BSPR 2022 Bursaries and Fellowships

MJ Dunn Fellowships

##John Mulvey (University of Oxford)

I would like to acknowledge and thank the British Society for Proteome Research for the award of the MJ Dunn Fellowship for the BSPR 2022 meeting.

The BSPR meeting this year was held at St Anne’s college at the University of Oxford, serving to bring together a diverse range of participants from both academia and industry with a shared interested in proteomics. The meeting provided an intense few days of technical discussions, exchange of ideas and social events.

The organisers had selected a program of presenters from across the spectrum of proteomics, from method development for sample preparation and computational approaches to those applying these technologies to drive new insight into biological problems. As ever, some of this was directly relevant to my own research: I particularly enjoyed hearing from Prof. Mike Gillette on his work integrating proteomics with other ‘omics - at scale - to both uncover novel biology and identify putative therapeutic targets. Some of the other highlights were however approaches that were not at all on my radar beforehand. Why not, for example, shine a laser through the ion path of the mass spec if you are studying a photoactive protein as presented by Prof. Perdi Barran. In addition to the melange of mass spec based research we also heard from Prof. Hagan Bayley who continues to develop a nanopore platform with the goal of probing single protein molecules for PTMs. This is certainly something that would complement our existing capabilities and make many additional hypotheses experimentally tractable.

The plenary lectures were delivered by Prof. Matthew Collins, who spoke of his work in applying proteomic methods to the study of archaeological material. In the process, delightfully balancing some very well- and poorly- conducted experiments in this field to make sure to cater for the sceptics in the audience. Sir Peter Ratcliffe covered his research past and present on protein hydroxylation during oxygen sensing, emphasising the value of antibodies during his career in addition to much of his mass spec work.

As ever, it is impossible to fully acknowledge everyone who made for such an interesting and productive meeting. I would like to close by thanking the organisers for their hard work that made the meeting a success, and to all participants for their input. I enjoyed talking to many of you, and I look forward to meeting those I did not have the opportunity to in Nottingham next year.

Bursaries

##Jasmine White (University of Manchester)

I am honoured to have received a Student Travel Bursary which allowed me to attend the BSPR Annual Scientific Meeting in the beautiful Oxford and present my poster during the lunch time sessions. Being a master’s student and not having been to a scientific conference before, I was nervous and unsure what to expect! I had a great time meeting people with the same interest for proteomics in cancer research and especially enjoyed discussing my research with such a knowledgeable audience. I received very helpful feedback and was able to take this back to improve my project, with suggestions probing different experiments I had not thought of myself. Importantly for me, I also gained a lot of confidence in talking about my research.

The talks were diverse and interesting, covering a variety of ways in which proteomics can be used in science today. I found the talks under ‘toward P5 medicine’ the most interesting with all the speakers (Manuel Mayr, Rosie Maher, and Melissa Grant) emphasising how important proteomics can be in the identification of disease progression and therefore specialization of treatment plans. For example, Melissa Grant used proteomics to identify new biomarkers that can aid the diagnosis of periodontitis, allowing doctors to distinguish disease severity and decide which treatments are most appropriate. I also really enjoyed the talks in which new methods were described, especially Melanie Bailey who has used ion beam imaging to analyse proteomes of live cells using nanocapillary sampling whilst maintaining geometric position. It’s astonishing to see what techniques are being developed and how they are being used today. Watching such confident and interesting speakers really solidified my interested in the field and even spurred me on to apply for PhD’s in proteomics.

Thank you to the British Society for Proteomic Research for organising such a great event and allowing the progression for early career scientists such as myself. And thank you to the speakers and other poster presenters for taking the time to share their research with us.

##Megan Ford (University of Liverpool)

I am a second year PhD student looking at drug hypersensitivity and specifically drug-protein adducts. I recently attended BSPR 2022 for three days in Oxford. The conference was titled ‘Next generation proteomics’. Here I presented a poster on my proteomics work and gave a 1-minute flask talk to encourage the audience to engage with me at my poster. I enjoyed the opportunity to present even for a short period of time. Over the three days I connected with many people including different PIs, students, Industry collaborators and the BSPR committee. I hope that these connections will make lasting collaborations in research in the future. It was also great to listen to all of the talks including those from students from different groups and fields of proteomics. I was very grateful to have been able to attend this conference thanks to the BSPR student bursary. This allowed me to attend, paying for my travel and accommodation. It was fun to be able to connect with so many different researchers (I even got a question right at the quiz!). I briefly visited the botanical gardens for my second love besides proteomics- plants. I look forward to attending next year in collaboration with EuPA in Newcastle, where I hope to give a short talk and improve my networking skills further.

