www.proteomic-forum.de
Proteomic Forum 2017 University Potsdam Campus Griebnitzsee 2–5 April 2017
Program 2 Notes Table of Contents 3
Proteomic Forum 2017
German Society of Proteome Research 4 Organization and Imprint 5 Welcome Note 6
Scientific Program 8 Program Overview 8 Sunday, 2 April 12 Monday, 3 April 16 Tuesday, 4 April 21 Wednesday, 5 April 26
Poster Sessions 29 Poster Session A – Sunday, 2 April 29 Poster Session B – Monday, 3 April 37 Poster Session C – Tuesday, 4 April 45
Lecture Abstracts of Young Investigator Award Session 55–63
Lunch Workshops 64 Monday, 3 April 64 Tuesday, 4 April 65 Wednesday, 5 April 67
General Information 68 Social Program 74 Sponsors and Exhibitors 75 Room Overview 77
Author List (Chairs, Speakers and Presenting Authors) 78
Key of Abstract IDs IS Abstracts of Invited Speaker YIA Abstracts of Young Investigator Session NC Abstracts of News Corner Session HUPO Abstracts of HUPO Workshop O Abstracts of Oral Abstract Presentations P Abstracts of Poster Presentations 4 DGPF
The German Society of Proteome Research
Objectives of the Society The German Society of Proteome Research as organizer coordinates and provides a network comprising academic institutions, commercial companies and special institutions at the national and international level in order to support the extension of scientific knowledge in the field of proteome research and protein analysis.
President: Albert Sickmann 1st Vice president: Uwe Völker 2nd Vice President: Stefanie Hauck Treasurer: Hans-Peter Braun Schriftführer: Dörte Becher
Organizing Committee
Ruedi Aebersold (Zurich/CH), Julia Bandow (Bochum/DE) Dörte Becher (Greifswald/DE), Karsten Boldt (Tübingen/DE) Christoph Borchers (Victoria/CA), Hans-Peter Braun (Hannover/DE) Stefanie Hauck (Neuherberg/DE), Christian Huber (Salzburg/AT) Friedrich Lottspeich (Stockdorf/DE), Helmut E. Meyer (Bochum/DE) Albert Sickmann (Dortmund/DE), Marius Ueffing (Tübingen/DE) Andrea Urbani (Rome/IT), Uwe Völker (Greifswald/DE)
Session Chairs & Pre-Conference Organizers
The organizers of the Proteomic Forum 2017 wish to thank all those who have been actively involved in the organization of the scientific program as pre-conference program organizer or session chair. Their involvement is highly appreciated and has greatly contributed to the quality of the final program. Organization and Imprint 5
Proteomic Forum 2017
Venue Conference Chairs University of Potsdam Prof. Dr. Albert Sickmann Campus Griebnitzsee, Haus 6 Leibniz-Institut für Analytische August-Bebel-Strasse 89 Wissenschaften – ISAS – e. V. 14482 Potsdam (DE) Dortmund (DE)
Date Prof. Dr. Uwe Völker 2–5 April 2017 Universitätsmedizin Greifswald Interfakultäres Institut für Genetik und Conference Website Funktionelle Genomforschung www.proteomic-forum.de Greifswald (DE)
Hosting Society Deutsche Gesellschaft für Proteomforschung e.V.
Professional Congress Organizer Conventus Congressmanagement & Marketing GmbH Nadia Al-Hamadi/Karoline Koch Carl-Pulfrich-Strasse 1 07745 Jena (DE) Phone +49 3641 31 16-315/-344 Fax +49 3641 31 16-241 [email protected] www.conventus.de
Imprint Layout Martina Kogler, Koma Design, Berlin/DE Pictures www.shutterstock.com © Iuliia Chugai, The German Society of Proteome Research, Einsteinturm auf dem Telegrafenberg © TMB Fotoarchiv Hans Bach, Brandenburger Tor Potsdam © TMB Fotoarchiv Ulf Boettcher, Landtag Potsdam © TMB Fotoarchiv Steffen Lehmann, Glienicker Brücke © TMB Fotoarchiv Bernd Kröger, terra press GmbH, Heilandskirche Sacrow © TMB Foto- archiv, Bernd Kröger, www.shutterstock.com © Andrew Buckin Print siblog – Gesellschaft für Dialogmarketing, Fulfillment & Lettershop mbH Circulation 500 Editorial Deadline 27 March 2017 6 Welcome Note
Dear Colleagues,
On behalf of the Organizing Committee it is a great pleasure to invite you to join the Proteomic Forum 2017. The Proteomic Forum will provide a unique opportunity to present and discuss progress in all fields of proteome research, including applications. In Potsdam in the vicinity of Sanssouci Palace you will have the chance to discuss your data with leading experts in the field. This time a special emphasis will be placed on options for analysis of complex proteomics data, both in hands on workshops performed by experts in the field as well as in special sessions by vendors in which dedicated software solutions for data analysis will be presented. Albert Sickmann Education will be a major theme of the conference and thus the program will feature besides the dedicated computational training courses and educational workshops, diverse activities ranging from a News Corner via a Doctor´s Office and a Young Investigator Session to a Career Session. On Sunday, two workshops organized by HUPO and the Top Down Consortium will focus on two special topics: i )Precision medicine and cardiovascular disease as well as ii) Strategies for the analysis of intact proteins. From Monday through Wednesday, a mix of plenary and parallel sessions will cover topics like: Interaction Proteomics, Mass Spectrometry Based Imaging, Phosphoproteomics, Prote- Uwe