Central European Proteomics Conference on Proteomics Driven Discovery and Applications
12-15 October, 2008
Jena, Germany

Organiser:

Aleš Svatos: Max Planck Institute for Chemical Ecology, Jena, Germany

Draft Report

Scientific Content

In mid-October researchers from proteomic laboratories operating in central and Eastern Europe region gathered to Jena, German city of science 2008. They come to Jena to discuss a progress in proteomics driven by a new mass spectrometry technology. This conference represents the second meeting of the Central European Proteomics Conference (CEEPC) series initiated by colleagues from Austria, the Czech Republic, Hungary, Germany, Russia, and Switzerland to promote interaction, partnership, and co-operation in this geographic region. The conference was kindly hosted by Beutenberg Campus Society eV. in the Abbe Zenter, the central lecture hall of the campus. The meeting was organised by Dr. Aleš Svatoš the leader of the Mass Spectrometry Research Group, Max Planck Institute for Chemical Ecology (MPI CE). The team of organisers were generously supported by administrative and technical service groups of MPI CE. Financial support comes from European Science Foundation (ESF) Programme in Functional Genomics, MPI CE, and exhibitors.

The meeting started with registration in the Abbe Zenter lobby on Sunday 12th October, followed by the opening ceremony. In the first welcome talk Prof. Wilhelm Boland, the Beutenberg Campus Society president and a director of MPI CE, told the participants on campus Institutes science, co-operation programs among them, and wishes the Conference a great success. He portrayed Jena as a place where the strong tradition in optic and glass meets new applications in biological sciences, genomics, proteomics, and natural product chemistry. Following speaker, Prof. David Heckle, the MPI CE deputy director, mentioned 450 year anniversary of the Friedrich Schiller University in Jena and tell the fascinated story how and why the University was established in Jena by Johann Friedrich I after loosing his university in Wittenberg and that Jena was elected the Germany City of Science 2008. The opening was closed by Dr. Hana Kovárová, organizer of the 1 st CEEPC meeting in Prague held in 2007. She explained origin of the idea of CEEPC conferences and remembered the last meeting in Prague. After the official opening all participants and quests were welcome to a mixer, where traditional “Bratwust” sausages and local beers were served. The same evening the scientific committee meets with invited speakers in a cosy atmosphere of “Zur Noll” historical restaurant to familiarise with each other and to plan the next CEEPC meeting.

Monday morning the scientific program started by Clinical Proteomic and Interactomics sessions. Opening lecture by Prof. Helmuth Meyer from Bochum (Germany) started with critical review of proteomic methods for protein identification, quatification, and clinical biomarkers discovery. He has stressed that the most likely solution for problems of nowadays proteomic technique is to work in a close cooperation with a clinic people to ensure high quality of samples and to prevent sample proteome degradation during sample handling and storage. Additionally, speaker highlighted laser micro-digestion for sample preparation and independent biomarker validation using orthogonal methods. Next key-note speaker, Dr. Hana Kovárová from Libechov (Czech Republic), reports on advance in proteomic of follicular fluid and plasma from women undergoing artificial fertilization. Her lab is using depletion of the major plasma proteins using IgY-12 columns and obtained fractions are further purified by 2-DE and 2D-LC separation. Proteins are determined after enzymatic digestion using mass spectrometry. The obtained patterns of proteins in follicular fluid could be potential biomarkers for Ovarian Hyperstimulation Syndrome. Slightly modified protocol was used for a study of mechanism of chemoresistance to cyclin-dependent kinase inhibitors in lymphoblastic leukaemia cells, reported by Jana Martinková from the same laboratory. Maria Vlasova (Moscow) discussed scope and limitation of MALDI-TOF/MS analysis for cancer biomarker discovery. Two technical notes from K. Compson (Waters) and V. Kruft (Applied Biosystems) reported on latest development in the field of label-free protein quantification and validation of biomarkers for neurodegenerative diseases, respectively.

