LPDG

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

Next Webinar
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

Webinar Programme


Proteomics: The Role Of Bioinformatics

08th October 2021 14:00 GMT

Dr Oliver Crook

Quantifying uncertainty in mass-spectrometry based proteomics

Uncertainties arise in mass spectrometry because of the technical variability inherent in the instruments we use, the biologically variability in the samples, as well as the choices made by filtering and preprocessing. These choices are often employed to control an error rate or prioritise “hits”. I will apply Bayesian statistics to model data and answer complex questions in spatial proteomics, thermal proteome profiling and hydrogen-deuterium exchange mass spectrometry and show what tools we have to deal with errors and uncertainties in mass spectrometry data science.

Dr Juan Antonio Vizcaino

Bringing proteomics data closer to biologists: disseminating and integrating public proteomics data into added-value bioinformatics resources

I will first briefly introduce the work we have done over the years to support open science practices in the proteomics field, highlighting the role of the PRIDE database (https://www.ebi.ac.uk/pride/), the world-leading public repository for mass spectrometry proteomics data. In this context, additionally, I will introduce the activities of the ProteomeXchange consortium (http://www.proteomexchange.org/) and of the Proteomics Standards Initiative (PSI, https://www.psidev.info/). Reuse of public proteomics datasets is increasing dramatically in recent years with multiple applications. In this context, our main focus is to disseminate and integrate public PRIDE proteomics data into added-value EMBL-EBI resources, namely UniProt (post-translational modification data), Expression Atlas (protein expression information) and Ensembl (proteogenomics data). We started to work with these resources and other collaborators in recent years, working in data reanalysis and dissemination pipelines. I will describe the status of these efforts, which are at a different state depending on each specific resource. I will also outline our future plans. These efforts are in my view required to bring proteomics data closer to a larger number of biologists, especially to those without any background in the field.

Proteomics Standards Initiative

Event Speakers

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

Juan Antonio Vizcaino
Juan Vizcaino
Juan Vizcaino EMBL-EBI
Cambridge

Dr Vizcaino leads the Proteomics team at the EMBL-European Bioinformatics Institute, responsible for the PRIDE database and related software tools. Juan co-led the establishment of the ProteomeXchange consortium of proteomics repositories and is currently chairing the Proteomics Informatics Working Group for the HUPO-Proteomics Standards Initiative. He co-founded the ELIXIR Proteomics Community coordinating computational proteomics activities in Europe. His overall goal is to help researchers make the most public proteomics data, including data re-use and integration between multi 'omics data types.

Oliver Crook
Oliver Crook
Oliver Crook Department of Statistics
University of Oxford

Olly is a Todd-Bird Junior Research Fellow in Biochemistry at New College Oxford and a Postdoctoral Researcher in the Department of Statistics, where he works on advanced computational methods for structural proteomics. He is supervised by Charlotte Deane from the University of Oxford and Chun-wa Chun of GSK. He completed his Ph.D in Bayesian methods for spatial proteomics with Prof. Kathryn Lilley, and an MMath at the University of Warwick. Olly's primary interest is to level-up mass spectrometry by developing models than can answer new questions of our challenging data.

Andrew Dowsey
Andrew Dowsey
Andrew Dowsey Bristol Veterinary School
University of Bristol

Prof Dowsey is Chair in Population Health Data Science and Chair in One Health Bioinformatics and Biostatistics at Bristol Veterinary School. Andrew’s research group focuses on the facilitation and acceleration of health sciences research through novel artificial intelligence and statistical data science methodology, as well as data collection and management platforms. He is Co-Director for Enterprise & Innovation in the Faculty of Health Sciences, is an Associate Director of the HDR-UK South-West Better Care Partnership, and a Turing Fellow.

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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.