The 4th Proteomic Forum
Technical University of Berlin, Berlin, Germany, 22–25 March 2015
The Biannual Proteomic Forum is an affordable place where PhD students from all over Europe, including eastern Europe and the Middle East, can taste proteomics, experience this exciting scientific specialty and engage in discussion with full-fledged players in the sphere. This digest presents the opinion of a newcomer to the field of proteomics, who enjoyed this to-see and to-be-seen event in Berlin, Germany.
The 4th Proteomic Forum, a traditional event that was a worthy continuation of a fortunate series of biannual meetings, was held in Berlin, Germany on 22–25 March 2015. Highly topical agendas provided platforms for the presentation and discussion of the current challenges and the immense progress made in the field of proteome science. With about 60 speakers, 470 attendees and 30 industrial representatives, the Forum strengthened the links between international proteomic societies and a pictorialized panoramic view of state-of-the-art proteomics. While a wide range of topics was enlightened during the scientific sessions, a number of evident trends sounded the most eloquent – critical prospects of biomarker discovery, novel proteomic techniques, multi-omic projects and the European Proteomics Association (EuPA) initiatives, which are presented in this synopsis.
Biomarkers
The great expectations and monumental efforts of proteomic society consist of translating fundamental research into clinical application by the discovery of novel biomarkers Citation[1]. In simplistic terms, two-thirds of conferees participated in a meeting that associated their scientific projects with the discovery and validation of biomarkers. In the Human Proteome Organization workshop, a number of talks and a plenitude of posters were dedicated to this daunting task. A majority of scientists were positively spirited and believed that current proteomic technologies and pipelines would deliver on the promise of clinically useful biomarkers.
The biomarkers for cardiovascular disease were the focus of the Human Proteome Organization workshop. Jochen Schwenk (SciLifeLab, KTH Royal Institute of Technology, Affinity Proteomics, Sweden) presented a hypothesis-free workflow Citation[2] for a systematic plasma protein exploration based on suspension bead array assays Citation[3] and antibodies from the Human Protein Atlas. He reported on intermediary results of the initiated VinnCARDIO project, indicating promising cardiovascular disease biomarkers; 720 targets were validated by immune-capture mass spectrometry and sandwich assays. Sandwich tests were implemented in a clinical routine laboratory to evaluate marker performance in prospective samples.
The complex process of finding the tangled knot in an oncogenic network hairball and potential tools for drug design was further addressed by Mohamed Ali Jarboui (Medical Proteome Centre, University Klinikum Tübingen, Germany), who gave a speech about cancer-specific mutation which perturbs the epidermal growth factor receptor’s network and leads to colorectal cancer phenotypes by rewiring the signaling landscape.
The most rousing talk on an innovative biochip for peripheral diagnostic tests of Alzheimer’s disease (AD) in a routine blood-based clinical screening was provided by Maria Zellner (Medical University of Vienna, Surgical Research Laboratories, Austria). The combination of four AD-regulated platelet proteins, including the most powerful genetic risk factor of late-onset AD, enabled identification of AD patients with an impressive-looking sensitivity of 94% and specificity of 89% Citation[4].
Following inspiring biomarker-polarized presentations, the speech of Tadashi Kondo had a sobering effect. He threw doubt upon conventional proteomic approaches to biomarker development, with a particular focus on the inefficiency of novel technology’s brute force in the absence of realistic theme setting and deep knowledge of cancer biology.
Proteomic techniques
Presentations of novel proteomic techniques as part of the top-level educational sessions and symposiums attracted interest from both industry and proteomics experts.
High-resolution data-independent acquisition techniques were one of the hottest topics of the Forum. The meeting started with a talk by Christina Ludwig (ETH Zurich, Institute of Molecular Systems Biology, Switzerland) on protein quantification by Sequential Window Acquisition of all Theoretical Mass Spectra and was followed by Stefan Tenzer (Universitätsmedizin Mainz, Institute for Immunology, Germany), who introduced the audience to label-free quantification using ion-mobility enhanced data-independent ultradefinition acquisition (UDMSE). UDMSE employs drift-time specific collision energy profiles that enhance precursor fragmentation efficiency and improve proteome coverage Citation[5].
The targeted analysis of proteins in a parallel reaction monitoring technique tailored on a quadrupole-orbitrap mass spectrometer was comprehensively addressed by Bruno Domon (L.I.H., Luxembourg Clinical Proteomics Center, Luxembourg) Citation[6]. He demonstrated a significant gain of method compared to selected reaction monitoring in terms of identification and selectivity.
