People

 

iMOP administration

Chair: Emøke Bendixen (Aarhus University)
Co-chairs: Andreas Tholey (Kiel University)
Dörte Becher (University of Greifswald)
Kathrin Riedel (University of Greifswald)
Joshua Heazlewood (The University of Melbourne)
Co-ordinator: Sabine Schrimpf (University of Zurich)


Active iMOP members

 

Scientist Species Summary Used Databases
Emøke Bendixen Pig (Sus scrofa), Cow (Bos Taurus), Horse (Equus caballus) Proteomics applied to farm animal sciences. Our research group has for the past 14 years focused on characterising farm animal proteomes, and related changes in proteome patterns to disease mechanisms and production traits in farm animals. We have recently focused on characterising metabolic disorders in pigs, because we believe pigs are adequate models for studying human metabolic disorders. An important aim of our quantitative proteomics studies is to provide information about differential expression patterns of specific proteins and pathways, and to integrate this information with genetic and physiological studies through a systems biology approach.Proteomics facilities:LC systems (Agilent, Thermo) for peptide separation. Mass spectrometry platform includes a Maldi-TOF/gTOF instrument (Bruker Daltonics) and a Q-star (a hybrid triple quadrupole-time of flight instrument) (AB-Sciex) and we are currently setting up a Q-Trap instrument (AB-Sciex) for use in SRM-based technology. Department website: http://agrsci.au.dk/en/institutter/institut_for_husdyrbiologi_og_sundhed/ Pig (Sus scrofa)
- www.genome.iastate.edu/community/other
- Peptide Atlas for pig
- http://www.uniprot.org/taxonomy/9823
- www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9823
- www.sanger.ac.uk/Projects/S_scrofa
- www.ensembl.org.Cow (Bos Taurus)
- Peptide Atlas for cow (The first build of the bovine peptide atlas will be public before 2012.)
- www.ensembl.org/Bos_taurus/Info/Index
- http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9913
- www.genome.iastate.edu/community/otherHorse (Equus caballus)
- Horse genome project: http://www.uky.edu/Ag/Horsemap/
- Horsemap database: http://locus.jouy.inra.fr/cgi-bin/lgbc/mapping/common/intro2.pl?BASE=horse
- ArkDB: http://www.thearkdb.org/arkdb/
- NCBl horse genome viewer: http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9796
- http://www.ensembl.org/Equus_caballus/Info/Index
- Model organism database for the horse:
http://www.equinegenome.org/Equinegenome.org.html
- BROAD Institute Horse genome project: http://www.broadinstitute.org/mammals/horse
- Horse cell lines: http://bioinformatics.istge.it/cldb/spe9.html
- www.uniprot.org/taxonomy/9796
Andreas Tholey The Tholey group works mainly on method development for bioanalytics, using model organisms for the establishment and validation of the methods; further, several ongoing applicative projects together with biologically oriented groups on different biological/biomedical questions are performed on model organisms. Research activities(i) Method development for (functional) protein analytics and proteomics- 2D-LC coupled to ESI and/or MALDI MS
- Protein identification
- Protein quantification: labeling methods (including metal labeling), label-free approaches
- Posttranslational modifications (phosphorylation, oxidative modifactions, ac(et)ylation, proteolytic processing)
- protein and peptide labeling
- novel matrices for improved MALDI MS(ii) Application on biotechnological and biomedical problems (host-pathogen interactions, antimicrobial peptides, model organisms for biomedical research (e.g. inflammatory processes)) http://www.iem.uni-kiel.de
C. elegans - Host-pathogen interactions
- Proteases: substrate identification
Worm-Atlas
E. coli - pathogenic E.coli
- studies of metabolisms
http://genprotec.mbl.edu/
S. pombe - bioproduction of recombinant proteins
- systems biotechnology
www.sanger.ac.uk/Projects/S_pombe/
Dictyostelium - Antimicrobial peptides http://dictybase.org/
Mycobacteria (e.g. C. glutamicum; M. tuberculosis) - host pathogen interactions
- phosphoproteomics
http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi
Mytilus edulis (sea mussle) - proteogenomics Non-public (in house) database
Joshua Heazlewood Arabidopsis thaliana, Oryza sativa, Panicum virgatum Our work examines subcellular partitioning of plant metabolism through organelle proteomics. We are currently applying these techniques to improve our understanding of plant cell wall biosynthesis.
Plant cell walls are a valuable carbon source for the large-scale production of compounds such as biofuels and our research uses proteomics to identify potential targets for future bioenergy crop manipulations.Webpage: http://www.jbei.org/feedstocks/sysbio.shtml
SUBA (http://suba.plantenergy.uwa.edu.au/) PhosPhAt (http://phosphat.mpimp-golm.mpg.de/)
MASCP Gator (http://gator.masc-proteomics.org/)
plants http://www.inppo.com/
Michael Hecker / Katharina Riedel / Dörte Becher Bacillus subtilis, Staphylococcus aureus, Bacillus licheniformis, Streptococcus pneumonia, other Gram-positive bacteria, Escherichia coli, Pseudomonas sp., Burkholderia sp., aquatic and terrestric microbial communities A broad variety of MS-based and gel-based techniques are used to answer physiological questions, until now mainly in Gram-positive bacteria. For these organisms we are working as reference laboratory. During the last year we have extended our model organism spectrum to Gram-negative bacteria as E. coli, Pseudomonas and Burkholderia species. We are able to cover the complete proteomes in high extent. Questions concerning pathogenicity are in the focus of our interest. Metaproteomics and tasks of environmental microbiology are rapidly growing fields in our institute. Mainly available techniques (including others) are: metabolic labeling / absolute quantification / label-free quantification / phosphoproteomics / analysis of unknown post-translational modifications / analysis of membrane proteins / secreted proteins / high throughput methods of gel-based proteomics. Moreover, our institute is developing software tools for data analysis and visualization. http://www.mnf.uni-greifswald.de/institute/fr-biologie/institute-und-forschung/institut-fuer-mikrobiologie.html
Günter Lochnit C. elegans, Ascaris suum, Schistosoma mansoni The Protein Analytics group is on one hand a service facility offering a wide range of methods for protein analysis. This includes HPLC separation techniques, 2D-gel electrophoresis,In-gel and on-membrane protein digest, protein identifications by MALDI-TOF-MS peptide mass fingerprint, LC-MALDI-MS coupling and the classical Edman-sequencing.On the other hand we are a research group which interested in the interaction between nematodes and the immune-system of their hosts. In this context, we are interested in post-translational modifications of nematodes, especially, in the modification of proteins and glycosphingolipids with the immunomodulatory compound phosphorylcholine. We investigate the structure of PC-epitopes, their biosynthesis and the function of these epitopes for nematode development and host-persistence. We have a large set of transformed E. colistrain in house for RNAi experiments.

