is crucial to understand the disease pathogenesis. The study aims to identify the metabolic alterations during IVD degeneration. Control and disease IVD tissues were collected and the metabolites were extracted from nucleus pulposus tissue (NP) using triple solvent mixture (Methanol: Acetonitrile: Methanol with 2:2:1 ratio) and profiled using UHPLC-ESI-MS/MS. Untargeted metabolomics identified 832 metabolites from control and disease samples. Differential analysis revealed alterations in amino acids and lipids predominantly. |
| Institute: | Ganga Orthopaedic Research and Education Foundation |
| Department: | Proteomics |
| Laboratory: | Proteomics |
| Last Name: | Tangavel |
| First Name: | Dr. Chitraa |
| Address: | Ganga Research Centre, 442, Vattamalaipalayam, NGGO Colony, Coimbatore-641022, Coimbatore, Tamil Nadu, 641022, India |
| Email: | cthangavel@gmail.com |
| Phone: | +91 8870009209 |
| Funding Source: | AO-Spine Start-Up research Grant 2023-2024 and Ganga Orthopaedic Research and Education Foundation (GOREF) Funding |
| Publications: | In Progress |
| Contributors: | Divya Arunachalam, Sharon Miracle Nayagam, Murugesh Easwaran, Sunmathi Rajendran, Karthik Ramachandran, Sri Vijay Anand, Chitra Tangavel, Rajasekaran Shanumganathan |
Subject:
| Subject ID: | SU004015 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | Wild |
| Age Or Age Range: | 22-76 |
| Gender: | Male and female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Condition |
|---|---|---|
| SA426647 | L34TC001 | Control |
| SA426648 | L5S1TC001 | Control |
| SA426649 | L5S1TC007 | Control |
| SA426650 | L45TC007 | Control |
| SA426651 | L34TC007 | Control |
| SA426652 | L34TC006 | Control |
| SA426653 | L34TC005 | Control |
| SA426654 | L34TC004 | Control |
| SA426655 | L34TC003 | Control |
| SA426656 | L34TC002 | Control |
| SA426657 | L45TC001 | Control |
| SA426658 | L5S1TC006 | Control |
| SA426659 | L5S1TC003 | Control |
| SA426660 | L45TC006 | Control |
| SA426661 | L45TC002 | Control |
| SA426662 | L45TC003 | Control |
| SA426663 | L5S1TC002 | Control |
| SA426664 | L45TC004 | Control |
| SA426665 | L5S1TC004 | Control |
| SA426666 | L45TC005 | Control |
| SA426667 | L5S1TC005 | Control |
| SA426668 | L45TD066 | Disease |
| SA426669 | L45TD048 | Disease |
| SA426670 | L45TD016 | Disease |
| SA426671 | L45TD022 | Disease |
| SA426672 | L45TD040 | Disease |
| SA426673 | L45TD037 | Disease |
| SA426674 | L45TD063 | Disease |
| SA426675 | L45TD051 | Disease |
| SA426676 | L45TD003 | Disease |
| SA426677 | L34TD031 | Disease |
| SA426678 | L34TD059 | Disease |
| SA426679 | L45TD043 | Disease |
| SA426680 | L45TD032 | Disease |
| SA426681 | L45TD052 | Disease |
| SA426682 | L5S1TD038 | Disease |
| SA426683 | L34TD067 | Disease |
| SA426684 | L45TD049 | Disease |
| SA426685 | L45TD047 | Disease |
| SA426686 | L45TD035 | Disease |
| SA426687 | L5S1TD024 | Disease |
| SA426688 | L45TD006 | Disease |
| SA426689 | L5S1TD009 | Disease |
| SA426690 | L45TD057 | Disease |
| SA426691 | L45TD028 | Disease |
| SA426692 | L5S1TD013 | Disease |
| SA426693 | L5S1TD010 | Disease |
| SA426694 | L45TD020 | Disease |
| SA426695 | L45TD007 | Disease |
| SA426696 | L5S1TD064 | Disease |
| SA426697 | L45TD065 | Disease |
| SA426698 | L34TD027 | Disease |
| SA426699 | L45TD044 | Disease |
| SA426700 | L34TD030 | Disease |
| SA426701 | L45TD001 | Disease |
| SA426702 | L45TD034 | Disease |
| SA426703 | L34TD023 | Disease |
| SA426704 | L45TD019 | Disease |
| SA426705 | L45TD025 | Disease |
| SA426706 | L45TD021 | Disease |
| SA426707 | L45TD029 | Disease |
| Showing results 1 to 61 of 61 |
Collection:
| Collection ID: | CO004008 |
| Collection Summary: | Control Intervertebral disc tissues were obtained from brain dead organ donors who have no history of any spinal trauma or diseases. Degenerated disc tissues were obtained from intervertebral disc disease patients undergoing micro discectomy for herniation and spinal fusion for degenerative stenosis with instability |
| Sample Type: | Intervertebral Disc Tissue |