Immuno-MALDI (iMALDI), a relatively new technology for targeted proteomics, was presented by Christoph Borchers (University of Victoria, Genome BC Proteomics Centre, Biochemistry & Microbiology, Victoria, Canada). Using the sensitivity of immunoaffinity capture combined with the specificity of mass spectrometry detection, he demonstrated results of plasma renin activity measurement, an established biomarker for primary aldosteronism Citation[7].
Multi-omics science
The integration of proteome/transcriptome/metabolome/lipidome profiles was the subject of multiple scientific projects presented at the Forum. Yibo Wu (ETH Zurich, Zurich, Switzerland) explained the complex nature of transcriptomics/targeted proteomics/metabolomics combinations and provided an example of an application to investigate mitochondrial activity in a mammalian genetic reference population Citation[8]. The expanded approach enabled a switch to a system-wide scale using Sequential Window Acquisition of all Theoretical Mass Spectra, providing an unprecedented comprehensive view of cellular processes in a population study.
Stefan Wallner (University Hospital Regensburg, Institute for Clinical Chemistry and Laboratory Medicine, Germany) presented results of a comparative lipidomic and proteomic analysis of the plasma elimination rate of current lipid apheresis methods. A combination of proteomics and lipidomics before and after apheresis allowed the therapeutic efficacy of different apheresis approaches to be measured.
Christian Moritz (University of Kaiserslautern, Department of Biology, Germany) presented the regiospecific transcriptome–proteome correlation analysis of rat brain. His findings emphasized the importance of comprehensive information about the biological sample, because the specialization of protein sets can strongly rely on their localization.
EuPA initiatives
EuPA day at the Forum delivered social insight into proteomics. Ingrained problems, for example, the moving target of standardization, were considered to be challenged using crowdsourcing. Lennart Martens presented a vision of risks which steadily accompany bioinformatics studies. Without standardized data formats and minimal required quality criteria, the sharing of in-home results and interpretation of experimental results obtained elsewhere around the world could turn into a Herculean task for researchers. Active proteomic communities can converge to find a common solution to this problem, driven by researchers, who provide and reuse data, scientific journals and software developers Citation[9]. According to Martens, connective infrastructure that links the crowdsourcing of needed proteomics bioinformatics tools and the crowdfunding of the development of these tools will bring value to bioinformatic pipelines. He also noticed that this initiative could be linked to the ELIXIR repository Citation[10] to match the demand of scientific society and supply of developers – may be in the shape of already materialized, but not yet popularized tools.
Emma Lundberg came up with the suggestion of affinity binder knock-down strategy, which consists of sharing antibody validation results with industrial partners and the whole proteomic society at Antibodypedia Citation[11]. This strategy will offset the costs of reagents to researchers and make it possible to standardize antibodies used in research Citation[12].
The coordinator of EuPA initiatives, Andrey Lisitsa, encouraged national societies to join a new format of socializing proteomics Citation[13]. He gave an example in targeted proteomics, where a solid communicative channel is supplied at LinkedIn by Biognosys AG, Switzerland. Recently, Biognosys AG has announced a research challenge. The aim is to discover the most forward-thinking research projects that may benefit from hyper reaction monitoring, a mass spectrometry-based technology, that enables reproducible and accurate quantification of several thousand proteins in a single sample. This is a good model of a business trigger for socializing proteomics.
Concluding remarks
The Forum provided a networking area for PhD students (approximately 30% of the total audience), postdoctoral researchers and established authorities to exchange ideas as well as to enjoy social interactions in Berlin. This event opened the door to face-to-face contact with peers of proteomics from all around the world during educational lectures. Real-life communication (mostly with PhD students of the same academic rank) during poster sessions was a powerful tool to break the ice.
At least three main take-home messages were obtained from the Proteomic Forum. First, proteomics itself and hand in hand with other OMICS still remains an evolving scientific field, but there are telling reasons to be enthusiastic about its ability to deliver practical outcomes. Second, the great efforts of technologists democratize high-performance proteomics and open the door to conduct state-of-the-art mass spectrometry experiments Citation[14] even in non-specialist laboratories. Third, realistic experiment design, which answers the biological question, is the most promising strategy of biomarker development. The audience was left with the view that crowdsourcing in proteomics is high on the priority list, and a cooperative effort, such as presented over the course of EuPA initiatives talks, shows great potential.
Taking all the aforesaid into consideration, the Proteomic Forum-2015 was absolutely worthwhile for highlighting advances and challenges that were addressed to high-caliber professionals as well as to newcomers in the sphere.
Acknowledgements
Financial support for participation at the Proteomic Forum 2015 in Berlin was provided by the Fundamental Scientific Research Program of the Russian Academy of Sciences for 2013–2020.
Financial & competing interests disclosure
The author has no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
No writing assistance was utilized in the production of this manuscript.
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