Participating laboratories

A network of collaborating laboratories will enable a comprehensive approach to capture, develop and disseminate knowledge on quantitative proteomics. Four courses will be developed on key areas of quantitative proteomics. In addition to the courses the Network will coordinate symposia and workshops in the network countries which will be accessible to all Life Scientists. Dates and further information will be accessible on the agenda.

Aebersold Lab ~ Zürich, Switzerland

The Aebersold lab is at the Institute of Molecular Systems Biology. Founded January 1st, 2005, the Institute of Molecular Systems Biology is a new Institute in the Department of Biology at the ETH Zurich.

The mission of the Institute is to develop, apply and teach the emerging science of Systems Biology. We understand Systems Biology as an approach to biological research that studies biological systems and processes as dynamic, integrated networks of interacting molecules. The underlying vision is that the structure and dynamics of such networks will provide insights into the function and control of biological systems that are not apparent from studying the systems’ components. Neither, the technologies to collect the data required to analyse molecular networks, nor the theory and tools to extract functional information from the data is well developed at present. A significant part of the activities in IMSB will therefore focus on the development of new technologies for the collection and analysis of quantitative data at high throughput and their integration into models that represent the behaviour of the systems studied.

IMSB scientists are involved in SystemsX, the Swiss Initiative in Systems Biology, which includes the Centre for Model Organism Proteomics (C-MOP) at the University of Zürich, the Competence Centre for Systems Physiology and Metabolic Disease (CC-SPMD) at the ETH Zürich as well as the Centre of Biosystems & Engineering (C-BSSE) of the ETH Zürich at Basel. The IMSB is also tightly linked to other international Systems Biology projects and institutes such as the Institute for Systems Biology (ISB) in Seattle, WA, the Yeast Systems Biology Network, and Advanced Systems Biology Courses.

Corthals Lab ~ Turku, Finland

The Corthals lab is at the Turku Centre for Biotechnology (CBT), a jointly funded institute of University of Turku and Åbo Akademi University. The CBT provides technical expertise and coordinates services for academic and industrial projects in several key areas of biotechnology, such as cell imaging, genomics and proteomics. Many cutting-edge high-tech biotech instruments are installed at the CBT. There are close to 200 people working at the CBT, which contains 15 group leaders, 80 postdoctoral fellows and graduate students, plus 75 other professionals. The main areas of focus for proteomics are on research, services and teaching.

Research – Biological Mass Spectrometry
The role of biological mass spectrometry (MS) is central to our research. MS is employed for qualitative and quantitative measurements on biomedical applications, which are used to drive the development of new technologies and computational tools. Key areas of interest are:
. 1.Quantitative analysis of proteins
. 2.Characterisation of dynamic protein complexes
. 3.Dynamic phosphorylation analysis
. 4.Mass spectrometry imaging

Proteomics Service – CBT VTT Proteomics Facility
The Facility forms part of the regional infrastructure, where it acts as a knowledge centre for proteomics and systems biology through training, service, consulting, and general promotion and diffusion of proteomics related sciences. In its role as a regional knowledge centre it has 3 primary roles:
. 1.To provide top class analytical proteomics services to bioscience researchers in academia and industry in the Turku region and strengthen the national competence in protein research
. 2.To educate and disseminate information on proteomics, bioscience applications and technology development to all scientists
. 3.To enhance and develop enhanced proteomic technologies for biosciences applications

Network available technology
The laboratory is equipped with five highly sensitive MS instruments, of which three will be used for this network. Our MALDI-TOF/TOF (Bruker), ESI-Q-TOF (ABI/Sciex), ESI-IT (Bruker) instruments that will be used are capable of identification and quantitation using MALDI or ESI based MS. There is also a dedicated teaching wet lab for protein and peptide separations. 1-DE, peptide-IEF and LC (C18), and LC/LC (SCX/C18) procedures will be predominantly used for sample preparation. Protein identification and quantitation is afforded through existing in-house commercial software (Mascot v2.2 (Matrix Science) and ProteinPilot v 2.0 (AppliedBiosystems)) as welll as X!Tandem (open-source) that runs from within the CPAS utility (Computational Proteomics Analysis System, open-source). Data management, archiving and retrieval of all MS and proteomics data will be made available to the network via our LIMS systems(Genologics).