PTMs in C. elegans

Analysis of PC-epitopes

Investigation of PC-epitope biosynthesis

Analysis of nematode host interactions

 

http://www.uni-giessen.de/cms/fbz/fb11/institute/biochemie/forschung/protein-analytik

 

http://www.wormbase.org / http://www.nematode.net/NN3_frontpage.cgi http://www.genedb.org/Homepage/Smansoni
Michael Hengartner /
Sabine Schrimpf
C. elegans Current work of the Hengartner lab focuses on:
engulfment, germ cell death, DNA damage, microbial glycobiology, neurobiology, and systems biology:
www.imls.uzh.ch/research/hengartner.htmlProteomics projects: shotgun comparison of different C. elegans wild-type strains, targeted analysis of microRNA regulation and targeted analysis of cancer pathways. These projects are part of a University
Research Priority Program Systems Biology/Functional Genomics
(www.sysbio.uzh.ch/index.html), a Sinergia project of the Swiss National
Foundation, and the EU FP7 project PANACEA: http://www.panaceaproject.eu/UK/.
http://www.wormbase.org, http://www.peptideatlas.org, http://www.ebi.ac.uk/pride, http://pax-db.org/.
Henning Hermjakob All The EBI Proteomics Services Team provides databases and tools for the deposition, distribution and analysis of proteomics data. We contribute to the development of community standards for proteomics data in the context of the HUPO Proteomics Standards Initiative (PSI), and develop reference implementations for these standards. The three major databases provided by the team are:IntAct – Molecular Interactions, http://www.ebi.ac.uk/intactPRIDE – Protein Identifications by Mass Spectrometry, http://www.ebi.ac.uk/prideReactome – Manually Curated Human Pathways, http://www.reactome.org