Völker omics in Health and Disease, Integrative OMICs, Systems Biology, Computational OMICs, Native and Top Down Mass Spectrometry, Structural Proteomics, Extracellular Vesicles and Protein Secretion, Host-Pathogen-Interaction, Plant-, Agricultural and Microbial Proteomics, Epigenetics and Histone Landscape up to Glycomics and Post-Translational Modifications. Thus, a broad spectrum of technical fields and application of proteomics will be covered by talks of invited speakers and short talks selected from submitted abstracts. Each of the participants will have the opportunity to present latest results in three poster sessions from Sunday through Tuesday. Complementing the scientific program, an industrial exhibition will cover the latest products and developments in proteomics technologies. You are cordially invited by the German Society of Proteome Research and we will be delighted to welcome you in Potsdam! With best regards,
Albert Sickmann Uwe Völker Conference Chair Conference Chair President of the DGPF Vice-President of the DGPF Welcome Note 7
Proteomic Forum 2017 Program Overview
Sunday, 2 April Monday, 3 April H04 H01 H02 S16 H04 H01 H02 S18 09:00–11:30 09:00–10:30 09:00–10:30 Educational Day Interaction Proteomics Training Course: Session I Computational OMICs Oliver Kolbacher
p. 16 p. 16
11:00–12:30 11:00–12:30 p. 12 Mass Spectrometry Training Course: Based Imaging Computational OMICs Martin Eisenacher 12:00–13:45 Educational Day p. 16 p. 16 Session II 12:45–13:45 12:45–13:45 12:45–13:45 Thermo Fisher Scientific GmbH Bruker Daltonik GmbH Waters GmbH
p. 12 p. 17/64 p. 17/64 p. 17/64
14:00–15:30 14:00–15:30 14:00–15:00 14:00–15:00 14:00–15:30 14:00–15:30 Workshop: HUPO Workshop: Moving Native and Top Down Computational OMICs Career Session Training Course: Top Down Consortium to Precision Medicine: Solv- Mass Spectrometry Computational OMICs ing Cardiovascular Disease p. 17 p. 17 Bruker Daltonik GmbH 15:00–16:30 p. 12 p. 13 Poster Session B and Industrial Exhibition p. 18 p. 18 15:45–17:45 Mass spectrometry Technologies | Plant and Microbial Proteomics I | Post-Translational News Corner Modifications I | Proteomics for Human Health II | Quantitative Proteomics I | Top Down 16:00–17:30 16:00–17:30 Proteomics and Macromolecular Complexes 16:00–17:30 Workshop: HUPO Workshop: Moving p. 37 ff. Training Course: Top Down Consortium to Precision Medicine: Solv- 16:30–17:30 16:30–17:30 16:30–17:30 Computational OMICs ing Cardiovascular Disease Extracellular Vesicles Plant and Agricultural Host-Pathogen Interaction Waters GmbH and Protein Secretion Proteomics and Antibiotical Resistance and Microbial Proteomics p. 12 p. 13 p. 20 p. 19 p. 20 p. 19 p. 14 17:30–18:30 General Assembly DGPF p. 20 18:00–19:30 Welcome and Opening Lecture p. 15 19:30–20:30 Poster Session A and Get-together Affinity Proteomics | Bioinformatics | Free Topics | Proteogenomics | Proteomics for Human Health I | Proteomics in Biotechnology | Standardization in Proteomics and Industrial Exhibition p. 29 ff.
Plenary Session Symposium Training Course News Corner, YIA, Career Session Lecture Poster Session Workshop Lunch Symposium Social Program Meeting DGPF Sunday, 2 April Monday, 3 April H04 H01 H02 S16 H04 H01 H02 S18 09:00–11:30 09:00–10:30 09:00–10:30 Educational Day Interaction Proteomics Training Course: Session I Computational OMICs Oliver Kolbacher
p. 16 p. 16
11:00–12:30 11:00–12:30 p. 12 Mass Spectrometry Training Course: Based Imaging Computational OMICs Martin Eisenacher 12:00–13:45 Educational Day p. 16 p. 16 Session II 12:45–13:45 12:45–13:45 12:45–13:45 Thermo Fisher Scientific GmbH Bruker Daltonik GmbH Waters GmbH p. 12 p. 17/64 p. 17/64 p. 17/64
14:00–15:30 14:00–15:30 14:00–15:00 14:00–15:00 14:00–15:30 14:00–15:30 Workshop: HUPO Workshop: Moving Native and Top Down Computational OMICs Career Session Training Course: Top Down Consortium to Precision Medicine: Solv- Mass Spectrometry Computational OMICs ing Cardiovascular Disease p. 17 p. 17 Bruker Daltonik GmbH 15:00–16:30 p. 12 p. 13 Poster Session B and Industrial Exhibition p. 18 p. 18 15:45–17:45 Mass spectrometry Technologies | Plant and Microbial Proteomics I | Post-Translational News Corner Modifications I | Proteomics for Human Health II | Quantitative Proteomics I | Top Down 16:00–17:30 16:00–17:30 Proteomics and Macromolecular Complexes 16:00–17:30 Workshop: HUPO Workshop: Moving p. 37 ff. Training Course: Top Down Consortium to Precision Medicine: Solv- 16:30–17:30 16:30–17:30 16:30–17:30 Computational OMICs ing Cardiovascular Disease Extracellular Vesicles Plant and Agricultural Host-Pathogen Interaction Waters GmbH and Protein Secretion Proteomics and Antibiotical Resistance and Microbial Proteomics p. 12 p. 13 p. 20 p. 19 p. 20 p. 19 p. 14 17:30–18:30 General Assembly DGPF p. 20 18:00–19:30 Welcome and Opening Lecture p. 15 19:30–20:30 Poster Session A and Get-together Affinity Proteomics | Bioinformatics | Free Topics | Proteogenomics | Proteomics for Human Health I | Proteomics in Biotechnology | Standardization in Proteomics and Industrial Exhibition p. 29 ff.
