our metabolomics services

We provide high quality metabolomics consultancy services, delivering expertise and advice to guide you through your metabolomics studies. From conception and experimental design, through data acquisition, data analysis and guidance in interpreting the results, we provide outstanding input into your research.

How we are different — our support structure

Scientific Lead: One of our highly experienced academic leads will work with you from project conception and planning to guide through the interpretation of the results.

Operations Team: Our professional operations team support all aspects of your project, from set-up through to billing. We will provide regular updates and are on hand to answer any questions relating to your project.

Experienced Researchers: Our team of Experimental Officers and Research Associates are all post-doctoral level researchers with extensive experience of applying metabolomics.

SOPs & Resources: We have substantial experience of working with a range of different sample types and will provide Standard Operating Procedures (SOP's) for the collection and transportation of your samples.

Our metabolomics consultancy services offers you access to world renowned experts in the field, state-of-the-art instrumentation, outstanding operational support, and a high level of service including:

Advice and support from leading scientists in the metabolomics field to design and plan your metabolomics study.

Face-to-face meetings or teleconferences with your scientific lead.

Analysis performed using state-of-the-art instrumentation and data analysis tools.

Guidance to interpret the study results and ensure you have all the information to answer your biological questions.

Outstanding operational and scientific support to deliver your results within a defined timescale.

Our service packages are comprehensively detailed below, but don't worry if you are not sure which choice is best for you. Contact us today and one of our experts will get in touch to advise which option is best suited for your project.

Option 1: Untargeted Metabolomics Service

Untargeted metabolomics is applied when a broad survey of different metabolite classes is required, typically used in discovery based studies when you have no previous knowledge of the metabolites of interest. We recommend two complementary chromatography methods and analysis in both positive and negative ion modes to maximise the number of metabolites detected. Each assay provides the relative quantification of low thousands of metabolites. We apply robust and rigorous quality assurance across all steps in the project workflow.

Our price per sample is all inclusive of the below, from your initial project consultation through to your final report.

What we provide

Your scientific lead can discuss the most suitable technique with you upon initial project consultation and experimental design.

Analytical

We have established analytical workflows that apply state of the art analytical techniques including:

Ultra-high performance liquid chromatography coupled to high resolution mass spectrometry (UHPLC-MS)
Producing high quality data representing thousands of metabolites present in diverse areas of metabolism including amino acid metabolism, lipid metabolism and purine metabolism.
Nuclear magnetic resonance (NMR) spectroscopy
For a broad coverage of high concentration lipophilic and hydrophilic metabolites; typically up to a hundred metabolites are detected.
Direct infusion mass spectrometry (DIMS)
Applied when sample amounts are limited, polar and non-polar assays are available.

Computational

With years of research and development experience in the field of computational metabolomics, we have established an extensive portfolio of computational solutions to process and analyse high dimensional metabolomics data.

Our computational services at a glance:

Well-established, standardised and reproducible workflows.
Workflows cover a broad range of methods and approaches, including data processing and quality control, biostatistics and machine learning, and metabolite identification.
We adapt and optimise our workflows to match the experimental design and exploit the full potential of the data.
Leveraging our pre-existing workflows, and scalable and robust compute resources we have the ability to provide a quick and reliable turnaround time.
A detailed and standardised project report, summarising the results and findings, will be generated and provided.
We apply and use standards and best practices to help our customers achieve regulatory compliance.

How we provide it

Analytical

Ultra-high performance liquid chromatography coupled to high resolution mass spectrometry (UHPLC-MS)

Our suite of High Mass Resolution Mass Spectrometers includes:

Three Thermo Scientific™ UltiMate™ 3000 UHPLC systems coupled to Q Exactive™ Focus mass spectrometers.

Three Waters™ ACQUITY UPLC® systems coupled to Xevo™ GS-XS QToF mass spectrometers.

Each instrument is assigned to a specific UHPLC assay to provide parallel analysis of your samples. Three assays are available:

Hydrophilic interaction liquid chromatography (HILIC) UHPLC-MS providing a broad coverage of hydrophilic metabolites.

Two reversed phase UHPLC-MS assays providing broad coverage of lipophilic metabolites, one method for cells or tissue samples and one method for urine analysis.

