Centre for Arthritis Diagnostic and Therapeutic Innovation - Core Facilities

Metabolomics Core Facility

As an emerging field in systems biology and a new branch in the field of "omics", metabolomics – which is the study of all the small molecules (<1500 Da) within a system – is gaining much interest in the scientific community, particularly in clinical research. Due to the close and near-instantaneous relationship of the metabolome with a biological state (healthy vs. disease), metabolites generally present as rapid indicators of perturbances within a dynamic biological system. As such, metabolomics can be used as a tool in clinical research for determining disease pathology, thereby helping to pave an alternative path towards improved engineering of treatments of various diseases.

At the Schroeder Arthritis Institute's Centre for Diagnostic and Therapeutic Innovation – Metabolomics Core Facility, liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) is the platform of choice for conducting metabolomics studies. Our LC-HRMS equipment – a Thermo Scientific™ Vanquish™ Flex Binary UHPLC system utilized in combination with a Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap™ mass spectrometer (MS) – is dedicated to the evaluation and elucidation of metabolites from biological cells, tissues and fluids. This metabolomics platform provides high accuracy, precision and reproducibility via the high-throughput capabilities of the robust and reliable UHPLC system that can perform superior separation of metabolites originating from complex biological sources. In addition, the MS boasts technology for optimal precursor ion selection, molecular fragmentation, and is equipped with an Orbitrap™ mass analyzer with a resolution of up to 140 000, making it the ideal instrumentation for the identification and analysis of known and/or unknown small molecules.

The Metabolomics Workflow

The Schroeder Arthritis Institute's Metabolomics Core Facility stands as a cornerstone of innovation and research, supervised by Dr. Vinod Chandran and Dr. Mohit Kapoor, and expertly managed by Nikita Looby, Ph.D., a specialist in Solid Phase Microextraction (SPME), Mass spectrometry and Metabolomics.

The steps of the metabolomics workflow are as outlined below.

 

Whether you're considering a new study, hypothesis- (targeted) or non-hypothesis- (untargeted/discovery) driven or seeking to integrate metabolomics into your research, reaching out to the facility is your first step towards achieving significant scientific advancements.

A general price list can be found below. A more accurate quote that is specific to your research needs can be generated by filling out the Request for Quotation.

Schroeder Arthritis Metabolomics Core Facility Price List

Sample Preparation using SPME

LC- HRMS Analysis

Sample Requirements

• For targeted metabolomics projects using a kit, a minimum of 70 µL of sample, per sample is required for targeted analysis. A minimum of 25 samples are required for half kits and a minimum of 65 samples are required for full kit use. A premium will apply for ≤ 25 samples and ≤ 65 samples respectively.
• For untargeted metabolomics projects, a minimum of 48 independent samples is required for sample preparation using SPME. For ≤ 48 samples, a premium will apply.
• Projects with many samples qualify for a high volume discount.

Data Processing

• Compound discoverer 3.3 for untargeted analysis - Included. Additional processing platform (R/R studio) available at additional cost, please inquire if interested.
• LC-Autofit for Metabolomix kits (targeted analysis) - Included
• MetIDQ Oxygen for Biocrates Kits (targeted analysis) - Included

Compound Identification

Tentative compound identification via annotation and preliminary compound fragmentation for untargeted metabolomics analysis is available at additional cost, please inquire.

Data analysis

Not currently available – Coming Soon. All prospective clients are encouraged to have their own biostatistician or statistical team for data analysis UHN offers biostatistics services. Please inquire for more information.

Prices are subject to readjustment.

A more customized and accurate quote can be drafted for your specific needs. Please fill out the “request for quote” form telling us more about your project and research goals to get started!

SAI Metabolomics Core Facility Manager

 

Nikita Looby PhD, with over 7 years of experience, adeptly navigates the facility from complex biological investigations to practical outcomes, overseeing its daily functions, pioneering new analytical techniques, and leading scientific projects. More than her scientific contributions, Dr. Looby is committed to mentoring students, advancing business goals, and enhancing the profile of metabolomics, thereby increasing its visibility and impact. For more information or to start a conversation about potential collaborations, please contact Dr. Looby at Nikita.Looby@uhnresearch.ca

Publications

The Schroeder Arthritis Institute Metabolomics Core Facility has been instrumental in providing metabolomics services for a number of projects.