Plenary Session Symposium Training Course News Corner, YIA, Career Session Lecture Poster Session Workshop Lunch Symposium Social Program Meeting DGPF Program Overview
Tuesday, 4 April Wednesday, 5 April H04 H02 S16 S18 H04 H01 H02 09:00–10:30 09:00–10:30 09:00–10:30 Phosphoproteomics Training Course: Integrative OMICs Computational OMICs Robert Ahrens/ Dominik Kopczynski p. 21 p. 21 p. 26
11:00–12:30 11:00–12:30 11:00–12:30 Proteomics in Health Training Course: Systems Biology and Disease Computational OMICs Thermo Fisher Scientific GmbH p. 21 p. 21 p. 26
12:45–13:45 12:45–13:45 12:45–13:45 12:45–13:45 12:45–13:45 Thermo Fisher Scientific GmbH Biognosys AG SCIEX Training Course: Doctor’s Office: Computational OMICs Serva Electrophoresis GmbH SCIEX
p. 22/65 p. 22/65 p. 22/66 p. 26 p. 26/67
14:00–15:00 14:00–15:00 14:00–15:30 14:00–15:30 14:00–15:00 14:00–15:00 14:00–15:00 Proteomics for Plant and Microbial Proteomics Training Course: Training Course: Structural Proteomics Glycomics and Post-Translational Epigenetics and Histone Landscape Human Health Computational OMICs Computational OMICs Modifications Waters GmbH Thermo Fisher Scientific p. 22 p. 23 GmbH p. 27 p. 27 p. 28 15:00–16:30 Poster Session C and Industrial Exhibition p. 23 p. 24 15:15–16:15 Integrated OMICs/Systems Biology | Plant and Microbial Proteomics II | Post-Translational Modifications II | Proteomics Award Ceremony for Human Health III | Quantitative Proteomics II | Structural Proteomics | Subcellular Proteomics and Closing Lecture p. 45 ff. 16:00–17:30 p. 28 Training Course: 16:30–18:00 Computational OMICs Young Investigator SCIEX Session p. 24
p. 25
from 19:30 Congress Party (Mensa) p. 74
Plenary Session Symposium Training Course News Corner, YIA, Career Session Lecture Poster Session Workshop Lunch Symposium Social Program Meeting DGPF Tuesday, 4 April Wednesday, 5 April H04 H02 S16 S18 H04 H01 H02 09:00–10:30 09:00–10:30 09:00–10:30 Phosphoproteomics Training Course: Integrative OMICs Computational OMICs Robert Ahrens/ Dominik Kopczynski p. 21 p. 21 p. 26
11:00–12:30 11:00–12:30 11:00–12:30 Proteomics in Health Training Course: Systems Biology and Disease Computational OMICs Thermo Fisher Scientific GmbH p. 21 p. 21 p. 26
12:45–13:45 12:45–13:45 12:45–13:45 12:45–13:45 12:45–13:45 Thermo Fisher Scientific GmbH Biognosys AG SCIEX Training Course: Doctor’s Office: Computational OMICs Serva Electrophoresis GmbH SCIEX p. 22/65 p. 22/65 p. 22/66 p. 26 p. 26/67
14:00–15:00 14:00–15:00 14:00–15:30 14:00–15:30 14:00–15:00 14:00–15:00 14:00–15:00 Proteomics for Plant and Microbial Proteomics Training Course: Training Course: Structural Proteomics Glycomics and Post-Translational Epigenetics and Histone Landscape Human Health Computational OMICs Computational OMICs Modifications Waters GmbH Thermo Fisher Scientific p. 22 p. 23 GmbH p. 27 p. 27 p. 28 15:00–16:30 Poster Session C and Industrial Exhibition p. 23 p. 24 15:15–16:15 Integrated OMICs/Systems Biology | Plant and Microbial Proteomics II | Post-Translational Modifications II | Proteomics Award Ceremony for Human Health III | Quantitative Proteomics II | Structural Proteomics | Subcellular Proteomics and Closing Lecture p. 45 ff. 16:00–17:30 p. 28 Training Course: 16:30–18:00 Computational OMICs Young Investigator SCIEX Session p. 24
p. 25
from 19:30 Congress Party (Mensa) p. 74
Plenary Session Symposium Training Course News Corner, YIA, Career Session Lecture Poster Session Workshop Lunch Symposium Social Program Meeting DGPF 12 Scientific Program Sunday, 2 April
09:00–11:30 Educational Day Session I Room H 01 Chairs Nina Overbeck, Falk Baberg (Düsseldorf/DE) 10:00 Applications of click-chemistry in proteomics Jeroen Krijgsveld (Heidelberg/DE) 10:45 Selective proteomic proximity labeling Johanna Rees (Cambridge/GB) 11:30–12:00 Break
12:00–13:45 Educational Day Session II Room H 01 Chair Christine von Törne (Munich/DE) 12:00 Data analysis using skyline Michael MacCoss (Seattle, WA/US) 12:45 Protein cross-linking and MS Fan Liu (Utrecht/NL) 13:45–14:00 Break
14:00–15:30 Workshop: Top Down Consortium Room H 01 14:00 Top Down Proteomics – Strategy and Implementation Neil Kelleher (Evanston, IL/US) 15:30–16:00 Break
16:00–17:30 Workshop: Top Down Consortium Room H 01 16:00 Top Down MS – Tools and Tricks for Data Processing Neil Kelleher (Evanston, IL/US) 16:30 Top-down Case Study – analysis of human body fluid with nanoLC quadrupole-orbitrap, ProSight and TDViewer Peter Verhaert (Herentals/BE) Scientific Program • Sunday, 2 April 13
Proteomic Forum 2017
14:00–15:30 HUPO Workshop: Moving to Precision Medicine: Solving Cardiovascular Disease Room H 02 Chair Jennifer van Eyk (Los Angeles, CA/US) 14:00 Introduction and Welcome Christoph Borchers (Victoria/CA) 14:05 Connecting the dots – digital objects in cardiovascular diseases Peipei Ping (Los Angeles, CA/US) 14:35 Scalability of antibodies use in tracking chronic disease Jochen Schwenk (Solna/SE) 15:05 Longitudinal Proteomics of Cardiac Tissue Highlights HUPO3 Decrease of Matricelullar Proteins in Left Ventricular Assist Device Therapy Jasmin Hasmik Shahinian (Basel/CH), Bettina Mayer, Stefan Tholen, Hannah Füllgraf, Selina Kiefer, Peter Bronsert, Kerstin Brehm, Martin L. Biniossek, Ulrike Heizmann, Claudia Heilmann (Freiburg/DE), Florian Reuter, Martin Grapow, Oliver Thomas Reuthebuch, Friedrich Eckstein (Basel/CH), Friedhelm Beyersdorf, Matthias Siepe, Oliver Schilling (Freiburg/DE) 15:16 In-depth Protein Expression Analysis of Histamine Stimulated HUPO4 Human Umbilical Vein Endothelial Cells to Evaluate Functional Selectivity of Histamine Receptor Ligands Pelin Esma Emirbayer (Erlangen/DE), Ankit Sinha, Vladimir Ignatchenko, Thomas Kislinger (Toronto/CA), Monika Pischetsrieder (Erlangen/DE) 15:30–16:00 Break