iMOP founding members

Christian Ravnsborg www.thermo.com
We work on biological interpretation of proteomics data. ProteinCenter is a web-based tool that enables scientists to compare and interpret proteomics data sets in minutes and overcomes the hurdle of proteins existing under different names and accession keys in different databases. Regularly updated from all major protein databases, ProteinCenter provides a consolidated, biologically annotated, protein sequence database to enable filtering, clustering and statistical bioinformatic analysis from single, combined or comparison data sets.
http://www.proxeon.com/productrange/data_interpretation/introduction/index.html
- TAIR, http://www.arabidopsis.org- FlyBase, http://flybase.bio.indiana.edu/- SGD, http://www.yeastgenome.org/- Pseudomonas Genome Database, http://www.pseudomonas.com/- TubercuList, http://genolist.pasteur.fr/TubercuList/- CMR, http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi- PlasmoDB, http://plasmodb.org/plasmo/
Katja Bärenfaller Arabidopsis thaliana,
Manihot esculenta (in collaboration with the Cassava group lead
by Herve Vanderschuren)
Both me and Herve Vanderschuren work in Willi Gruissem’s group of Plant Biotechnology at ETH Zurich:
http://www.pb.ethz.ch/ Our research is aimed at understanding how proteins, their levels and their activity are regulated, and how this is related to their function and their localisation inside the cell and the plant. The main technology we are employing in our work is quantitative mass spectrometry and for comprehensive analysis of the proteome data we had developed the pep2pro database. The capacity of that database has been demonstrated with the genome-scale organ-specific proteome maps of Arabidopsis thaliana (available at
www.pep2pro.ethz.ch) providing expression evidence for more than 50% of all predicted proteins and new datasets are continually added and made available through the pep2pro website in which we also provide a proteogenomic mapping of the peptides to the genome sequence.The website for my work on Arabidopsis is
http://www.swissplantscienceweb.ch/nc/research/home/portfolio/baerenfaller/
and the website of our collaborating group on Cassava is
http://www.swissplantscienceweb.ch/nc/research/home/portfolio/vanderschuren/
The database for Cassava is downloaded from: http://www.phytozome.net/cassava.php
Steve Briggs Maize (Zea mays), Arabidopsis thaliana, Chlamydomonas reinhardtii, Homo sapiens, mouse, E. coli, Dictyostelium discoideum We primarily study immune signaling in plants and algae; we study the proteomics of development in maize; we study genome annotation using proteogenomics in maize; we study post-transcriptional regulation of differentiation in murine and human embryonic stem cells; as collaborators, we study chemotaxis signaling in Dicty; as collaborators, we study B cell pathology of patients with chronic lymphocytic leukemia; as collaborators, we study the evolution of the genetic code in E. coli.
http://www.biology.ucsd.edu/labs/briggs/
Chlamy
(http://www.phytozome.net/chlamy
Arabidopsis (http://www.masc-proteomics.org/mascp/index.php/Main_Page ;
http://www.phytozome.net/arabidopsis.php; http://www.arabidopsis.org/)Maize (http://www.phytozome.net/maize.php; http://www.maizegdb.org/)Human (http://david.abcc.ncifcrf.gov/home.jsp)Mouse (http://www.informatics.jax.org/)E. coli (http://www.genome.wisc.edu/)Dictyostelium (http://dictybase.org/)
Alex Jones Arabidopsis thaliana, Nicotiana benthamiana, various oomycetes such as Phytophthora infestans, Albugo laibachii I work mainly on Arabidopsis thalianaI also work on Nicotiana benthamiana (no genome sequence yet, I use a collation of available EST and cDNA sequences) and keep an eye on http://solgenomics.net/ In collaboration with Peter Shaw and Graham Moore at the John Innes Centre I have some involvement with wheat/rye proteomics. The John Innes Centre has recently released the first draft of the wheat genome but prediction of the proteome is still under development.I also work with various oomycetes such as Phytophthora infestans, Albugo laibachii. I use sequence data from collaborations with The Sainsbury Laboratory group leaders and keep a eye on http://pmgn.vbi.vt.edu/index.phpMy research interests are deciphering changes to receptor-like kinases and their complexes during plant-pathogen interactions. I specialise in the identification and quantification of phosphorylation, amongst other post-translational modifications and I am also interested in changes to protein subcellular localisation during signalling.My address and lab page:The Sainsbury Laboratory
Norwich Research Park
Norwich
Norfolk NR4 7UH, UK
http://www.tsl.ac.uk/proteomics.htm
http://www.arabidopsis.org http://solgenomics.net/ http://pmgn.vbi.vt.edu/index.php
Christian Ahrens 1) Bartonella henselae
2) Burkholderia cenocepacia complex strains A) strain J2315
B) strain H1113, Arabidopsis thaliana4) Drosophila melanogaster