##Katie Dunphy (Maynooth University)

I would like to express my sincere gratitude to the committee of the British Society of Proteome Research for awarding me a Student Conference Bursary to attend the Annual EuPA 2022 Congress. The congress was held over 5 days from April 3rd to April 7th in Leipzig, Germany. My attendance at this conference was especially significant as it was the first in-person conference I attended since the beginning of my PhD in February 2020. The conference was attended by proteomics experts and early career researchers from all over Europe and even America. Plenary sessions were given by long-standing proteomics experts including Prof. Matthias Mann, Prof. Albert Heck, and Prof. Kathryn Lilley, among others. The opportunity to interact with and learn from individuals working in similar areas was invaluable. Symposiums consisted of a wide range of topics from top-down proteomics to clinical applications which ensured every individual could attend talks that were of personal interest. In addition, the conference organisers arranged an educational day for early career researchers to learn more about R programming, working abroad, grant writing and deciphering protein lists. The career session provided insight into the many career paths available for proteomics researchers. I had the opportunity to discuss my future career with industry including Thermo Fisher and Bruker, as well as with professors and laboratory leads who took the academia route. I was honoured to present my research in the form of a poster presentation at the conference. During my poster session, I received valuable feedback and interacted with many individuals in similar research areas. The casual coffee and poster sessions offered casual discussion on projects and interests, as well as allowing the formation of new friendships and collaborations. Attending this conference was hugely exciting and motivating for me. Seeing the progress that is being made in the field of proteomics and being a part of this amazing community is a privilege. Attendees came together with one goal: Advancing proteomics research for the benefit of individuals and patients all over the world. Travel grants and bursaries are essential for early career researchers to advance their professional career and make connections with others for future collaborations or career moves. Finally, I would like to again thank the BSPR for providing this bursary for early career researchers.

##Charlotte Hutchings (Cambridge University)

I first wish to thank the British Society for Proteome Research for awarding me a travel grant to attend the BSPR Annual Scientific Meeting 2022 at St Anne’s College, Oxford.

This was the first conference I have had the opportunity to attend, and what a way to start. Having only ventured into the world of proteomics at the start of my PhD last October, it was wonderful to hear talks from peers and meet so many of the names I constantly see on papers (and academic twitter, of course). I’d always wondered what a conference would be like, and part of me was even nervous upon arrival. Luckily, the BSPR Meeting turned out to be the perfect combination of learning and networking, both with an open, informal atmosphere.

The topic of this year’s meeting was “Next generation proteomics”, and on this it delivered. The first talk from Anne-Claude Gingras was a perfect start to the meeting. In fact, the discussion of using proximity-dependent sensors was particularly interesting to me as I was already in the process of planning a similar proximity-labelling experiment as part of my own work. Despite setting a high bar, the following speakers rose to the challenge. We heard from early career researchers, Claire Eyers (this year’s BSPR lecturer), Hagan Bayley (founder of Oxford Nanopore Technologies), and even Nobel Laureate Sir Peter Ratcliffe. The meeting was nothing short of impressive from start to finish.

On a personal level, the BSPR Meeting was hugely important. I was the only member of my lab to attend this year and felt honoured to be able represent and discuss our ongoing work with peers. I had huge fun networking, especially at the BSPR quiz and open bar (kindly funded by Waters). As I sit at my desk reflecting on the experience, I am grateful to the BSPR for the opportunity to attend and I feel genuinely inspired to continue my work in the field of proteomics. What an exciting time.

Here’s to next year – BSPR 2023 in Newcastle.

##Alejandro Brenes (Dundee University)

BSPR 2022 was set among the timeless spires of Oxford University, where the top proteomics scientists in the UK met in person for the first time in 3 years.

The pre-conference activities started with a workshop on protein-protein interactions lead by Sandra Orchard from EBI, and Ed Huttling from the Gygi lab, before kicking off the following day. The symposium was opened with a keynote from Anne Claude Ginras focussed on the spatiotemporal element of signal transduction focussing on her work with BioID, mentioned the strength and limitations and introducing her idea of pre-prey pearson correlation analysis as a more robust way to build networks. She also highlighted that all the data her lab generated on HEK293 cells was available in the resource humancellmap.org.

The enabling technologies session saw great talks from Perdi Barran and Alex von Kriegsheim one exploring protein structures using native mass spectrometry and the other talking the power of multi-omics to discover new insights in hepatocellular carcinoma. The first day ended with the chemical biology session, where Sabine Flitsch, Ed tate and Aini Vourinen discussed a wide array of topics ranging from biocatalysts for proteins and peptides, proteins S-acetylation networks to profiling cysteine fragment reactivity against deubiquitinases.