16:00–17:30 HUPO Workshop: Moving to Precision Medicine: Solving Cardiovascular Disease Room H 02 Chairs Christoph Borchers (Victoria/CA) 16:00 Start at the end – developing and delivering mass spectrometry diagnostic tests of clinical utility Stephen Pennington (Dublin/IR) 16:30 Plasma Proteomics in Epidemiology: HUPO6 Very Low-Density Lipoprotein Associated Apolipoproteins Predict Cardiovascular Events and Are Lowered by Inhibition of ApoC-III Manuel Mayr (London/GB) 17:00 Exogenous blood plasma peptides HUPO7 Georgij Arapidi, Maria Osetrova, Tatjana Saveleva, Polina Pavlovich, Olga Ivanova, Victoria Shender, Ivan Butenko, Nikolay Anikanov, Rustam Ziganshin, Vadim Ivanov, Vadim Govorun (Moscow/RU) 14 Scientific Program Sunday, 2 April
17:11 Proteomic and Lipidomic differences of the plasma elimination HUPO8 rate of current lipoprotein apheresis methods Gerd Schmitz, Stefan Wallner, Silke Matysik (Regensburg/DE), Jürgen Gräßler (Dresden/DE), Christoph Borchers (Victoria/CA), Ulrich Julius (Dresden/DE), Helmut E. Meyer (Dortmund/DE) 17:22 Summary Jennifer van Eyk (Los Angeles, CA/US) 15:45–17:45 News Corner Room S 16 Chairs Helmut E. Meyer (Bochum/DE) 15:45 Comparison of different proteomic sample preparation protocols NC01 for quantity limited material Ute Distler, Malte Sielaff, Stefan Tenzer (Mainz/DE) 15:55 Detecting the special ones – automated identification of NC02 modifications and mutations in MS/MS VIRUS proteomics data using tag-based searching Felix Hartkopf, Thilo Muth, Jörg Doellinger, Bernhard Y. Renard (Berlin/DE) 16:05 Integrated reporting of search results from sequence databases NC03 and spectral libraries John Cottrell, David Creasy, Ville Koskinen, François Ripp (London/GB) 16:15 Accelerating data independent acquisition with microflow NC04 chromatography Zuzana Demianova, Joerg Dojahn (Darmstadt/DE), Nick Morrice (Warrington/GB), Remco Van Soest, Christie L. Hunter (Redwood Shores, CA/US) 16:25 QuiC – a fast, easy to use QC monitor that allows you to generate NC05 QC readouts in real time from raw files of various vendors and workflows (MRM, PRM, DIA, DDA) Ian Lienert, Florian Marty, Lukas Reiter (Schlieren-Zurich/CH) 16:35 Microfluidic free-flow electrophoresis for protein separation NC06 Pedro Novo, Margherita Dell’ Aica, René P. Zahedi, Dirk Janasek (Dortmund/DE) 16:45 Proteotyping enables grouping and classification of biogas NC07 plant microbiomes Robert Heyer, Fabian Kohrs, Dirk Benndorf, Kay Schallert (Magdeburg/DE), Jo de Vrieze (Ghent/BE), Erdmann Rapp, Udo Reichl (Magdeburg/DE) 16:55 Protein arginine phosphorylation in Staphylococcus aureus NC08 Sabryna Junker, Timo Sachsenberg (Tübingen/DE), Robert Starke Nico Jehmlich, Martin von Bergen (Leipzig/DE), Oliver Kohlbacher (Tübingen/DE) Scientific Program • Sunday, 2 April 15
Proteomic Forum 2017
17:05 Identifying coding genomic variants in proteome analysis without NC09 the customized genomic databases Mark V. Ivanov (Moscow, Dolgoprudny/RU), Lev I. Levitsky, Anna A. Lobas, Sergei A. Moshkovskii (Moscow/RU), Mikhail V. Gorshkov (Moscow, Dolgoprudny/RU) 17:15 Tissue homogenization for proteomics by laser ablation NC10 with the picosecond infrared laser Hartmut Schlüter, Marcel Kwiatkowski, Marcus Wurlitzer, Manka Marceline Fuh, Laura Heikaus, Pascal Steffen, Refat Nimer, Andrey Krutilin, Nils-Owe Hansen, Stephanie Uschold, Hannes Petersen, Dwayne Miller (Hamburg/DE) 17:25 Adaptation of the filamentous fungus Aspergillus nidulans NC11 to low temperature stress Benjamin Hanf, Thomas Krüger (Jena/DE), Boyke Bunk (Braunschweig/DE), Derek Mattern (Jena/DE), Jörg Overmann (Braunschweig/DE), Olaf Kniemeyer, Axel A. Brakhage (Jena/DE) 17:35 MSqRob – analysis of label-free proteomics data NC12 in an R/Shiny environment Ludger Goeminne, Emmy Van Quickelberghe, Kris Gevaert, Lieven Clement (Gent/BE) 17:30–18:00 Break
18:00–19:30 Welcome and Opening Lecture Room H 04 Chair Albert Sickmann (Dortmund/DE) 18:00 Proteome centric precision health – Changing medicine? IS01 Jennifer van Eyk (Los Angeles, CA/US) 19:30–20:30 Poster Session A and Get-together Room 1st Floor Affinity Proteomics P002–P008 p. 29 Bioinformatics P011–P031 p. 30 Free Topics P032–P038 p. 32 Proteogenomics P100–P103 p. 32 Proteomics for Human Health I P104–P117 p. 33 Proteomics in Biotechnology P149–P157 p. 34 Standardization in Proteomics P193–P196 p. 35 16 Scientific Program Monday, 3 April
09:00–10:30 Interaction Proteomics Room H 04 Chair Karsten Boldt (Tübingen/DE) 09:00 A physical map of a human cell IS02 Anne-Claude Gingras (Toronto/CA) 09:45 Amino acid hydroxylation – a common and sometimes IS03 misunderstood post-translational modification Alex von Kriegsheim (Edinburgh/GB) 09:00–10:30 Training Course: Computational OMICs: OpenMS/knime Room S 18 Chair Oliver Kohlbacher (Tübingen/DE) 10:30–11:00 Break
11:00–12:30 Mass Spectrometry Based Imaging Room H 04 Chair Uwe Völker (Greifswald/DE) 11:00 Molecular microscopy – employing mass spectrometry to image IS04 biomolecules in their native state Richard Caprioli (Nashville, TN/US) 11:45 Instruments and Methods – new achievements and perspectives IS05 in high-performance mass spectrometry imaging Bernhard Spengler (Giessen/DE) 11:00–12:30 Training Course: Computational OMICs: Special Aspects of Bioinformatics for Proteomics Room S 18 Chair Martin Eisenacher (Bochum/DE) 12:30–14:00 Lunch Workshops and Break Scientific Program • Monday, 3 April 17
Proteomic Forum 2017