Nuclear magnetic resonance (NMR) spectroscopy

1D ¹H- and 2D J resolved ¹H-NMR spectroscopy in the untargeted analysis using two Bruker™ 600MHz IVDr NMR spectrometers each equipped with a room temperature 5 mm probe and a SampleJet automatic sample changer.
Various 2D NMR spectroscopic methods, such as 2D J-res, COSY, TOCSY, NOESY, HSQC and HMBC are available for the identification of metabolites.

Direct infusion mass spectrometry (DIMS)

One LTQ-Orbitrap Elite mass spectrometer with nanospray infusion via an Advion Triversa Nanomate is applied in our direct infusion assays.

Computational

Our robust, scalable and secure informatics infrastructure includes:

BlueBEAR supercomputer - high performance computing cluster employs some of the latest solutions and technology to deliver fast and efficient processing capacity.

Well-established, standardised and reproducible workflows build from a combination of open-source and proprietary software and tools.

Sample types

Sample Types

Our team of researchers have developed and evaluated standard operating procedures to prepare samples from a diverse range of biological samples. We have robust SOPs to extract metabolites from all types of clinical samples, cells, culture media and many model organisms.

If your sample type is new to us, our team of experienced researchers will develop a new SOP for your study.

Sample Collection and Shipping

Appropriate sample collection, storage and shipping is essential to guarantee the quality of your samples when working in the metabolomics space. Our operations manager will provide sample collection and shipping guidelines to ensure your samples reach us in optimal conditions.

Sample Type Examples:

Serum/ Plasma
Urine
Cells (mammalian, suspension or adherent)
Cerebrospinal fluid (CSF)
Dried Blood Spots (DBS)
Tissue
Saliva
Model organisms; (e.g. Daphnia magna)

Metabolite Identification

Metabolite annotation / identification is a recognised major challenge in metabolomics. The Phenome Centre Birmingham Directors have been working on this challenge for the last 17 years, and continue to push boundaries, leading and engaging with collaborative networks and partnerships - such as the Metabolomics Society Metabolite Identification Task Group (Dunn - Chair) - to maximise coverage and confidence in the identifications we provide.

For Phenome Centre Birmingham workflows, we address this challenge in several ways:

We have incorporated the latest analytical developments and bioinformatics tools in our annotation / identification workflows, and continue to update and optimise workflows as new developments and tools are created.

We run all data collected through our in-house annotation workflow, Birmingham mEtabolite Annotation for Mass Spectrometry (BEAMS).

We run multiple Data Dependent Analysis experiments on project specific pooled QCs to maximise MS/MS data collected during the initial analysis. The MS/MS data is used to search external databases including Thermo Scientific™ LipidSearch™, mzCloud™, and our in-house spectral library containing ~300 metabolites.

We apply accurate mass and MS/MS data and retention time (for metabolites in our in-house database) to provide confidence in the metabolites we identify.

View our Untargeted Metabolomics project workflow

Our facility has established workflows in place, designed to provide optimal support on a stage-by-stage basis, ensuring that you receive the best possible results from our service.

1. Scientific Lead

Your scientific lead is the primary contact for the duration of the project. They will guide you through the experimental design and select the appropriate methods for your study.

2. Project Setup

Our operations manager will support your project set-up including ethics, contracts and any specific project requirements and once complete, provide guidance on how samples should be shipped to us.

3. Sample Preparation & Data Acquisition

Sample preparation and data acquisition will be undertaken by a dedicated analytical specialist using our optimised methods.

4. Metabolite Identification

Accurate mass, retention time and MS/MS data acquired via Data Dependent Analysis on project specific pooled QCs is applied to search internal and external databases.

5. Data Processing & Data Analysis

Our bioinformatics and biostatistics team will process the data, run our quality assurance procedure and perform the data analysis using defined workflows.

6. Our team will compile a report

Your report will be complied by our team of experts and reviewed by your scientific lead.

7. Delivering your results

Your scientific lead will communicate directly with you via face-to-face meeting or teleconference to aid your interpretation of the results.

Contact us about your project

Do you need an outstanding collaborative metabolomics service?

Get in touch with us about your project today!

Option 2: Targeted Metabolomics Service

In targeted metabolomics we focus on a small number of specific metabolites. This approach is typically applied to validate results from discovery-based studies and in translational studies. Our assays are developed for research use only and provide absolute quantification of the metabolites.

With our targeted metabolomics service using an assay from our portfolio, our price per sample is all inclusive of the below, from your initial project consultation through to your final report. If we do not have a targeted method suitable for your project, we can design a new assay to suit your project.

