Babraham Institute

The Mass Spectrometry Facility uses the latest approaches and develops novel methods to analyse biological molecules, particularly proteins and nucleic acids.

The Babraham Institute Mass Spectrometry Facility staff have many years of hands-on experience, performing experiments using a wide range of mass spectrometry techniques and instruments. The team can help with all aspects of mass spectrometric analysis including, experimental design, input into grant writing, sample preparation, generating the mass spectrometry data and data interpretation.

Technology Overview

Mass spectrometry is a very powerful technique which can be used for the analysis of biological molecules. It is used extensively to detect and quantify molecules of interest, even at very low concentrations and in extremely complex backgrounds, but it can also be used in the determination of molecular structure - from precise details of primary structure, to protein folding and 3D structure. It is also the standard means for data acquisition in various “omics” methods (e.g. proteomics, metabolomics etc.). The Mass Spectrometry Facility works with colleagues in the Institute research groups to utilise the power of mass spectrometry to help understand the molecular processes that drive key biological functions.

Facilitiy Expertise

The Facility has expertise in all aspects of mass spectrometric analysis and is able to meet a wide range of analytical challenges, for example:

• Accurate mass measurement of an intact protein (<10ppm)
• Peptide mapping by LC-MS/MS
• Protein identification (and relative quantification) in:
  • Purified samples (e.g. gel band)
  • Moderately complex samples (e.g. immunoprecipitated protein complex)
  • Highly complex samples (e.g. subcellular fraction or total cell lysate)
• Identification and localisation of protein post-translational modifications
• Development of quantitative LC-MS/MS assays for the analysis of specific proteins in complex matrices
• Quantification of modified bases (e.g. 5-methylcytosine and 5-hydroxymethylcytosine in DNA and oxidation in RNA) 

The Mass Spectrometry Facility also offers some services to external scientists from academia and industry, including:

• Consultancy
• Fee-for-service standard analyses of proteins (e.g. protein identification and peptide mapping)

Equipment

The Facility is equipped with three state-of-the-art high‑resolution tandem mass spectrometers, all with nanoLC systems for online LC-MS analyses.

• Thermo Scientific Orbitrap Astral mass spectrometer
• Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer
• Thermo Scientific Q Exactive Plus hybrid quadrupole-Orbitrap mass spectrometer

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The Genomics facility at the Babraham Institute provides researchers with access to cutting‑edge technology to advance their research.

The Facility can advise researchers on the sequencing platform and run type that provides the sequencing depth, read length and turnaround time that best suits their project. Facility staff also analyse sequencing library Quality Control results and provide guidance on their interpretation and expected sequencing results. The Facility has recently expanded their library preparation offering both in 10x Genomics and bulk RNA library preparation areas.

The Babraham Institute established the Genomics Facility in 2009, with investment from the Biotechnology and Biological Sciences Research Council (BBSRC) and Medical Research Council (MRC), in partnership with the University of Cambridge’s Centre for Trophoblast Research. The Facility has grown since and is playing a crucial role in the Institute’s research projects on epigenetics, chromatin regulation, cell signalling and immunology.

Technology Overview

Genomics Facility Services:

• Sequencing:
  • Short-Read Sequencing: Available on Element Biosciences AVITI and Illumina MiSeq instruments, supporting both single- and paired-end runs. Sequencing workflows are tailored to suit your research needs.
  • Long-Read Sequencing: Conducted using Oxford Nanopore Technologies library preparation kits and sequenced on our PromethION P2 devices, offering solutions for projects requiring extended read lengths.
• Library Preparation:
  • Comprehensive library preparation services for diverse sample types, including DNA, RNA, single cells, and cDNA, across various input amounts.
  • Bulk RNA-seq: Prepared using Watchmaker Genomics kits for poly(A) enrichment or rRNA depletion. Ultra-low input libraries are created with Takara’s SMART-seq mRNA library prep kit.
  • 10x Genomics Applications: Includes library preparation for gene expression, immune profiling, Multiome ATAC + gene expression, and the Flex fixation assay, enabling high-resolution single-cell experiments.
• Sample Quality Control
  • Advanced quality control with instruments for fragment analysis, qPCR-based quantification, and automated size selection.
  • Services include:
    • Agilent TapeStation for fragment analysis.
    • qPCR Quantification assays for accurate library measurements.
    • BluePippin for automated size selection to meet project specifications.

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The Babraham Gene Targeting Facility offers expert advice in genome editing, particularly embryo targeting and genotyping strategies, as well as methodologies for producing your own gene‑targeting reagents. The Facility provides a bespoke service for genotyping your gene-edited cell lines.