12:45–13:45 Thermo Fisher Scientific GmbH Lunch Workshop Room H 01 p. 64 12:45–13:45 Bruker Daltonik GmbH Lunch Workshop Room H 02 p. 64 12:45–13:45 Waters GmbH Lunch Workshop Room S 18 p. 64 14:00–15:00 Native and Top Down Mass Spectrometry Room H 04 Chair Kai Stühler (Düsseldorf/DE) 14:00 Native mass spectrometry for the revelation of highly complex IS06 glycosylation in protein therapeutics Christian Huber (Salzburg/AT) 14:20 Native top-down proteomics IS07 Neil Kelleher (Evanston, IL/US) 14:50 Complexome analysis – identification of old and new complexes O01 Katja Seidel, Chang Ding, Joana Karbe, Lorenz Adrian (Leipzig/DE) 14:00–15:00 Computational OMICs Room H 01 Chair Martin Eisenacher (Bochum/DE) 14:00 Computational strategies for improving the quantitative analysis IS08 of peptide mixtures by tandem mass spectrometry Michael MacCoss (Seattle, WA/US) 14:20 Computational strategies for deep proteomics and IS09 proteogenomics datasets Alexey I. Nesvizhskii (Ann Arbor, MI/US) 14:40 Mass spectrometrists should search for all peptides, but assess only O03 the ones they care about Ariaan Sticker, Lieven Clement, Lennart Martens (Ghent/BE) 14:50 Workflows for unified MS1- and MS2-based protein inference O04 in a Bayesian framework Julianus Pfeuffer (Tübingen/DE), Xiao Liang, Oliver Serang, Knut Reinert (Berlin/DE), Oliver Kohlbacher (Tübingen/DE) 18 Scientific Program Monday, 3 April
14:00–15:30 Career Session Room H 02 Chair Christian Moritz (St. Étienne/FR) Employability has been one of the main goals of the Bologna process. However, many universities neglect to train their students’ skills in career planning, especially beyond academia. The Career Session can help to fill this gap. Well-known companies of the proteomics sector present their focuses and inform about requested competences for candidates. Current job vacancies will be presented. In addition, the chances and obstacles of academic careers will be addressed in one of the talks. The following companies and their representatives will present during the session: 14:00 Petra Blankenstein, Sales (Darmstadt/DE)
14:13 Lukas Reiter, Chief Technology Officer (Schlieren/CH)
14:26 Tobias Börsig, Talent Acquisition Manager (Dreieich/DE)
14:39 Michael Schroda (Kaiserslautern/DE)
14:52 Norbert Chlup, Human Resources Manger, Central and Eastern Europe (Eschborn/DE) 14:05 tba 15:18 tba 14:00–15:30 Training Course: Computational OMICs: Bruker Daltonik GmbH Room S 18 The glycopeptide detection and characterization workflows offered by the Glycoquest software will be illustrated, before providing a practical illustration of MALDI imaging data processing. 15:00–16:30 Poster Session B Room 1st Floor Mass spectrometry Technologies P050–P055 p. 37 Plant and Microbial Proteomics I P056–P063 p. 38 Post-Translational Modifications I P072–P085 p. 39 Proteomics for Human Health II P118–P132 p. 40 Quantitative Proteomics I P158–P175 p. 42 Top Down Proteomics and P213–P216 p. 43 Macromolecular Complexes Scientific Program • Monday, 3 April 19
Proteomic Forum 2017
16:00–17:30 Training Course: Computational OMICs: Waters GmbH Enhanced Discovery ‘Omics Workflow in Complex Biological Matrices – Finding the Needle in the Haystack Room S 18 Discovery ‘Omics analysis is the first and most complex step in the overall workflow for Biomarker discovery. It involves quantitative analysis and comparison of all analytes in complex mixtures between two or more conditions to discover what is changing expression and may therefore be considered candidate biomarkers. The normal method of discovery ‘Omics analysis, is compared with the more efficient co-detection method used in Progenesis QI for Proteomics software. After discussing the benefits of co-detection, a “live” demonstration of Progenesis QI for Proteomics will be given to illustrate the speed, ease of use and power of the Progenesis workflow. Agnes Corbin (Newcastle upon Tyne/GB) 16:30–17:30 Plant and Agricultural Proteomics Room H 01 Chair Hans-Peter Braun (Hannover/DE) 16:30 The plant mitochondrial proteome IS10 Ian Max Møller (Skagekse/DK) 16:50 Plant phosphoproteomic resources and technologies – from IS11 discovering phosphorylation sites to identifying kinase clients Jay Thelen (Columbia, SC/US) 17:10 Deep proteomics reveals genome-wide protein expression O05 dynamics in Arabidopsis immunity and development Mona Bassal, Petra Majovsky, Domenika Thieme (Halle/DE), MHD Rami Al Shweiki (Ulm/DE), Ali Hmedat, Tobias Herr, Jörg Ziegler, Steffen Neumann, Wolfgang Hoehenwarter (Halle/DE) 17:20 A large-scale approach to study the mitochondrial protein-protein O06 interactome of Arabidopsis thaliana Silvia Martinez Jaime, Alexander Graf (Berlin/DE) 20 Scientific Program Monday, 3 April
16:30–17:30 Host-pathogen Interaction and Antibiotical Resistance and Microbial Proteomics Room H 02 Chair Uwe Völker (Greifswald/DE) 16:30 Metaproteomics and integrated multi-omics – What do they IS14 tell us about microbial community function? Paul Wilmes (Esch-sur-Alzette/LU) 16:50 Infectoproteomics for the characterisation of the interaction IS13 of the human pathogenic fungus Aspergillus fumigatus with immune cells Axel A. Brakhage (Jena/DE) 17:10 Ribosome-targeting antibiotics and mechanisms IS12 of bacterial resistance Daniel N. Wilson (Munich/DE) 16:30–17:30 Extracellular Vesicles and Protein Secretion Room H 04 Chair Helmut E. Meyer (Bochum/DE) 16:30 Confounding factors and contaminants of extracellular IS15 vesicle preparations Edit Buzas (Budapest/HU) 16:50 Exosome-mediated release of Alzheimer’s disease amyloid IS16 Lawrence Rajendran (Zurich/CH) 17:10 Secretome analysis during cardiomyogenic differentiation O07 of human pluripotent stem cells Hanna Wolling, Sarah Konze, Anne Höfer, Andreas Pich, Falk Buettner (Hannover/DE) 17:20 The role of ubiquitylation on the phagosome – a tale of O08 inflammatory responses and vesicle trafficking Orsolya Bilkei-Gorzo (Dundee/GB), Anetta Härtlova, Julien Peltier, Matthias Trost (Newcastle upon Tyne, Dundee/GB) 17:30–18:30 General Assembly of the DGPF Room H 01 Scientific Program • Tuesday, 4 April 21
Proteomic Forum 2017
09:00–10:30 Phosphoproteomics Room H 04 Chair Stefanie Hauck (Munich/DE) 09:00 Building models of signaling networks from phosphoproteomics to tackle cancer Julio Saez-Rodriguez (Aachen/DE) 09:45 Neuro-phosphoproteomics – application of sensitive IS18 phosphoproteomics strategies in neurobiology Martin Larsen (Odense/DK) 09:00–10:30 Training Course: Computational OMICs: SearchGUI, PeptideShaker Room S 18 Chairs Robert Ahrens, Dominik Kopczynski (Dortmund/DE) 10:30–11:00 Break