What we provide

Targeted Assays

We can develop and validate customized assays on request in a variety of biological matrices, including biofluids (serum, plasma, urine), tissue, cells and cell media. C ontact us today and one of our experts will get in touch to discuss developing a suitable assay for your project.

Our portfolio of current assays includes:

Amino acids
- Measures free amino acid
- Validated in plasma, urine, tissue

Bile acids
- For the quantification of Taurocholic acid, Glycodeoxycholic acid, Taurodeoxycholic acid, Ursodeoxycholic acid, Taurolithocholic acid, 3-oxo-7a,12a-hydroxy-5b-cholanoic acid
- Validated in plasma

Caffeine related metabolites
- For the quantification of caffeine, paraxanthine, theobromine, theophylline
- Validated in plasma and urine

One carbon metabolism metabolites
- For the quantification of methionine, pyridoxine, homocysteine, S-adenosylhomocysteine (SAH), S-adenosyl methionine (SAM), folic acid, 5-methyltetrahydrofolate (5MTHF), vitamin B12
- Validated in tissue

Citrulline quantification
- Validated in plasma

Sugars
- Mannitol, lactulose and sucralose
- Validated in urine for gut permeability testing

Β-Aminoisobutyric acid
- Validated in plasma, α and ϒ forms also detected

Sphingosine-1-phosphate
- Validated in plasma

How we provide it

Analytical

Ultra-high performance liquid chromatography coupled to high resolution mass spectrometry (UHPLC-MS)

Two Thermo Scientific™ UltiMate™ 3000 UHPLC systems coupled to TSQ Quantiva™ triple quadrupole mass spectrometers are applied in the UHPLC-MS/MS assays to quantify metabolites in the targeted panels.

Data Processing

Data is processed using Thermo Scientific™ TraceFinder™ software and reviewed by our targeted specialist and the scientific lead.

Sample Types

If your sample type is new to us, our team of experienced researchers will develop a new SOP for your study.

Sample Collection and Shipping

Sample Type Examples:

Serum/ Plasma
Urine
Cells (mammalian, suspension or adherent)
Cerebrospinal fluid (CSF)
Dried Blood Spots (DBS)
Tissue
Saliva
Model organisms; (e.g. Daphnia magna)

View our Targeted Metabolomics project workflow

Our facility has established workflows in place, designed to provide optimal support on a stage-by-stage basis, ensuring that you receive the best possible results from our service.

1. Scientific Lead

Your scientific lead is the primary contact for the duration of the project. They will work with you to decide if we have a targeted method suitable for your project and if not design a new assay for your project.

2. Project Setup

Our operations manager will support your project set-up including ethics, contracts and any specific project requirements and once complete provide guidance on how samples should be shipped to us.

3. Sample Preparation & Data Acquisition

Our targeted specialist will develop and validate a new assay (if required), prepare and analyse your samples.

4. Data Processing & Data Analysis

Our targeted specialist will process the data, calculate the concentrations in your samples and perform quality assurance checks according to FDA guidance.

5. Our team will compile a report

Our targeted specialist and the project scientific lead will compile a report.

6. Delivering your results

Your scientific lead will communicate with you directly to aid your understanding of the results.

Contact us about your project

Do you need an outstanding collaborative metabolomics service?

Get in touch about your project today!

Option 3: Additional Metabolomics Services

We are able to support many requirements; offering a fully bespoke service. Please contact us to see if we can help.

View our Additional Services

Data Submission to Repositories

We are able to provide submission of data to MetaboLights and/or Metabolomics Workbench.

Metabolite Identification

We can also offer a bespoke service to identify unknown metabolites using a combination of solvent / SPE / chromatographic fractionation, NMR spectroscopy and sequential mass spectrometry fragmentation (MSⁿ) experiments.

Biocrates - AbsoluteIDQ^® p400 HR Kit

Phenome Centre Birmingham acted as one of the test sites for the international ring trial to evaluate the reproducibility of the AbsoluteIDQ^® p400 HR Kit in human serum and plasma.

The kit provides quantification of up to 408 metabolites and lipids form 11 compound classes covering central metabolic pathways.

Want to learn more about our methods?

We use thoroughly developed, established, state-of-the-art, peer-reviewed analytical and computational methods, some of which are listed below:

Metabolomics Services

How we are different — our support structure