Day 2 began with an explanation of the ever-expanding collection of P’s in medicine, which had gone from P3 to P5. This session had talks from Manuel Mayr who discussed the complexities of clinical proteomics and revealed one of the big bottle necks in the cardiovascular proteomics field was the lack of datasets with a large number of patients enrolled. Edward Emmott followed and he spoke about the sputum proteomics and finding biomarkers correlated within the data and finally Melissa Grant looked at gingival crevicular fluid and also found biomarkers relating to the regulation of immune cell and in particular neutrophils.

The imaging and spatial proteomics session kicked off by Melanie Bailey with element imaging to look at the distribution of elements within a cell as well as subcellular compartments. Harry Whitwell talked about the challenges and methodologies they used to analyse low sample amounts and how the quantitation of some peptides doesn’t follow the normal dilution pattern that most do, which can affect quantitation. The low sample amounts theme was also central to the talk from Covaris which closed the session.

The systems/networks session was kicked off with a tour de force by Mike Gillette where he presented the vast amount of deep proteogenomics data that was acquired within CPTAC and how this was already helping to further characterise cancer, stratify patients and refine the molecular taxonomy. Charlie Barker, also focussed on cancer, presented his work on melanoma looking at constitutively active BRAF mutations. The session was closed with a talk from Aymen Al-Rawi looking at the how different binding partners of the CDK1 kinase can affect the phosphorylation dynamics and motif preferences.

The last session in the day was the Bioinformatics session. Here after some struggle with zoom, Evangelia Petsalaki discussing probabilistics networks for kinases and their substrates. Anjan Venkatesh then talked about using proteomics to study paralogs looking at what happens to the abundance of one when the other is lost. The plenary session on Tuesday saw a fascinating talk from Matthew Collins, discussing the challenges and opportunities of studying ancient proteins, ranging from T-rex sequencing down to the boom of proteomics in archaeology which took off in 2021.

Tuesday night also hosted the BSPR dinner and the legendary pub quiz, which maintained the spirit Kathryn Lilley imbued into it, and became a challenging but fun evening for all attendees, with some of the organisers featured in the quiz itself.

Wednesday was the last day, and first session was the collaborative segment between the BSPR and the British Mass Spectrometry Society. The first talk in the session was from Claire Eyers, showing us that the world of phosphorylation was not only centred around serine, threonine and tyrosine, but that there were important roles for non-canonical phosphorylation and that the traditional phosphor-proteomics methods are not well suited to study many of these. The second talk was from Jack Penny who discussed using gas phase fractionation to generate DIA libraries and how these provided impressive results when paired with diaPASEF. The final talk of the session was from Alejandro Brenes and it looked at the neutrophil proteomes in COVID19 and how saw a phenotype of long covid and found value in “contaminants” as potential clinical biomarkers.

The mid morning session was One health research, and this had talks from Alfredo Costello, Jenny Ho from Thermo and Sarah Hart. Alfredo talked about the interplay between viruses and the hosts and talked about the importance of studying the interactomes of virion RNA and some of the issues to think about when understanding and interpreting the results from these interactomes. Sarah Hart then talk about Leishmaniasis Mexicana, showing the dire consequences the disease can cause and her approach of studying the surface proteome of the parasite after knocking down components of the BBSome complex.

The final session was started by the announcement of the Young Investigator awards, where the society recognised the contributions of young investigators. This was followed by the Next Gen Tech session. This was started by Hagan Bailey who discussed the process of development of Nanopores to study proteins but promised the Mass Spectometrists in the room that their jobs were not quite a risk just yet. Xiao Qin then talked about mass cytometry and the analysis of PTMs in organoids with the last talk being from Edward Emmott talking about his single cell proteomics work using SCoPE-2 to study post translational modifications in Norovirus infection and how the virus needed to use PTM’s to replicate.

The final talk in the meeting was a Plenary by the Nobel prize winner Peter Radcliffe, who discussed his journey to discover the oxygen sensing and signalling with hydroxylation and offered career advice to the young investigators in the room. With that the meeting was over, great science, great talks, great posters and phenomenal organisation, BSPR 2022 was done.