11:00–12:30 Proteomics in Health and Disease Room H 04 Chair Gerd Schmitz (Regensburg/DE) 11:00 Dynamic proteome organization and host defense IS19 during viral infection Ileana M. Cristea (Princeton, NJ/US) 11:45 Advances in Protein Biomarker Research for quantity IS20 limited material Ruedi Aebersold (Zurich/CH) 11:00–12:30 Training Course: Computational OMICs: Thermo Fisher Scientific Discovery Proteomics workflows in Proteome Discoverer Room S 18 In the workshop you will learn about the study management system and advanced quantitative workflows (including associated statistical tools) which were recently introduced in Proteome Discoverer for labeled and label-free quantification. Bernard Delanghe, André Muller (Dreieich/DE) 12:30–14:00 Lunch Workshops and Break 22 Scientific Program Tuesday, 4 April
12:45–13:45 Thermo Fisher Scientific GmbH Lunch Workshop Room H 02 p. 65 12:45–13:45 Biognosys AG Lunch Workshop Room S 16 p. 65 12:45–13:45 SCIEX Lunch Workshop Room S 18 p. 66 14:00–15:00 Proteomics for Human Health Room H 04 Chair Friedrich Lottspeich (Stockdorf/DE) 14:00 Landscape of nuclear transport receptor cargo specificity O11 Marie-Therese Mackmull (Heidelberg/DE), Alessandro Ori (Jena/DE), Martin Beck (Heidelberg/DE) 14:10 Refining the human proteome – integrated analysis of human O12 tissues with a multi-omics approach Hannes Hahne, Dongxue Wang (Freising/DE), Basak Eraslan (Munich/DE), Thomas Wieland (Freising/DE), Björn Hallström (Stockholm/SE), Lihua Li (Freising/DE), Anna Asplund, Frederik Ponten (Uppsala/SE), Mathias Uhlen (Stockholm/SE), Julien Gagneur (Munich/DE), Bernhard Kuster (Freising/DE) 14:20 Protein array enabled profiling of autoantibody repertoires O13 within health and disease Peter Nilsson (Stockholm/SE) 14:30 Social network architecture of human immune cells unveiled O14 by quantitative proteomics Jan C. Rieckmann (Martinsried/DE), Roger Geiger (Bellinzona/CH), Daniel Hornburg (Martinsried/DE), Ksenya Kveler (Haifa/IL), Tobias Wolf, David Jarrossay, Federica Sallusto (Bellinzona/CH), Shai S. Shen-Orr (Haifa/IL), Antonio Laanzavecchia (Bellinzona/CH), Matthias Mann, Felix Meissner (Martinsried/DE) 14:40 Highly parallelized, automated and precise native sample O15 preparation for proteome analysis and biomarker search: comprehensive search for altered proteoforms as potential biomarkers Heidrun Rhode (Jena/DE) Scientific Program • Tuesday, 4 April 23
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14:50 MASP1, THBS1, GPLD1 and ApoA-IV are novel biomarkers O16 associated with prediabetes – the KORA F4 study Christine von Törne, Cornelia Huth, Tonia de las Heras Gala (Neuherberg/DE), Florian Kronenberg (Innsbruck/AT), Christian Herder (Neuherberg, Düsseldorf/DE), Wolfgang Koenig (Ulm, Munich/DE), Christa Meisinger (Neuherberg, Augsburg/DE), Wolfgang Rathmann (Neuherberg, Düsseldorf/DE), Melanie Waldenberger (Neuherberg/DE), Michael Roden (Neuherberg, Düsseldorf/DE), Anette Peters, Barbara Thorand, Stefanie Hauck (Neuherberg/DE) 14:00–15:00 Plant and Microbial Proteomics Room H 02 Chair Dörte Becher (Greifswald/DE) 14:00 N-terminal phosphorylation of LHCSR3 is light triggered IS21 and synergistic and operates as a molecular switch for LHCB4 phosphorylation and LHCSR3 multi-protein complex association Michael Hippler (Münster/DE) 14:20 Using 15N metabolic labeling for the accurate quantification IS22 of changes in proteome composition in Chlamydomonas cells Michael Schroda (Kaiserslautern/DE) 14:40 Probing the global kinome and phosphoproteome in O09 Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics Leslie Hicks, Emily Werth, T. S. Karim Gilbert, Lee Graves (Chapel Hill, NC/US) 14:50 The proteomics response of the human-pathogenic fungus O10 A.fumigatus to the antifungal drug caspofungin Olaf Kniemeyer, Thomas Krüger, Theresia Conrad, Sebastian Henkel, Reinhard Guthke, Jörg Linde, Axel A. Brakhage (Jena/DE) 14:00–15:30 Training Course: Computational OMICs: Waters GmbH Enhanced Discovery ‘Omics Workflow in Complex Biological Matrices – Finding the Needle in the Haystack Room S 16 Discovery ‘Omics analysis is the first and most complex step in the overall workflow for Biomarker discovery. It involves quantitative analysis and comparison of all analytes in complex mixtures between two or more conditions to discover what is changing expression and may therefore be considered candidate biomarkers. The normal method of discovery ‘Omics analysis, is compared with the more efficient co-detection method used in Progenesis QI for Proteomics software. After discussing the benefits of co- detection, a “live” demonstration of rogenesis QI for Proteomics will be given to illustrate the speed, ease of use and power of the Progenesis workflow. Agnes Corbin (Newcastle upon Tyne/GB) 24 Scientific Program Tuesday, 4 April
14:00–15:30 Training Course: Computational OMICs: Thermo Fisher Scientific GmbH Structural Proteomics in Proteome Discoverer Room S 18 In this workshop you will learn about new nodes available in Proteome Discoverer for data processing of Top-Down (ProSightPD) and Cross- Linking (XlinkX) experiments Bernard Delanghe, Sonja Radau (Dreieich/DE) 15:00–16:30 Poster Session C Room 1st Floor Integrated OMICs/Systems Biology P040–P049 p. 45 Plant and Microbial Proteomics II P064–P071 p. 46 Post-Translational Modifications II P086–P098 p. 47 Proteomics for Human Health III P133–P148 p. 48 Quantitative Proteomics II P176–P192, P217 p. 50 Structural Proteomics P197–P202 p. 52 Subcellular Proteomics P203–P212 p. 53 16:00–17:30 Training Course: Computational OMICs: SCIEX Germany GmbH Room S 16 We will give you an introduction in the principles of the Paragon™ algorithm, which is used for protein identification in ProteinPilot™ software. You will learn how to navigate through the software to identify proteins, peptide modifications as well as protein classes and their isoform specific peptides. We will show you how ProteinPilot™ software could be used for relative quantitation of proteins by labeling strategies like iTRAQ® reagents and SILAC. Scientific Program • Tuesday, 4 April 25