1. Li, S., Looby, N., Chandran, V., & Kulasingam, V. (2024). Challenges in the Metabolomics-Based Biomarker Validation Pipeline. Metabolites 2024, Vol. 14, Page 200, 14(4), 200. https://doi.org/10.3390/METABO14040200
   
2. Koussiouris, J., Looby, N., Kotlyar, M., Kulasingam, V., Jurisica, I., & Chandran, V. (2024). Classifying patients with psoriatic arthritis according to their disease activity status using serum metabolites and machine learning. Metabolomics, 20(1), 1–12. https://doi.org/10.1007/S11306-023-02079-7/TABLES/4
3. Choksi, H., Li, S., Looby, N., Kotlyar, M., Jurisica, I., Kulasingam, V., & Chandran, V. (2023). Identifying Serum Metabolomic Markers Associated with Skin Disease Activity in Patients with Psoriatic Arthritis. International Journal of Molecular Sciences, 24(20), 15299. https://doi.org/10.3390/IJMS242015299/S1
4. Koussiouris, J., Looby, N., Kulasingam, V., & Chandran, V. (2023). A Solid-Phase Microextraction—Liquid Chromatography-Mass Spectrometry Method for Analyzing Serum Lipids in Psoriatic Disease. Metabolites, 13(8), 963. https://doi.org/10.3390/METABO13080963/S1
5. Koussiouris, J., Looby, N., Anderson, M., Kulasingam, V., & Chandran, V. (2021). Metabolomics studies in psoriatic disease: A review. Metabolites, 11(6). https://doi.org/10.3390/METABO11060375​
   

Informatics Core Facility

The Informatics core brings cost-effective integrative computational biology solutions to the Schroeder Arthritis Institute. We aim to foster collaboration and to help advance the research of Schroeder Investigators working across spectrum of arthritis conditions. The Informatics core is directed by Dr. Igor Jurisica

 

The collaborative process begins by consulting with the Computational Biologist to plan, design and budget for the analyses of interest. Our Computational Biologist will work closely with lab personnel to identify the analyses more appropriate to answer the research questions at hand and will be providing updates at specific checkpoints. After completion of the analyses, details about methods and resources used as well as results in table and publication-ready image format will be provided to the lab contact person.

For quotes and initial consultation, please contact our Computational Biologist, Dr. Chiara Pastrello.​

Biobank Core Facility

 

The Schroeder Arthritis Institute Biobank is one of the largest biobanks with over 500,000 high-quality samples. This biobank is comprised of biospecimens collected from our clinics, national and international collaborators and represents various forms of arthritis:

1. Orthopaedics and Osteoarthritis (OA) Biobank:
   Cohorts include: end-stage OA knee, hip OA, spine OA, ankle OA, shoulder OA, elbow OA and hand OA; early OA knee; post-traumatic knee OA; normal cartilage spine patients; conservative hand patients and a healthy control group from volunteers.
   Samples include longitudinal biofluids such as plasma, urine and whole blood, as well as surgical tissues and synovial fluid.
2. Rheumatology Biobank
   Cohorts include: psoriatic arthritis (PsA); psoriasis (Ps); ankylosing spondylitis (AS); Systemic Lupus Erythematosus (SLE) and healthy controls.
   Samples include derivatives from bio-fluids such as blood, synovial fluid, urine, semen and stool as well as tissue biopsies.

All biospecimens are located in a key-card access, remote temperature monitored location until further analysis is requested. The sample request undergoes ethical monitoring and governance to ensure compliance with all policies and guidelines from the Research Ethics Board and principal investigators are met.

If you are interested in more details about this biobank, please contact our biobank operations co-chairs Kim Perry and Julie Gagnier.​​