LPDG

-- The London Proteomics Discussion Group --
Proteomics seminar series for the South East

Next Webinar LPDG-YPIC Mini Challenge
Proteomics seminar series for the South East
Discussion
Networking
Methods Challenge
---Registration is free---

About the LPDG

We are a free, local proteomics seminar series in the South East,
with a focus towards networking, discussion and supporting early career researchers.

The LPDG...

was founded to bring together the large community of proteomics scientists all working in and around London. We aim to provide a space for discussion, with a focus on methods and early career researchers (two fundamental building blocks of good research!), on all topics related to proteomics. The meetings comprise of research talks framed by a proteomics methods challenge, lunch, refreshments and pizza - they are free to attend thanks to sponsorship.


Meeting Dates:

Next Meeting

Sponsors

These seminars would not be possible without our amazing sponsors.
If you are interested in sponsoring an LPDG seminar,
please get in touch at sponsor@londonproteomics.co.uk

LPDG-YPIC Mini Challenge

The LPDG have teamed up with YPIC to produce a proteomics-challenge with Prize money sponsored by Matrix Science. To find out more and view the current challenge,

click here!

Webinar Programme


Proteomics: Protein-Protien Interactions

04th December 2020 14:00 GMT

Dr Isabell Bludau

Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect and quantify protein complexes with high selectivity and statistical error control via the computational framework CCprofiler (https://github.com/CCprofiler/CCprofiler). Complex-centric proteome profiling captures most proteins in complex-assembled state and reveals their organization into hundreds of complexes and complex variants observable in a given cellular state. The protocol is applicable to cultured cells and can potentially also be adapted to primary tissue and does not require any genetic engineering of the respective sample sources. At present, it requires ~8 d of wet-laboratory work, 15 d of mass spectrometry measurement time and 7 d of computational analysis.

Publication

Dr Andreas Damianou

Profiling dynamic K-Ras interactomes via optimised APEX-2 proximity labelling

Several recently developed proximity labelling techniques such as BioID, TurboID and APEX-2 add to the arsenal of methods that enable the capture of protein-protein interactions as well as the exploration of different molecular and cellular environments. A hallmark of APEX-2 proximity labelling is that it occurs at a timescale of seconds, which is advantageous for the capture of transient interactions as well as fast molecular changes. In this study, APEX-2 proximity labelling was applied in conjunction with LC-MS/MS to investigate the dynamic protein-protein interactions of the oncogene K-Ras. K-Ras is a small GTPase which acts as a transductor protein to deliver signals from an external environmental stimulus to the cell nucleus, controlling several essential functions such as progression of cells through the cell cycle, promotion of angiogenesis, cellular adhesion, migration and cell invasion. Ras GTPases have the ability to bind either to GTP or GDP, which is essential for its role as a molecular switch. This role is apparent in the case of serum-starved cells, where it primarily binds to GDP, which inactivates K-Ras and shuts down its signal transduction. K-Ras activating mutations have been previously described as cancer driving mutations that can lead to cellular transformation as well as an increase in chemotherapy resistance. Here, APEX-2 labelling was used to compare wild type K-Ras to three activating mutations, G12D, G13D and Q61H, respectively, under both starvation and FCS stimulation conditions. These conditions allowed for the clear elucidation and comparison of the environment and interacting partners of K-Ras, both in its active and inactive forms. This study gives us the opportunity to evaluate several steps that are critical for a successful proximity labelling experiment such as correct localisation of the bait protein as well as appropriate protein expression levels. Additionally, data were analysed using different methods, including SAINTexpress, to identify which method is more appropriate and reliable. The identification of several known interactors of K-Ras including a-RAF and LZTR1 indicate the ability of this approach to capture interaction partners. We further examine how these protein’s interactions and the K-Ras environment vary with the different mutations, revealing unique protein interactors of different K-Ras mutants under different environmental conditions.

Event Speakers

Would you like to present at an LPDG meeting? Email: speaker@londonproteomics.co.uk
Research presentations from:

Dr Isabell Bludau
Dr Isabell Bludau
Dr Isbell Bludau Max Planck Institute of Biochemistry,
Munich

Dr Bludau is a postdoctoral researcher in Prof. Matthias Mann’s lab at the Max Planck Institute of Biochemistry near Munich. During her Ph. D. with Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology, ETH Zurich, Isabell contributed to the development of software for analyzing large-scale data-independent acquisition (DIA) mass spectrometry datasets. She specifically focused on computational strategies for detecting and quantifying protein complexes from data generated by native co-fractionation coupled to DIA. In her postdoctoral research, Isabell studies molecular signaling pathways mediated by post-translational modifications and their crosstalk.