Proteomic Forum 2017
16:30–18:00 Young Investigator Session Room H 04 Chair Kai Stühler (Düsseldorf/DE) 16:30 Profiling the phosphotyrosine interactome of receptor YIA1 tyrosine kinases Runsheng Zheng, Chen Meng, Bernhard Kuster (Freising/DE) 16:45 Dynamics of protein synthesis and degradation in FLG22-stimulated YIA2 arabidopsis Phillip Ihmor, Wilhelm Gruissem, Mark Robinson, Katja Baerenfaller (Zurich/CH) 17:00 Optimised de novo peptide sequencing and proteogenomics YIA3 workflows to refine ab initio gene prediction Bernhard Blank-Landeshammer, Laxmikanth Kollipara, Karsten Biß (Dortmund/DE), Tilman Schell (Frankfurt a. M./DE), René P. Zahedi (Dortmund/DE), Markus Pfenninger (Frankfurt a. M./DE), Albert Sickmann (Dortmund/DE) 17:15 Deciphering acute cellular response to X-ray-, proton- and carbon ion YIA4 irradiation via quantitative proteomics and phosphoproteomics Martin Winter, Ivana Dokic, Ramona Mayer, Uwe Warnken, Amir Abdollahi, Martina Schnölzer (Heidelberg/DE) 17:30 Impact of gene overdosage in the hippocampus and cerebellum YIA5 proteome and phosphoproteome Mireia Ortega, Ilario De Toma, Eduard Sabidó, Mara Dierssen (Barcelona/ES) 17:45 Protein complex identification using combination of fractionation YIA6 methods and label-free quantification of complexome changes Michał Górka, Alexander Graf (Potsdam/DE), Sebastian Streb (Zurich/CH) 19:30–23:00 Congress Party Room Mensa p. 74 26 Scientific Program Wednesday, 5 April
09:00–10:30 Integrative OMICs Room H 04 Chair Albert Sickmann (Dortmund/DE) 09:00 From integrative OMICS to predictive, mechanistic models IS23 Lars Kaderali (Greifswald/DE) 09:45 The other side of integration – proteomics as a vital tool IS24 in other omics Lennart Martens (Ghent/BE) 10:30–11:00 Break
11:00–12:30 Systems Biology Room H 04 Chair Marius Ueffing (Tübingen/DE) 11:00 First and second derivative proteomics – how speed and IS25 acceleration in protein synthesis and degradation provide a critical energy use window required for a systems biology understanding of cellular function and potential Harvey Millar (Crawley/AU) 11:45 tba IS26 Rob Russell (Heidelberg/DE) 12:30–12:45 Lunch Workshop and Break
12:45–13:45 Doctor’s Office: Serva Electrophoresis GmbH Room H 02 12:45–13:45 Training Course: Computational OMICs: SCIEX Room H 01 We will show you how to navigate through PeakView® and MarkerView™ software for SWATH® processing and give you an overview on our cloud based data processing solution – the OneOmics™ project. You will learn how to generate SWATH® ion libraries, process and review your SWATH® data as well as doing statistics on it and visualize the results. 13:45–14:00 Break Scientific Program • Wednesday, 5 April 27
Proteomic Forum 2017
14:00–15:00 Structural Proteomics Room H 04 Chair Albert Sickmann (Dortmund/DE) 14:00 Developing structural interactomics and its application IS27 in cell biology Fan Liu (Utrecht/NL) 14:20 Structural systems biology – towards a complete 3D map IS28 of molecular structures in living systems Matthias Wilmanns (Hamburg/DE) 14:40 Selective Proteomic Proximity labelling using Tyramide O17 (SPPLAT) – a novel proteomic method to identify protein interactors and neighbours in microenvironments Johanna Rees, Kathryn Lilley, Tony Jackson (Cambridge/GB) 14:50 RNP-ID generates a picture of the molecular interactions O18 during shuttling and mRNP export Florian Richter, Anfisa Solovyeva, Ilka Wittig, Micheala Müller-McNicoll (Frankfurt a. M./DE) 14:00–15:00 Glycomics and Post-Translational Modifications Room H 01 Chair Friedrich Lottspeich (Stockdorf/DE) 14:00 Disease-associated glycosylation changes in colorectal cancer IS29 and autoimmune diseases Manfred Wuhrer (Leiden/NL) 14:20 MS-based glycomics and glycoproteomics – crossing the IS30 isomer barrier Yehia Mechref (Lubbock, TX/US) 14:40 A dynamic picture of the ubiquitinome upon O19 proteasome inactivation Jeroen Demmers (Rotterdam/NL) 14:50 Studying protein phosphorylation with ultra-high temporal O20 resolution using a µicroMixing µicroFluidic device Margherita Dell Aica, Pedro Novo, Janeseck Dirk, René P. Zahedi (Dortmund/DE) 28 Scientific Program Wednesday, 5 April
14:00–15:00 Epigenetics and Histone Landscape Room H 02 Chair Gerd Schmitz (Regensburg/DE) 14:00 Identification of protein interactions in chromatin to understand IS31 decision-making in the control room Jeroen Krijgsveld (Heidelberg/DE) 14:20 Establishment versus maintenance of specialised IS32 chromatin domains Robin Allshire (Edinburgh/GB) 14:40 Age and tissue dependent changes in the epigenome measured O21 by middle-down MS Veit Schwämmle, Andrey Tvardovskiy, Giorgio Oliviero, Adelina Rogowska-Wrzesinska, Ole N. Jensen (Odense/DK) 14:50 Pharmacoproteomics of brain disorders O22 Stefan Lichtenthaler, Martina Pigoni, Stephan Müller (Munich/DE) 15:00–15:15 Break
15:15–16:15 Award Ceremony and Closing Lecture Room H 04 Chair Uwe Völker (Greifswald/DE) 15:15 Award Ceremony for Young Investigator Prizes, Promotion Prize and Poster Prizes 15:30 Exploration and Exploitation of Human Proteomes Bernhard Küster (Freising/DE) Poster Sessions 29
Proteomic Forum 2017
Poster Session A – Sunday, 2 April
Affinity Proteomics P002–P008 p. 29 Bioinformatics P011–P031 p. 30 Free Topics P032–P038 p. 32 Proteogenomics P100–P103 p. 32 Proteomics for Human Health I P104–P117 p. 33 Proteomics in Biotechnology P149–P157 p. 34 Standardization in Proteomics P193–P196 p. 35
