Proteomics Research Translational Technology Platform

The Proteomics Research Translational Technology Platform (TTP) offers collaborative proteomics research support for projects at the Cancer Institute and within the CRUK City of London Centre.

The Proteomics Research TTP provides infrastructure for the identification and quantification of proteins and their post-translational modifications (PTMs). This includes expertise in PTM enrichment strategies, peptide separations, state-of-the-art mass spectrometry (MS) for discovery-driven experiments as well as targeted workflows for sensitive and consistent quantitative monitoring of pre-selected sets of proteins. The platform continuously develops new sample preparation techniques, MS approaches and software tools to provide optimal analytical solutions for research projects. The PRTTP should be involved in all stages of a project to facilitate the use of an appropriate experimental design leading to accurate data interpretation.

How do I start a proteomic collaboration?

Please request a proposal form by email to s.surinova@ucl.ac.uk. Proposals are reviewed by the scientific committee and successful proposals will be further discussed between proteomic experts and researchers. Typically, details of experimental conditions, analytical strategies, tailored data analysis and expected results interpretation will be determined prior to collaboration starting.

Equipment

Q-Exactive Plus coupled to EASY nLC 1200

Thermo Fisher Scientific

Liquid Chromatography Mass Spectrometry (LC-MS) used for discovery- and hypothesis-driven peptide-level workflows

Ultimate 3000 BioRS UHPLC

Thermo Fisher Scientific

Offline LC optimised for high pH Reversed Phase peptide fractionation

ScanVac vacuum centrifuge and freezer dryer

Speedvac capable of drying down protein/peptide solutions to dryness in both Eppendorf tube and Falcon tube formats. For booking, please refer to the attached documentation.

SpeedVac Booking Instructions

SpeedVac Booking Instructions

Orbitrap Exploris 480 coupled to EASYnLC 1200

Experimentation

Protein extraction and proteolytic digestion

Generation of digests from whole proteomes or protein complexes

Enrichment of post-translational modifications

Generation of enriched sub-proteomes (phosphorylated, ubiquitinated, ...)

Peptide separation

Fractionation of peptidic mixtures to achieve deep sequencing

Isotopic labelling of peptides

Employed for sample multiplexing and downstream fractionation

Data Analysis

Database searching

To identify proteins and their modifications (Proteome Discover, MaxQuant)

Quantification

To determine protein abundance (MaxQuant, Skyline) in a label-based (e.g. TMT labelling) or label-free manner

Statistics and bioinformatics

Significance analysis of abundance changes (MSstats, Perseus)

Functional bioinformatics

Contacts

Dr Silvia Surinova

Head of the Proteomics Research Translational Technology Platform

Amandeep Bhamra

Mass Spectrometry and Proteomics Specialist

• Location: Lab 502, 4th Floor MS Labs: 425, 426, Paul O'Gorman Building
• TTP contact: ci.proteomicsresearch@ucl.ac.uk

Non-Mass Spec Proteomics

We offer a platform for researchers to purify the protein samples or cell lysates for subsequent measuring of protein-protein interactions or protein detection. We have Akta (Micro and Prime Plus from GE Healthcare) and Octet Red96 (Fortebio) instruments available. In addition, we operate Ettan IPGphor 3 and a Typhoon imager (GE Healthcare) for 2D-DIGE imaging.

Instruments and specifications

Akta Prime

Lab 106

Akta is equipment used for the protein purification via ion exchange, size exclusion or affinity chromatography. Affinity chromatography is the most common way of purifying recombinant proteins. The proteins are genetically modified to contain various tags (His, GST, etc.). Tags have affinity for the molecules on the column (nickel or cobalt ions or glutathione). By applying high pH or high concentration of buffer (imidazole) the purified protein is eluted. Akta Prime maximum pressure applied on the column and the flow rate: max. pressure 1 MPa, max. flow rate 50 ml/min.

Contact: Nicole Jhala (n.jhala@ucl.ac.uk)

Octet Red96

Lab 106

Octet Red96 is used for measuring protein-protein/small molecule affinity and kinetics and the protein concentration. It uses disposable biosensors in the 96 well plate format. The advantage is low operational cost due to the possibility to regenerate the biosensors and absence of micro-fluidic system.

Dip and Read Biosensors - fortebio.com

Typhoon Trio+

Lab 132

Typhoon Trio+ is used for imaging of fluorescent protein gels (SYPRO Ruby, Deep Purple), fluorescent western blots (ECL Plus, ECL Plex), fluorescent nucleic acid stains (SYBR-green). It can also be used as phosphor imager for developing phosphor storage screens.

Contact: Kim Chia (k.chia@ucl.ac.uk)

Book this equipment

Following appropriate training, you will be given access to the relevant booking calendars on the Clustermarket Bookkit system.

---

If you have any comments or queries regarding the CI Translational Technology Platforms please contact us at: ci.ttpfeedback@ucl.ac.uk or come along to one of our drop-in clinics.

Check out our leaflet! 

proteomics_ttp_leaflet

proteomics_ttp_leaflet