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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 pathform continuously develops and adapts new sample preparation techniques, MS approaches and software tools to provide optimal analytical solutions for individual 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.

Proteomic research at the Cancer Institute is led by Silvia Surinova - Team Lead in Proteomics, supported by Amandeep Bhamra - Mass Spectrometry and Proteomics Specialist and overseen by a scientific committee

How do I start a proteomic collaboration?

In order to establish a proteomic collaboration, you will need to submit a project proposal. Please request a proposal form by email (s.surinova@ucl.ac.uk). Proposal requests 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

Orbitrap Exploris 480 coupled to EASYnLC 1200 

 

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.

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

Would you like to work with us?

The Proteomics Team also includes PhD and MSc students and visiting post-doctoral researchers. If you would like to work with us and have your own funding, do get in touch by email with a brief letter of motivation.

CRUK UCL Centre Proteomic Seminar Series

Our seminars showcase the latest proteomic developments and research highlights from global leaders in the field.

Previous seminars

Proteomics beyond protein expression analysis: Proteomes in 3D

Professor Paola Picotti, Institute of Molecular Systems Biology, ETH Zurich, Switzerland

 Monday 26th of April 2021, 12:00-13:00

Using Network Bioinformatics to Reveal Disease Pathways and Therapies from Proteomic and Genetic Data: Applications to SARS-CoV-2

Dr Mehdi Bouhaddou, University of California, San Francisco

Monday 14th of June 2021, 15:00-16:00

Proximity interactomes: using a reference map of a human cell to navigate cancer signaling and viral infections

Prof Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute of Sinai Health System, Toronto

Thursday 16th of September 2021, 13:00-14:00

Light-mediated discovery of surfaceome nanoscale organization and inter-cellular receptor interaction networks.

Prof Bernd Wollscheid, Institute of Translational Medicine, ETH Zurich, Switzerland

Wednesday 23rd of March 2022, 12:00-13:00