##Ruth Walker (Newcastle University)

Conference: British Society for Proteome Research (BSPR) 2022, St Anne’s College Oxford (3-6 th July) Theme: Next Generation Proteomics Sessions: Native/Structural Proteomics, Systems Biology/Networks, Towards P5 medicine, Chemical Biology, Bioinformatics, Imaging and Spatial Proteomics, One Health Research, Next Generation Technology Keynote Speakers: Sir Peter Radcliffe, Perdi Barran, Evangelina Petasalki, Manuel Mayr, Sabine Flitsch, Christopher Tape, Matthew Collins, Anne-Claude Gingras, Mike Gilette, Melanie Bailey, Claire Eyers, Alfredo Castello Why did I attend BSPR 2022 Conference? I attended BSPR2022 because I am very interested in next generation proteomics, especially in how spatial and therefore the underlying structural information can enrich the depth of information able to be obtained. I am also interested in how proteomic data can be linked to other omic data such as transcriptomics providing greater insight into the mechanisms underlying disease and how treatments can be tailored to patients using a personalised approach. It was also a valuable experience to share one of my current projects as a poster, discuss different proteomic advances with other and gain insight into the cutting-edge research being carried out. Conference Highlights I enjoyed so many talks, learnt so much and heard about lots of interesting applications of proteomics it was hard to narrow down my highlights of the BSPR2022 conference, but below are a few standouts.

1. Matthew Collins – The Challenges and Opportunities of studying ancient proteins A fascinating talk by the inventor of the ZooMS (quick) method wrongly described as referring to as zoo archaeology on Wikipedia, describing how he applies MALDI-TOF MS to archaeology. A technique “so easy kids can do it”! Using MALDI-TOF MS in my drug discovery research, whilst I’d read about its ability to type meat, animals and remains e.g. skeletal remains found, I had not before connected this to medieval manuscripts - written on animal skins, but with the information of when and where they were published, so a far more value source of archaeological information. The ability of the technique to solve questions which have confounded zoologists or other types of archaeologists for hundreds of years such as are Thunderbirds more related to chicken’s or other bird species? However, preserving artefacts from the past is important and it was astonishing to hear the wealth of data provided from protective cleaning waste e.g. eraser rubbings/bone chips or electrostatics technics used to pull molecules off the surface of artefacts without damaging them.
2. How important are neutrophils in human health and disease? Throughout the conference, other than proteomics, the importance of neutrophils and the instrumental role they play in inflammation was highlighted, as neutrophils were a key part of every oral presentation in the ‘Towards P5 medicine’ session from cardiovascular to cystic fibrosis to periodontal disease. Furthermore, later in the conference, Alejandro J Brenes, Dundee University discussed the effect of COVID-19 on proteomic neutrophil signature – showing that in early infection those patients who are more severely ill and have delayed recovery do not have robust interferon signals and a lot more changes in the proteome resulting from impaired killing and survival of neutrophils. Interestingly, when isolating neutrophils the population contains ~3% eosinophils and PRG 2 & 3 proteins are highly expressed in eosinophils but not neutrophils and change with disease severity making these good biomarkers.
3. Solvent precipitation SP3 (SP4) enhances proteomics sample preparation without magnetic beads (Poster) Harvey Johnston, Babraham Institute presented an improved method for performing proteomics sample preparation at a much reduced cost which he has termed ‘SP4’. SP4 uses 4x volumes of 80% acetonitrile captured with centrifugation instead of magnetic beads but glass beads did improve the SP4 handling. SP4 matched or outperformed SP3 and was comparable with S-TRAP for inputs 1-5000 µg. Moreover, it was much more compatible with detergents and salts, producing a deeper proteome coverage, offering a faster and much cheaper method which we are looking forward to trying in our own lab.
4. Networking Event run by Young Proteomics Investigators Club (YPIC) YPIC offered a rare opportunity to chat with some inspirational proteomics professionals over lunch, discussing our research and gaining insights both into future steps we could take in both our research and careers. One piece of advice that has really stuck with me was from Professor Claire Eyers, paraphrased – follow research that interests you, and allow it to shape your career.
5. Sir Peter Radcliffe – Signalling oxygen levels by protein hydroxylation Hearing from Sir Peter Radcliffe was the perfect close to the conference, discussing his research into hypoxia – the reason why your mothers/ partners/ friends plants die when you overwater them is due to hypoxia, and the gene responsible also works in human cells! It was interesting and inspirational to hear from someone who made a Nobel Prize-winning breakthrough. He challenged us to tackle unfashionable problems, answerable in your hands and emphasised that scientifically one of the hardest things to learn is when to call negative results and to understand their importance in the big picture of the research being carried out. Conclusions Overall, attending BSPR provided me with an invaluable opportunity for both my research and career development. I was very grateful to be able to discuss my work with others, gain insight into their different methods and how they applied them in their own research. Moreover, amongst so much exciting research, it was amazing to be awarded the best poster prize at the conference.

No reports provided

#Lucy Bedwell (Imperial College London)

#Myrto Mavrotas (Imperial College London)

#Sophie Lellman (University of Readin)

#Athansia Yiapanas (University of Edinburgh)