Another part of this section discussed methods for study protein-ligand interactions. Prof. Andrea Sinz from Halle presented cross linking strategy using linkers of different length to study 3D structure of proteins and protein-protein(peptide) complexes. The crosslinked proteins are digested and peptides using 2D-nanoLC chromatography separated and fractions analyzed using MALDI-TOF/TOF/MS and ESI-MS (Orbitrap). Calmodulin, laminin and PRARa receptor were studied. Dr. Melle from Jena has been using antibodies linked to SELDI surfaces and analyzed the antibody-bound proteins using SELDI-TOF/MS to study protein-protein interaction in vivo. Different members of S100 Ca2+-binding family and E2F transcription factor and the co-repressor Alien interactomes were detected. Another two lectures used mass spectrometry to observe and study protein-ligands interactions. Prof. Neil Oldham (Nottingham) discussed requirement for successful experimental setup, determination of binding stoichiometry, binding constants, and enzymatic reaction inhibition using lysozyme and a model example. He further reports on a large-scale study of histamine receptor ligands/inhibitors, where high productivity and throughput was achieved using Triversa Nanomate robotic system. Jaroslava Svobodová (Jena) extends previously mentioned measurements on lysozyme moving the assay on a micro-fluidic chip. It obviates needs for low sample consumption and integration to automatic workflow for study enzymatic reaction inhibitors. Her clear and concise presentation was awarded by the best lecture price sponsored by Thermo-Fisher.

Prof. Roman Zubarev (Upsala) has opened afternoon session New Technology for High Throughput Clinical Proteomics with his plenary lecture on development of Pathway Search Engine (PSE) for expression proteomic. So far we have been dealing with identification of individual proteins and problems with database hits validation limits correct assignment of proteins which are regulated in the cell. In the PSE the data from gene mapping and transcription factors analysis are combined with proteomic results and the output is constructed on the level of signalling pathways, rather than on an individual protein level. This approach was shown to be more robust a many fall positive protein identification could be eliminated. This new method was well accepted by the conference audience and the lecture initiated interesting discussion. The section continued by three lectures on proteomic technology. Ingy Petry-Podgorska (Brno) has presented use of monolithic LC columns for Top-down protein regulation study, on the electron transfer dissociation workflow for analysis of posttranslational modifications (K. Scheffler, Thermo Fisher), and finally utility of pMALDI planar chips for sample preparation, enrichment of phosphopeptides, enzymatic on-chip digestion, and multi read out of proteins or DNA was presented by A. Ibanez (Münster). The section ended by a talk on side reactions of N- terminal cysteine after treatment with diverse alkylation agents reported by Pavel Rehulka (Brno).

Tuesday morning Prof. Richard Caprioli had open Spatially Resolved proteomic, Imaging of Biomarkers section. There will not be a better speaker for such plenary lecture as Prof. Caprioli had laid foundation of this area in 1991. He has summarized the basic principals of MALDI-TOF/MS imaging of proteins, the use of this method in cancer diagnostic, and in study of spatial localization of peptides/proteins in the biological tissues (brain, lung, kidney), mostly from human and rats. Lately, he presents recent development in imaging and combination of MALDI imaging with NMR imaging also in 3D space. He argued for MALDI imaging as important tool for clinicians and histologists to recognize the grade of cancer and to direct the extent of cancer tissue removal. Rich discussion followed. Ferdinand von Eggeling (Jena) presents alternative method to study spatial distribution of proteins in tissues using laser micro dissection protocol and subsequent proteomic analysis based on SELDI technique. State-of–art single cell peptidomics of fruit fly presented by Susanne Neupert (Jena) was used to identify peptides in hugin -expressing neurons. Arnd Ingendoh (Bruker) has reviewed novel application in MALDI imaging using matrix spotter, imaging software, and Ultraflex II MALDI to provide an effective workflow for molecular histology.