Dr Andreas Damianou
Dr Andreas Damianou
Dr Andreas Damianou Target Discovery Institute,
University of Oxford

Dr Damianou studied at the University of Leicester for both his Bachelor’s degree in Medical Microbiology and his master’s degree in Infectious and Immunity. He then received an MRC Doctoral Training studentship to join Prof. Jeremy Mottram’s lab at the University of Glasgow. During his PhD, he focused on identifying and characterising Leishmania Deubiquitinase enzymes. After the completion of his PhD he moved to a postdoc position with Prof. Benedikt Kessler in the Nuffield Department of Medicine, Oxford where he is currently using proximity labelling techniques to reveal the possible role of DUBs in both cancer and immunity.

Dr Karen Colwill
Dr Karen Colwill
Dr Karen Colwill, Guest Chair Lunenfeld-Tanenbaum Research Institute
Toronto

Dr. Karen Colwill joined Dr. Tony Pawson's laboratory in 2002 to help coordinate large-scale projects and collaborations. Work in the Pawson laboratory is centred on understanding how signals originating from outside the cell are interpreted by components within the cell to generate the appropriate cellular response. This cellular response is dictated in large part by the interaction between proteins that are dynamically organized into vast networks - aberrations within these networks can lead to complex diseases such as cancer.

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FAQ

Here is a list of answers to frequently asked questions for speakers, delegates and sponsors

If you still have unanswered questions after reading this page, wish to present a talk, suggest a venue or sponsor a meeting, please contact us.

Organising Committee

The organising committee is made up of early and "not-so-early" career scientists
from academia and industry.
If you are interested in joining the committee, please get in touch.

Dr Harvey Johnston
Dr Harvey Johnston Chairperson, Founder

After my PhD in blood plasma cancer proteomics I moved to the Cancer Proteomics Group at UCL. I founded the LPDG as a focus group for the SE. I am currently at the Babraham Institute investigating protein degradation pathways using proteomics.

Dr Harry Whitwell
Dr Harry Whitwell Communications Officer

I am a post doc at ICL, developing mass spectrometry and data analysis methodology for the study of protein PTMs, in particular methylation. My research is multidisciplinary, using chemistry, bioinformatics and biology. For more info, click here.

Dr Lukas Krasny
Dr Lukas Krasny Secretary

I am a post-doc at the ICR in Paul Huang’s group. My research interest is in extracellular matrix remodelling during cancer progression. From an analytical point of view, I am interested in protein quantification by DIA mass spectrometry.

Dr Roberto Buccafusca
Dr Roberto Buccafusca Treasurer

I manage an MS lab at QMUL. I graduated from Drexel University (USA) in Biomedical Science, completing my PhD work at Harvard University. After a long stint in the private sector, I re-joined academia here in the UK researching lipidomics and proteomics.

Danai Kati
Danai Kati
Danai Kati Committee Member

Danai studied biology and biomedical sciences in Greece. She has worked in numerous labs in England, Singapore, the Netherlands and Greece. Now she is focusing on her PhD at UCL in Primary Biliary Cholangitis analyzing human samples using Mass spectrometry.

Suniya Khatun
Suniya Khatun Committee member

I am a PhD student at UCL on the CellX project in the Thalassinos Lab studying competition in cellular populations using mass spectrometry-based proteomics.

Dr Daniel Conole
Dr Daniel Conole Committee member

Daniel is a post-doc in the lab of Prof. Ed Tate at Imperial College London. His research interests lie in the use of chemical proteomics for better understanding of drug targets, protein function, and post-translational modification dynamics.

Tom Ruane
Tom Ruane Committee member

Tom works for SCIEX in the London region helping customers with MS and 'OMICS applications. He gained an interest in MS from working with Prof Roy Goodacre, Manchester Institute of Biotech. applying -omics and chemometric approaches for rapid food authenticity determination.

Joanna Kirkpatrick
Dr Joanna Kirkpatrick
Dr Joanna Kirkpatrick Committee member

Joanna Kirkpatrick
Crick Insitute

London and the South East
United Kindgom

Please email with any questions.
Particularly welcome are venue suggestions,
speaker suggestions or if you are thinking of sponsoring a meeting.

This seminar series is run by volunteers from academia and industry. We will try to reply to your email as quickly as possible, but please allow at least 5 days.