Our Services

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

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, standardized 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, summarizing the results and findings, will be generated and provided.
• We apply and use standards and best practices to help our customers achieve regulatory compliance.

• 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.

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

 

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 and develop a new SOP for your study.

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. 

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.

 

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. Contact 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

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

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 and develop a new SOP for your study.

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.