After coffee break Glycomic, Glycoproteomic and Diseases section was opened by a plenary lecture for Prof. Jasna Peter-Katalinic (Münster), a pioneer of the glycomic field. Importance of glycomic for understanding and treatment of diseases was stressed followed by an overview of sample preparation methods and the methods for glycoproteins structural elucidation. FTMS and ion mobility measurements were shown to unravel the glycoprotein complexity in diagnosis of diseases. All data handling and de novo glycane sequencing is supported by in-house developed software. New software, named GlycoMiner, for glycoprotein structure elucidation was presented by Lazlo Drahos (Budapest). Aberrant glycosylation pattern of hinge region of IgA1 was studied by Marek Šebela (Olomouc) using a combination of nanoLC-MS/MS with Q-tof and MALDI TOF analyses. The complete glysosylation pattern was characterized. Oliver Ozohanocs (Budapest) have used similar methods to study a glycosylation pattern of a-1 acid glycoprotein related to cancer.

The late afternoon was fully devoted to poster section, where all the topics of the CEEPC sections were presented. It has started with 1 min. short presentations of the poster topic to give PhD students a chance to advertise her/his work in the bigger audience. After initial hesitation of students to present very short information (only one slide) it was a great success and it will be adopted for upcoming CEEPC conferences. The poster of Daniela Schmid (Jena) on comparative analysis of male/female brown algal gametes was lately awarded by a poster price (kindly sponsored by Thermo Fisher). Local food and drinks were served during the poster session.

The evening conference dinner organized in MPI for Chemical Ecology started with informal lecture on the development of planetarium by Carl Zeiss Jena and on construction of the first commercial operation in Jena in 1921. Dinner was served from the “Zur Noll” local restaurant and music was provided by a local music band playing a mixture of Latin, soul, and jazz music. Many participants had stay late to discuss the conference lectures and posters, and to start new co-operations.

The last day of 2 nd CEEPC was focussed on Plant and Insect Proteomics. The session was open by Prof. Ian Baldwin (Jena) by an eloquent presentation of insect-plant interaction topic. An amount of data here presented show the dept of study performed in MPI-CE. Recent results of dynamic changes of plant (Nicotiana attenuata) leaf proteome upon insect herbivory were discussed. Surprisingly, plants react on herbivory my modulating internal resources and e.g. the most abundant proteins from photosynthetic apparatus (Rubisco family) seems to be degraded in the early stage to get enough energy to activate plant defence (e.g. inhibitors of insect digestive enzymes called PIs). Lately (within 48-72 h) the loss of photosynthetic capacity is fully compensated. Yannick Pauchet (Peryn, UK) showed insect side of the story. In his presentation methods for isolation and identification of insect digestive enzymes was discussed. Helena Rehulková (Brno) reports on identification of aminoethylated hordenins, barley proteins important for beer production. The section was closed by Alexander Muck's presentation on differentional proteomic of horse chestnut challenged by Cameraria ohridella herbivory. Using de novo sequencing (no genomic information available for horse chestnut) he was able to identify a handful of proteins up-regulated in leaves upon insect larvae infestation, mostly related to stress response and signalling.

The conference scientific program was finished by Dr. Bela Paizs plenary lecture on peptide fragmentation in a gas phase. His fundamental understanding of gas-phase chemistry was presented with many important implications for practical proteomic. He is using CID spectra of model peptides and quantum chemical calculation to explain typical fragmentation patterns. It will be still a long way to go, but the understanding of fragmentation of peptides might replace the genomic database-dependency of proteomics for the true de novo sequencing programs. This final lecture was surely one of the highlights of the conference.

Programme

The full programme and photos from the scientific and social events are to be seen on the conference web: www.ceepc.eu

Future Directions

The 2nd CEEPC was surely a successful event fulfilling the major role of the conference series: to promote interaction, partnership, and co-operation in this geographic region. Sixty three participants attend the conference more than 80% actively. The conference series will continue in 2009 in Budapest, Hungary. We were successful to attract leading persons from different areas of proteomic. Next time we should try even harder to attract more people from Russia, Romania, Poland, Baltic, and Balkan countries. The fall of 2008 year was unfortunately were competitive and several major conferences (HUPO) were organised. As the groups from this geographic region are operating with limited budget, they likely went to larger conference instead of CEEPC. For the conference success the financial support from ESF was vital, and is greatly acknowledged.