5) Caenorhabditis elegans

Summary of research interests:- Achieving extensive/”complete” proteome coverage by discovery proteomics approaches
- membrane proteome
- data integration proteomics/txomics/metabolomics
- protein inference
- support targeted quantitative proteomics workflows:
1) peptide information content (Qeli& Ahrens, Nat Biotechnol July 2010)
2) peptide detectability predictionWebsite link: http://www.mop.uzh.ch/
Erich Brunner Drosophila melanogaster Our work mainly focuses on the development of methods that can be used to quantify protein levels in specific subsets of cells of a tissue (in collaboration with Bernd Wollscheid IMSB ETH Zurich). With these methods we investigate how the position of cells in the Drosophila wing imaginal disc affects their ability to respond to developmental or environmental signals. These technology developments are complemented with mass spectrometry-based imaging in collaboration with Ron Heeren, AMOLF, University of Amsterdam, The Netherlands. flybase.org
peptideatlas.org
http://www.mop.uzh.ch/peptideatlas
http://www.primexs.eu/
http://www.wingx.ch/
http://www.imls.uzh.ch/
Klaas van Wijk Primarily plants: Maize, Arabidopsis, rice and also Bienertia sinuspersici
Others: pea aphid Acyrthosiphon pisum and its obligate symbiont the γ-proteobacterium Buchnera aphidicola
Biology of photosynthetic organs in C3 and C4 plants, with particular attention for development, differentiation and protein homeostasis of chloroplasts that are essential photosynthetic organelles. Where possible, these biological processes are studied in a quantitative manner, taking a ‘systems biology’ approach. Primarily three different plant species, namely Arabidopsis thaliana (a C3-type dicotyledon), rice (a C3 type grass) and maize (a C4 type grass) are studied in our lab. We maintain our own mass spectrometers and proteomics infrastructure, and together with colleagues in computational biology, we developed an extensive bioinformatics infrastructure to process these mass spectrometry and proteomics data. We created a freely accessible online Plant Proteomics Database (PPDB) in which protein information for Arabidopsis, maize and rice is integrated. We also provide mass spectrometry and proteomics support and expertise to collaborating labs. (lab web site: http://cbsuss03.tc.cornell.edu/vanwijk/) The Plant Proteomics Database (PPDB at http://ppdb.tc.cornell.edu/)
Ueli Grossniklaus Arabidopsis thaliana, Zea mays, Lilium longiflorum, Ophrys spp., Dionaea muscipula, Nepenthes spp., Pinguicula sp. Our general interest is in plant development and we have used proteomics approaches to get a comprehensive overview on how proteins are expressed, regulated, and partitioned in specific tissues or cells of interest. Most of our work is with Arabidopsis thaliana, where we focus on reproductive tissues. We have contributed proteomics data on various stages of seed development and pollen to the pep2pro database (see K. Bärenfaller’s entry). In the context of plant reproduction, we focus on pollen, where we study proteome dynamics during development, the phosphoproteome, as well as histone modifications in various species (Arabidopsis, maize, lily). We have extended our work to the level of individual cell types and performed shot-gun proteomics on sperm cells and individual cell types of the Arabidopsis root (in collaboration with P. Benfey’s lab, Duke University). In addition, we have also done proteomics experiments on secreted proteins of several carnivorous plants and floral tissues of closely related orchid species (in collaboration with F. Schiestl’s lab, University of Zürich).
Websites: http://www.botinst.uzh.ch/research/development/grossnik.html, http://www.swissplantscienceweb.ch/nc/research/home/portfolio/grossniklaus
Plants: http://www.phytozome.net
Arabidopsis: http://www.arabidopsis.org, http://www.pep2pro.ethz.ch, http://phosphat.mpimp-golm.mpg.de
Maize: http://www.maizegdb.org