| Collection Method: | IVD tissues from brain dead organ donors and degenerated IVD tissues were collected in the 2ml cryo vials and immediately snap frozen in liquid nitrogen in the clinic (Ganga Hospital, coimbatore). The samples from clinic were transported to research laboratory in the liquid nitrogen storage container. |
| Collection Location: | Intervertebral disc |
| Volumeoramount Collected: | 0.5 mg to 1 mg |
| Storage Conditions: | -80℃ |
| Collection Vials: | Cryovials |
| Storage Vials: | Cryovials |
Treatment:
| Treatment ID: | TR004024 |
| Treatment Summary: | The study involves no treatment. The study compares the metabolomic profile between control and disease intervertebral disc tissues |
Sample Preparation:
| Sampleprep ID: | SP004021 |
| Sampleprep Summary: | Human nucleus pulposus tissue of 200 mg was homogenized into fine powder with liquid nitrogen using pre-chilled mortar and pestle. The powdered tissue was dissolved in a 1ml of triple solvent mixture (Methanol: Acetonitrile: Methanol with 2:2:1 v/v/v ratio) and incubated for one minute at RT. The suspension was vortexed for 10 min, sonicated for 2 min using a probe sonicator and incubated overnight at -20°C freezer. The samples were centrifuged at 5000 xg for 15 min at 4°C and the supernatant collected was dried in a vacuum concentrator. |
| Sampleprep Protocol Filename: | Protocol_IVD.pdf |
| Processing Method: | Tissue homogenization using mortar and pestle with liquid nitrogen |
| Processing Storage Conditions: | 4℃ |
| Extraction Method: | Solvent based extraction using triple solvent mixture (Methanol: Acetonitrile: Methanol with 2:2:1 v/v/v ratio) |
| Extract Enrichment: | Vacuum drying using speed vaccum concentrator |
| Extract Cleanup: | Filtration of the extract using 0.22 micron filter and centrifugation to remove residual tissue debris |
| Extract Storage: | -20℃ |
| Sample Derivatization: | NIL |
Chromatography:
| Chromatography ID: | CH004835 |
| Chromatography Summary: | Metabolite samples were reconstituted with 50% methanol in 0.1% formic acid spiked with 20ng caffeine. Control and disease individual samples and pooled QC samples (Control pool, disease pool, control+disease pool), and blanks (50% methanol in 0.1% formic acid with 20ng caffeine) (for each sample) were injected and fractionated on to Vanquish Ultra-high performance liquid chromatography (UHPLC) coupled with reverse-phase Q ExactiveTM Plus Hybird Quadrupole-OrbitrapTM mass spectrometer (Thermo scientific, Germany) equipped with heated electrospray ionization (HESI) source. The system maintains the column temperature of 40°C. Metabolites were separated into a Hypersil GOLD™ 1.9 UM 100x2.1 mm column (dim. 100x2.1mm, particle size 1.9 micrometer, C18 column) with a pore size of 175Å. The mobile phase solvents include: Solvent -A: 0.1% formic acid; Solvent -B: 100% methanol, with a flow rate of 0.250 mL/min. The metabolites were eluted with a linear gradient of 30 min (2.0% B for 2 min, 2-50% B for 3 min, 50-75% B for 13 min, 75-95% B for 2 min, 95% B for 5 min, 95-2% B for 2 min, and 2% B for 3 min). |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Hypersil GOLD C18 (100 x 2.1mm, 1.9um) |
| Column Temperature: | 40 |
| Flow Gradient: | 2.0% B for 2 min, 2-50% B for 3 min, 50-75% B for 13 min, 75-95% B for 2 min, 95% B for 5 min, 95-2% B for 2 min, and 2% B for 3 min |
| Flow Rate: | 0.250 mL/min |
| Injection Temperature: | 10 |
| Internal Standard: | Caffeine |
| Retention Time: | 8.54 |
| Sample Injection: | 4 microlitre |
| Solvent A: | 100% water; 0.1% Formic acid |
| Solvent B: | 100% Methanol |
| Analytical Time: | 30 min |
| Capillary Voltage: | 3500 V |
| Oven Temperature: | 40 |
| Transferline Temperature: | 350 |
| Washing Buffer: | 90% Acetonitrile |
| Target Sample Temperature: | 10 |
| Sample Loop Size: | 20 microlitre |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006373 |
| Laboratory Name: | Proteomics |
| Analysis Type: | MS |
| Analysis Protocol File: | IVD_Analysis_protocol.pdf |
| Software Version: | Compound Discoverer 3.3 |
| Operator Name: | Dr. Chitraa Tangavel |
| Detector Type: | Thermo Q Exactive quadrupole orbitrap mass spectrometer |
| Data Format: | .RAW |
| Chromatography ID: | CH004835 |
| Num Factors: | 2 |
| Num Metabolites: | 3187 |
| Units: | Abundance |