Fladmark Lab ~ Bergen, Norway

The Fladmark lab is located at the Department of Molecular Biology at University of Bergen. In 2007 we established a new proteomics lab together with our collaborators from Department of Biology, Institute of Marine Research and Bergen University College.

The Fladmark Lab’s research focuses on identifying key signalling proteins in toxin-induced apoptotic cell death. These marine algal toxins seem to target well-conserved signalling pathways of apoptotic cells death and are important tools in dissection of mammalian cellular signalling.

James Lab ~ Lund, Sweden

The James lab was launched in January 2002 under the auspices of the SWEGENE consortium which was funded by the Wallenberg Foundation to develop ‘omics’ technologies in Sweden. The centre consists of two parts: a research and development laboratory and a service facility which is part of SCIBLU. The centre is open to all scientists and provides both analytical and educational services. Currently monthly day-long courses in ‘do-it-yourself’ proteomics (practical instruction on protein separation and identification and experimental design) in addition to four one-week long courses on the four fundamental areas of proteomics: electrophoretic and chromatographic protein and peptide separation, mass spectrometry and bioinformatics.

Jensen Lab ~ Odense, Denmark

The Jensen lab is at the University of Southern Denmark and provides a state-of-the-art proteomics platform for this project. The research is focused on the development of highly sensitive mass spectrometry based technology for protein identification, characterization and quantitation, and proteome wide analysis of post-translational modifications (PTMs). Several sensitive and specific affinity-enrichment methods for quantitative phosphoproteomics studies of cellular signal transduction were developed in the Jensen group.

Ole N. Jensen and the Protein Research Group participates in the EU Marie-Curie Research Training Network ’DNA Enzymes’ (9 partners) and is part of the Danish National Research Foundations Center-of-excellence in Epigenetics. The Protein Research Group participates in several other EU projects and a HFSP project in the areas of aging and neurobiology.

Network available technology
Mass spectrometry platforms, including several MALDI MS/MS and ESI MS/MS instruments. The newest acquisitions include a Thermo LTQ-Orbitrap XL MS/MS instrument, a Waters Synapt IMS-MS/MS instrument and an Agilent iontrap ETD MS/MS system. In addition, several QTOF and TOF-TOF instruments are available. Chromatography and electrophoresis equipment for protein and peptide separations is used in conjunction with mass spectrometry for detailed characterization of proteins. Hydrogen-deuterium exchange mass spectrometry (HX-MS) and surface plasmon resonance analysis (Biacore) is applied to the study of protein-protein and protein-ligand interactions. Laser microcapture dissection equipment was recently installed for preparation of tissue samples for proteomic analysis. Bioinformatics tools are developed and applied to the study and interpretation of complex proteomics datasets.

Loog Lab ~ Tartu, Estonia

The Loog lab is at the Institute of Technology at the University of Tartu, which is a new and modern research institute, that was built in 2005. The institute hosts a collection of independent research laboratories and several core facilities. In 2006 we launched the graduate program which offers Ph.D positions in different fields of science and technology, including biochemistry, proteomics, cell and molecular biology, organic chemistry, plant biology, robotics, applied mathematics etc. The Protein Kinase Laboratory at the Institute of Technology was launched in 2006 by group leader Mart Loog Ph.D. Currently there are 6 members and 3 Ph.D projects are in progress. The projects involve different themes connected to phosphoproteomics, including the studies of protein kinases involved in cell-cycle regulation. The proteomics facility at the Institute of Technology was launched in 2007. Currently there are two research scientists working in the facility using Orbitrap LTQ.

Nordic Quantitative Proteomics