To produce new mouse models, we target mouse zygotes directly using CRISPR/Cas9 technology. Using this approach, we can generate a wide variety of mouse models, including knockouts, deletions and knock-ins. Typically projects can be completed within 6 months with a high success rate. Further, we have extensive experience with gene tagging i.e. adding specific tags such as HaloTag and MiniTurbo on to genes. Every newly generated mouse line undergoes extensive QC including sequencing by Nanopore and checking copy number by ddPCR.

Technology Overview

Training and Support

The experienced gene targeting specialist at the Gene Targeting Facility can provide expert guidance in CRISPR/Cas9-based genome editing. The GTF can assist making any type of genome modification, including single point mutations, deletions, gene tagging and creating Cre/Dre driver models. The Facility can assist from all stages; project genesis, CRISPR/Cas9 reagent procurement, transfection methodology, genotyping and QC. Projects that depend on homology directed repair (HDR), the GTF can assist in donor design DNA templates for knock-in projects. The Facility provides practical advice and design strategies for advanced cloning strategies including Gibson assembly.

Services

• Guidance on using Cas proteins to genome engineer your own cell line.
• Developing high through-put genotyping strategies.
• ddPCR for checking Copy Number (CN) and concatemers.
• Troubleshooting strategies.

Use of CRISPR/Cas9 technology to produce gene‑edited mouse models

To produce new mouse models, The Facility targets mouse zygotes directly using CRISPR/Cas9 technology. Using this approach, The Facility can generate a wide variety of mouse models, including Knock-outs, deletions and Knock-ins. These models can typically be completed with 6 months with a high success rate. Further, The Facility staff have extensive experience with gene tagging i.e. adding specific tags such as HaloTag, MiniTurbo or NanobiT on to genes. Every newly generated mouse line undergoes extensive QC.

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The Babraham Institute Flow Cytometry facility provides services to support the work of scientists from both the Institute and external companies. These include an expert cell sorting service, analyser training and use, help with experimental design, panel design, analysis of samples, troubleshooting, and data analysis.

Headed by Dr Rachael Walker, the knowledgeable flow cytometry team have a combined cytometry experience of over 30 years and extensive knowledge in a variety of flow cytometry applications. Within the facility there are both self-use analysers (after training) and cell sorters that are run as a service. Expert advice is available on experimental design, training on machine, post-acquisition analysis of data, help with interpreting the data and producing figures for publication.

Consultancy work on panel design, buying your own cytometer and bespoke training in flow cytometry is also available.

Technology Overview

Analysers:

• The Facility offers nine high-end analysers that are available for self-use after training or can be run as a service.
  • 3 x Cytek Aurora full spectrum analysers ( 5 lasers, 67 parameters)
  • Sony ID7000 full spectrum analyser (7 lasers, 188 parameters)
  • 2 x BD LSRFortessa analysers (5 lasers, 20 parameters)
  • ThermoFisher Attune CytPix (4 lasers, 16 parameters, and brightfield images)
  • Bio-Rad ZE5 high-throughput analyser (5 lasers, 30 parameters)
  • Cytek ImageStream MkII (4 lasers, 12 parameters) with the high gain mode and machine learning upgrades
• A FlowJo (flow cytometry analysis software) site licence is available for all commercial companies using the facility.

Cell Sorting Service:

• The Facility houses nine high-end cell sorters which are run as a service by experienced cytometrists. The Facility offers 96/384 well plate sorting as well as bulk sorting of populations (up to 500 million cells per instrument per day).
  • Cytek Aurora CS (full spectrum, 5 lasers, 67 parameters)
  • 3x ThermoFisher Bigfoot (full spectrum, 9 lasers, 58 parameters) housed in a containment hood
  • BD FACSAria III (4 lasers, 17 parameters)
  • BD FACS Aria Fusion (5 lasers, 20 parameters) housed in a BSL2 containment hood
  • 3x FACSJazz (3 lasers, 8 parameters) housed in a BSL2 containment hood

Flow Cytometry Training Courses:

These interactive lecture and exercise-based courses are given by experts in the field who share their in-depth knowledge of an evolving technology. Ideal for those using flow cytometry in industry and academic settings, these provide delegates with skills in designing, performing, analysing and presenting flow cytometry data.

The Babraham Institute is offering the following flow cytometry courses in 2025:

• Introduction to Flow Cytometry
• Advanced Flow Cytometry
• Practical Cell Sorting
• Practical Data Analysis
• Practical Spectral Flow Cytometry
• Practical Imaging Flow Cytometry

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The Biological Support Unit (BSU) is recognised as a leading facility in its field, providing housing and care for rodents at a highly defined health status. There are four internal units offering the highest standards of welfare with fully trained technicians offering excellence in husbandry and procedural technique to support both academic and commercial scientific research programmes.

