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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 UCL 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 facility continuously develops and adapts new sample preparation techniques, MS approaches and software tools to provide optimal analytical solutions for individual research projects. The PRCF 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 overseen by a scientific committee. The TTP activity is supported by a Mass Spectrometry and Proteomics Specialist, Amandeep Bhamra.

How do I start a proteomic collaboration?

In order to establish a proteomic collaboration, you need to submit a project proposal according to the guidelines below. 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 start.

Guidelines for project proposals

To minimise the evaluation of your proposal, please check that your project description features the following information and layout:

1. Cover page with project title, author(s) and affiliation including head of laboratory (PI).

2. Summary (up to half a page)

3. Project description with a brief introduction, preliminary data and desired objectives (up to 2 pages)

4. Project layout including a preliminary experimental design and detailed hypotheses (one page)

5. Requested technologies, support and training will be determined and added to the proposal upon project selection.

6. References.

7. Sources of project financing.

Please submit your proposal for review to: s.surinova@ucl.ac.uk

Equipment

Q-Exactive Plus coupled to EASY nLC 1000

Thermo Fisher Scientific

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

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.

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 1.4/2.0, 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