Proteomics - Articles and news items

An essential role for the Michael Barber Centre

Issue 5 2006, Past issues / 28 September 2006 / Simon J Gaskell, Director of the Michael Barber Centre for Mass Spectrometry in the School of Chemistry and the Manchester Interdisciplinary Biocentre and Isabel Riba-Garcia, Research Fellow, Michael Barber Centre.

The development of proteomics has been based very heavily on the suite of analytical techniques encompassed by mass spectrometry and associated methods. It is therefore appropriate that the work of the Michael Barber Centre for Mass Spectrometry (MBCMS, named for the inventor of, inter alia, the fast atom bombardment ionisation method) should now be largely driven by the needs of proteomics research and the broader field of systems biology.

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A showcase project for EU research

Issue 4 2006, Past issues / 20 July 2006 / Dr Anne Katrin Werenskiold, Project Manager, Interaction Proteome

The investigation of functional protein-protein interactions has been gaining momentum with recent technological innovations. The high-throughput era in genomics and proteomics research is essentially dependent on technological advancements to drastically increase capacities in both large-scale gathering of data; their interpretation and functional validation, as well as the compilation and storage of data in a standardised format. Contributions of the European Commission-funded ‘Interaction Proteome’, an integrated project in the field, are outlined in this article.

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Structure, function, interaction

Issue 3 2006, Past issues / 23 May 2006 / Walter Kolch, University of Glasgow & Beatson Institute for Cancer Research

In the last decade proteomics has revolutionised biology and now biology starts revolutionising proteomics.

We are at an exciting interface where the biological questions we can ask and answer with proteomics have become less limited by the available technology and push proteomics towards new frontiers. Exploring these frontiers is the topic of the upcoming joint BSPR/EBI conference entitled ‘Integrative Proteomics: Structure, Function, Interaction’. The conference focuses on the new challenges in proteomics, which are about functions, mechanisms and global contexts rather than cataloguing components. The programme addresses key developments and applications featuring topical sessions with eminent speakers and short talks chosen from submitted abstracts. The full programme is available from http://www.bspr.org

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The human plasma proteome: A biomarker pool too deep to explore?

Issue 3 2006, Past issues / 23 May 2006 / Susann Schenk, Center for Experimental Bioinformatics (CEBI) and Gary J. Schoenhals, Bioinformatics, Department of Biochemistry and Molecular Biology University of Southern Denmark

The human blood plasma harbors treasure, which, like most treasures, is not easily attained, and finding it requires ingenuity, endurance and possibly a grain of luck. The blood plasma is the largest (most proteins) and deepest (widest dynamic range) of the human proteomes. In order to ‘triumph over’ it, it is necessary to overcome an enormous protein concentration range to finally be rewarded with the possible discovery of biomarkers. But is this a realistic challenge we are facing or is this plasma pool too deep to explore?

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Identification and prevalidation of safety biomarkers

Issue 2 2006, Past issues / 24 March 2006 / Michaela Kroeger, Merck KGaA, Institute of Toxicology, Matthias Glückmann, Applied Biosystems, Mass Spectrometry and Proteomics

To date, hazard/risk assessment of new drugs and chemicals primarily relies on the investigation of toxicological endpoints from animal studies. In this field, the full range of genomics and proteomics technologies can be used in efforts to uncover the molecular mechanisms at work in response to xenobiotic exposure. These new disciplines, called toxicogenomics and toxicoproteomics, offer several practical benefits.

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The HUPO Brain Proteome Project

Issue 1 2006, Past issues / 2 February 2006 / Kai A. Reidegeld, Michael Hamacher, Helmut E. Meyer, Christian Stephan; MPC, Medical Proteom-Center, Ruhr-University of Bochum, Martin Blüggel, Gerhard Körting, Daniel Chamrad, Christian Scheer; Protagen AG, Herbert Thiele; Bruker Daltonik GmbH, Chris Taylor, Michael Müller, Rolf Apweiler, Philip Jones; EBI, European Bioinformatics Institute, Lennart Martens; Department of Medical Protein Research, Ghent University

The proteome analysis started by the Human Proteome Organization (HUPO)1 is the second big international consortium project after the sequencing of the human genome by the Human Genome Project (HUGO)2. The aim of the HUPO Brain Proteome Project (BPP)3 is to derive in depth knowledge of the brain from analysing samples with state-of-the-art proteomics techniques.

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Meeting the challenge with a new facility

Issue 4 2005, Past issues / 11 November 2005 / EPR

The conclusion of the Genome Sequencing Project – far from providing the solution to the problem of human disease – has created further questions that had not previously been considered. Hence, the age of genomics has initiated the need to examine the body’s real biochemical actors: proteins, to learn about their role in human health and disease.

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Plasma protein biomarker discovery

Issue 3 2005, Past issues / 22 August 2005 / Gilbert S. Omenn, M.D.,Ph.D University of Michigan

Less than a week after Nature and Science published the special issues on the ’blueprint‘ for the human genome sequence 15-16 Feb, 2001, the Financial Times of 21 February, 2001, ran a major article about proteomics, calling proteins “the real stuff of life”. Proteins are, indeed, the effector molecules for most cellular actions and interactions. As attention has migrated from genome sequences to genetic variation and functional genomics, proteomics has gradually emerged as a potentially powerful set of technologies for biomarker discovery and mechanistic studies important to drug development and drug safety surveillance1-4.

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Initiatives from Spain

Issue 3 2005, Past issues / 22 August 2005 / José M Mato, Isabel Pérez-Mato, Félix Elortza, CIC bioGUNE and Julio Font, Noray Bioinformatics, S.L

The availability of the complete sequence of some model organism genomes, including the human genome, offers new opportunities for biological research. The goal is to establish technology to identify all the proteins involved in a particular biological process and the interactions between them.

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Easy access for the scientific community

Issue 2 2005, Past issues / 20 May 2005 / Laura Hohmann, Research Associate, Daniel Martin M.D., Director, Proteomics Facility, The Institute for Systems Biology

The past decade has witnessed an explosion in the field of proteomics. This development has been driven by the development of database search algorithms, expansion of sequence databases and improvements in mass spectrometry instrumentation. Quantitative techniques using isotopic dilution have allowed quantitative experiments. The expanding opportunities have propelled the development of core facilities to provide services to biological researchers wishing to conduct proteomic experiments for themselves.

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A network of innovation from Canada

Issue 1 2005, Past issues / 7 March 2005 / Dr Daniel Boismenu, Team Leader, Mass Spectrometry Unit, Montreal Proteomics Network

The Réseau Protéomique de Montréal Proteomic Network (RPMPN) was created in the year 2000 through funding from Genome Canada, Genome Québec and the Canadian Foundation for Innovation. For the past five years, the RPMPN has been involved in the Cell Map Project, which involves cell biologists from the Université de Montréal and McGill University. The goal is to achieve the most exhaustive documentation (identification, localisation and function) of protein expressed in mammalian organelles challenged with hormones such as insulin and EGF, along with their respective control.

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