In April 2025 accreditation for AAALAC International was reconfirmed, following the facility's initial accreditation in February 2022. This voluntary accreditation is evidence that the Institute and the BSU is taking extra steps to achieve excellence in animal care and use. The BSU animal technicians hold Home Office Personal Licences enabling the BSU to provide technical support for researchers. The team have a commitment to up-hold the highest standards of animal welfare in all aspects of their work.

The BSU is made up of four bio-science units, each performing a unique role in the provision of flexible services to meet the ever-changing needs of biological research. The four units are arranged around a central services unit which utilises robotic cage-washing technology and automated sterilisation processes to provide equipment and consumables to each unit. The BSU has a mix of animal technicians and service technicians who perform daily husbandry duties and provide essential services to the facility.

Technology Overview

Areas of Expertise

Extensive expertise in the Facility provides researchers with substantial support:

• Facility animal technicians have in-depth knowledge of animal health barrier maintenance and husbandry, and are fully trained in the use of state-of-the-art animal housing systems and containment procedures. Technicians gain nationally recognised qualifications awarded by the Institute of Animal Technology and hold Home Office Personal Licences which permit them to perform regulated procedures.
• Key staff hold further positions of responsibility under the Institute Establishment Licence. These include NACWO (Named Animal Care and Welfare Officer) and NTCO (Named Training and Competence Officer) roles.

Equipment

• Independently ventilated caging systems and containment facilities
• High level bio-secure and independently ventilated caging systems and containment facilities
• Flexible film isolators
• Open cage environments
• Containment Level 2 suites
• Containment cabinets, change stations and down-draft benching

Services

• Rooms in the Facility are designed to offer flexible layout and usage options enabling the team to respond to changing user requirements, including multi-species housing.
• A range of services are available to external clients, including:
  • Rederivation of mouse lines,
  • Embryo cryopreservation,
  • Sperm freezing,
  • IVF
  • Procedure training and assessment
  • Management of experimental cohorts (key procedures include)
    • Microchipping
    • Body weights
    • Tumour studies
    • Multi-site/multi‑route injections and dosing
    • Blood sampling
    • Tissue dissection
    • Liver perfusion (rat)
    • Pharmacokinetic studies
    • Immunisation studies
    • Behavioural studies
    • Tissue sampling for genotyping

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The Babraham Bioinformatics Facility can support all your computational biology requirements. The team is composed of experienced bioinformaticians and statisticians, all of whom have a biological background. The Facility is happy to provide advice or practical assistance on how to apply computational methods to extract biological meaning from your data.

Technology Overview

The Babraham Bioinformatics Facility supports research through:

• Bioinformatics Services:
  • The facility’s experienced bioinformaticians can offer advice or practical assistance in the processing and analysis of a wide variety of different types of biological data.
  • The facility has extensive experience of analysing high-throughput sequencing data including RNA-Seq, ChIP-Seq, Hi-C and many epigenetic sequencing techniques, both on bulk and single cell data.
  • The facility can develop custom applications or pipelines to meet your specific requirements. The facility’s range of publicly available software is used by bioinformaticians worldwide and the bioinformaticians can bring their experience to your projects.
• Consultancy:
  • The facility has worked with over 170 individuals at the Babraham Institute and 22 external companies. The Bioinformatics Facility team can help with everything from experimental design to reporting, or just with one part of the process.
  • The facility can develop custom pipelines and applications to suit your needs.
• Training:
  • During 2021, more than 600 delegates from The Babraham Institute, Babraham Research Campus companies and other organisations around the world (including European Bioinformatics Institute, Institute of Cancer Research, University of Cambridge, The Crick Institute, ETH Zurich, Astra Zeneca, and CRAGenomica in Barcelona), were trained by the facility.
  • The facility offers a wide variety of practical bioinformatics and statistics training courses taught by experienced bioinformaticians.
  • The modular courses can be tailored to your needs at a convenient venue, alternatively delegates may attend the series of courses run at the Babraham Institute.
• Statistics:
  • The facility can provide the assistance of an experienced bio-statistician to help with experimental design, data analysis or grant applications.
• Infrastructure:
  • The facility can provide access to a large bioinformatics computer cluster to allow you to run large computationally demanding workflows.
  • The facility can assist with the design and implementation of data management and processing infrastructure for your own pipelines.
  • The facility team can write and host targeted infrastructure for researchers, such as an interactive web application to support publications.
  • The team are happy to provide assistance on how to apply computational methods to extract biological information from your data.

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