Study Data


MS Study

Project uploaded by: Joveeta
Project ID: IMP_100076
Title: Integrated Metabolite and Lipid Profiling of Human Vitreous Reveals Purine Metabolic Dysregulation and Inflammatory Lipid Remodeling as the Drivers of Bacterial Endophthalmitis
Project Description: Bacterial endophthalmitis, an intraocular infection and inflammation often progress rapidly and lead to irreversible vision loss especially in culture-negative cases where the diagnosis is delayed. We profiled infection-associated metabolomic and lipidomic alterations in the vitreous of patients with microbiological and clinically confirmed bacterial endophthalmitis to understand pathogenesis and identify distinct markers that drive infection and retinal injury.
Research Area: Biological Sciences
Funding Source: Hyderabad Eye Research Foundation
Project Contributors: Joveeta Joseph, Dhanwini Rudraprasad, Agimanailiu Khapuinamai, Sreyasi Maiti, Satyashree Gagan

Study uploaded by: Joveeta
Study ID: IMS_100076
Title: Integrated Metabolite and Lipid Profiling of Human Vitreous Reveals Purine Metabolic Dysregulation and Inflammatory Lipid Remodeling as the Drivers of Bacterial Endophthalmitis.
Summary: Bacterial endophthalmitis is a severe intraocular infection in which rapid inflammation, metabolic stress, and retinal injury can lead to irreversible vision loss. This study aimed to characterize infection-associated metabolic and lipid alterations in the human vitreous and identify biochemical signatures that may provide insight into disease pathogenesis and support culture-independent biomarker discovery. Undiluted vitreous samples were collected from 31 patients undergoing pars plana vitrectomy, including 16 patients with clinically and microbiologically confirmed bacterial endophthalmitis and 15 patients with non-infectious retinal conditions serving as controls. Samples were collected during surgery, processed rapidly, and stored at −80°C until analysis. Untargeted metabolomic and lipidomic profiling was performed using liquid chromatography–tandem mass spectrometry (LC–MS/MS), enabling broad characterization of small-molecule metabolites and lipid species. Following data normalization and statistical filtering, differential features were evaluated using multivariate analyses and pathway enrichment to identify biological processes associated with infection. The study revealed distinct metabolic and lipidomic profiles in infected vitreous, with alterations involving purine, amino acid, polyamine, redox, and vitamin metabolism, together with extensive remodeling of fatty acids, eicosanoids, bile acid derivatives, and membrane lipids. These findings provide a comprehensive view of the biochemical reprogramming associated with bacterial endophthalmitis and identify candidate molecular pathways for future diagnostic and therapeutic investigation.
Publication:
Release Date: Sept. 21, 2026
Study Type: Mass Spectrometry (MS)
Data Type: Untargeted
IEC/IBSC Approval Number : LEC-BHR-P-05-23-1045

Sr.No Sample ID Sample Name Organism Source Sample Preparation Protocol Sample Type Experimental Condition Time of treatment Variant/Variety Gender Age Replicates Storage Conditions Extraction Protocol Number of files per sample
21 IMSM_105435 Infected_6 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 31 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
22 IMSM_105436 Infected_7 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 51 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
23 IMSM_105437 Infected_8 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 40 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
24 IMSM_105438 Infected_9 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 48 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
25 IMSM_105439 Infected_10 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 50 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
26 IMSM_105440 Infected_11 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 61 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
27 IMSM_105441 Infected_12 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A F 72 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
28 IMSM_105442 Infected_13 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 66 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
29 IMSM_105443 Infected_14 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A M 67 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2
30 IMSM_105444 Infected_15 Homo sapiens | 9606 Human Vitreous Vitreous humor samples stored at -80°C were thawed on ice (4°C) prior to processing. 150 µL of thawed vitreous humor was used per sample for downstream extraction. Human Vitreous Infected N/A N/A F 61 3 -80℃

Untargeted metabolomic/lipidomic profiling via reverse-phase LC-MS/MS on a Zorbax SB-Aq RRHD column (3.0 × 150 mm, 5.0 µm). Mobile phases: water + 0.2% acetic acid (A), methanol + 0.2% acetic acid (B). Gradient: 5-35% B (0-15 min), 35-95% B (15-20 min), hold 95% B (20-25 min), re-equilibrate (25.1-32 min); flow 0.5 mL/min, 40°C column, 15°C autosampler. Analyzed on a TripleTOF 5600+ (Sciex) with DuoSpray source (550°C), positive/negative ESI, m/z 50-1000, IDA mode, collision energy 35.

 2

Sr.No MS Exp ID Sample Name/ID Mass Spectrometer Type MS Instrument Name MS Instrument type MS Ionization Method Ion Mode/Scan Polarity Data Transformation (Software/s Used)
1 IME_104526 Control_1 / IMSM_105415 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.6
2 IME_104527 Control_1 / IMSM_105415 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.6
3 IME_104528 Control_2 / IMSM_105416 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.7
4 IME_104529 Control_2 / IMSM_105416 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.7
5 IME_104530 Control_3 / IMSM_105417 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.8
6 IME_104531 Control_3 / IMSM_105417 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.8
7 IME_104532 Control_4 / IMSM_105418 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.9
8 IME_104533 Control_4 / IMSM_105418 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.9
9 IME_104534 Control_5 / IMSM_105419 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.10
10 IME_104535 Control_5 / IMSM_105419 Duo Spray Ion Source ABI Sciex 5500 QTrap Triple TOF Electrospray Ionization - ESI Positive;Negative Analyst TF 1.10

Sr.No First name Last name Email Organization Designation
1 Satyashree Gagan satyashree.gagan@gmail.com LV Prasad Eye Institute postdoctoral_researcher
2 Sreyasi Maiti sreyasideeni@gmail.com LV Prasad Eye Institute research_scholar
3 Agimanailiu Khapuinamai agimanailiu@gmail.com LV Prasad Eye Institute research_scholar
4 Dhanwini Rudraprasad satyashree.gagan@lvpei.org LV Prasad Eye Institute research_scholar
5 Joveeta Joseph joveeta@lvpei.org LV Prasad Eye Institute principal_investigator

Sr.No ftprun ID MS Exp ID MS Data Files
1 IMR_105130 IME_104526 Control_P1.xlsx
2 IMR_105131 IME_104527 Control_P2.xlsx
3 IMR_105132 IME_104528 Control_P3.xlsx
4 IMR_105133 IME_104529 Control_P4.xlsx
5 IMR_105134 IME_104530 Control_P5.xlsx
6 IMR_105135 IME_104531 Control_P6.xlsx
7 IMR_105136 IME_104532 Control_P7.xlsx
8 IMR_105137 IME_104533 Control_P8.xlsx
9 IMR_105138 IME_104534 Control_P9.xlsx
10 IMR_105139 IME_104535 Control_P10.xlsx

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