Affinity Proteomics P002 Species specific protein analysis of animal derived blood products by enrichment strategies and LC-MS Alicia Niedzwiecka, Lyes Boucharef, Lina Hanisch, Christel Rozycki (Berlin/DE), Andreas Steinhilber, Oliver Poetz (Tübingen/DE), Jutta Zagon, Albert Braeuning, Alfonso Lampen (Berlin/DE) P004 Screening of 1000 small molecule kinase inhibitors using chemical proteomics Maria Reinecke, Susan Klaeger, Stephanie Heinzlmeir (Freising, Munich, Heidelberg/DE), Mathias Wilhelm, Guillaume Médard (Freising/DE), Bernhard Kuster (Freising, Munich, Heidelberg/DE) P005 Identifying drug targets and target engagement biomarkers using proteome-wide CETSA and ITDR Gabriele Stoehr, Melanie Maschberger, Sandra Poser, Thomas Wieland, Bernhard Kuster, Hannes Hahne (Freising/DE) P006 Chemo-proteomics unravel how Sphingolipid derived small molecules alter protein phosphatase 2A activity and starve cancer from the inside and out Peter Kubiniok (Montreal/CA), Alison McCracken (Irvine, CA/US), Michael Perryman, Stephen Hanessian (Montreal/CA), Aimee Edinger (Irvine, CA/US), Pierre Thibault (Montreal/CA) P007 Proteome-wide identification of glycosylation-dependent interactors of Galectin-1 and Galectin-3 on mesenchymal retinal pigment epithelial cells Jara Obermann, Claudia Priglinger, Magdalena Götz, Juliane Merl-Pham, Arie Geerlof, Sigfried Priglinger, Stefanie Hauck (Munich/DE) P008 A peptide based interaction screen on disease related mutations Katrina Meyer, Marieluise Kirchner, Bora Uyar, Matthias Selbach (Berlin/DE) 30 Poster Sessions
Bioinformatics P011 Horizontal gene transfer detection directly from proteomic MS data Kathrin Trappe, Ben Wulf, Thilo Muth, Jörg Döllinger, Bernhard Y. Renard (Berlin/DE) P012 Physical modeling of the influence of phosphorylation and dephosphorylation processes the p53 protein on its binding with proteins Mdm2 and p300 Kirill Kulikov, Tetiana Koshlan (Saint-Petersburg/RU) P013 OpenProXL – an efficient and versatile XL-MS identification tool Eugen Netz, Timo Sachsenberg, Christian Johannes Gloeckner, Oliver Kohlbacher (Tübingen/DE) P015 Evaluating de novo sequencing in shotgun proteomics – Ready an accurate alternative to database-driven peptide identification with modern instrumentation? Thilo Muth, Bernhard Renard (Berlin/DE) P016 Proline – a software environment for label-free quantification data analysis and exploration David Bouyssié (Toulouse/FR), Anne-Marie Hesse (Grenoble/FR), Emmanuelle Mouton-Barbosa (Toulouse/FR), Alexandre Burel, Christine Carapito (Strasbourg/FR), Véronique Dupierris (Grenoble/FR), Charlotte Macron (Strasbourg/FR), Jean-Philippe Menetrey (Grenoble/FR), Aymen Romdhani (Strasbourg/FR), Jérémie Turbet, Odile Burlet-Schiltz (Toulouse/FR), Sarah Cianférani (Strasbourg/FR), Jérôme Garin, Myriam Ferro, Christophe Bruley (Grenoble/FR) P017 Glycomics@ExPASy to bridge glycomics and proteomics Alessandra Gastaldello, Davide Alocci, Elisabeth Gasteiger, Julien Mariethoz, Frederique Lisacek (Geneva/CH) P018 The MetaProteomeAnalyzer – a software suite for analysis of metaproteomic data in microbiome research Kay Schallert, Dirk Benndorf, Robert Heyer, Fabian Kohrs (Magdeburg/DE), Thilo Muth (Berlin/DE), Udo Reichl (Magdeburg/DE) P019 IdentiPy – an open-source search engine for shotgun proteomics Lev Levitsky, Mark Ivanov, Anna Lobas, Mikhail Gorshkov (Moscow/RU) P020 Imputation of missing data in quantitative proteomics using singular value thresholding Tjeerd Dijkstra, Timo Sachsenberg, Oliver Kohlbacher (Tübingen/DE) P021 Progenesis QI for proteomics for fast, simple and precise analysis of proteomic datasets Janusz Debski, Andy Borthwick, Agnes Corbin (Newcastle/GB) Poster Sessions 31
Proteomic Forum 2017
P022 Stable isotope probing of proteins (protein-SIP) with heavy water (D2O and H218O): a general marker for microbial activity Timo Sachsenberg (Tübingen/DE), Robert Starke, Nico Jehmlich, Martin von Bergen (Leipzig/DE), Oliver Kohlbacher (Tübingen/DE) P023 BioInfra.Prot – bioinformatics services for proteomics within the German Network for Bioinformatics Infrastructure (de.NBI) Michael Turewicz, Michael Kohl, Maike Ahrens, Gerhard Mayer, Martin Eisenacher (Bochum/DE) P024 A survey to characterize the German Proteomics Community and to identify the scientists needs regarding Bioinformatics Julian Uszkoreit, Michael Kohl, Michael Turewicz, Gerhard Mayer, Maike Ahrens, Martin Eisenacher (Bochum/DE) P025 Reliable protein quantification in the OpenMS software framework Lars Nilse, Ursula Kern (Freiburg/DE), Jonas Grossmann, Christian Trachsel (Zurich/CH), Tino Polen, Pitter Huesgen (Jülich/DE), Oliver Schilling (Freiburg/DE) P026 MasPy – mass spectrometry-based proteomics data analysis with python David Hollenstein, Jakob Hollenstein (Vienna/AT) P027 Diving deeper – iterative and automatic strain identification of microbial tandem mass spectra Mathias Kuhring, Thilo Muth, Bernhard Y. Renard (Berlin/DE) P029 Phylogeny and expression insights into the interaction preference of trans-membrane receptor/co-receptor pairs Lin Xi, Zhaoxia Zhang, Xuna Wu, Waltraud Schulze (Stuttgart/DE) P030 De novo identification and taxonomic analysis of human blood peptides, not being a product of known human genes Maria Osetrova, Georgij Arapidi (Dolgoprudny, Moscow/RU), Olga Ivanova (Moscow/RU), Tatiana Savel’eva (Dolgoprudny/RU), Ivan Butenko (Moscow/RU), Vadim Govorun (Dolgoprudny, Moscow/RU) P031 A mathematical model of temperature aggregation of protein structures in aqueous solutions Tetiana Koshlan, Kirill Kulikov (Saint-Petersburg/RU) 32 Poster Sessions
Free Topics P032 Retrospective study of antibiotic resistance among Salmonellatyphi Isolated from a Tertiary Hospital of Mid Western Nepal Tarani Paneru (Kathmandu/NP) P033 Black vs White merino wool fibre – a proteomics study using iTRAQ Jeffrey Plowman (Basseterre/KN), Ancy Thomas (Lincoln/NZ), Tiago Perloiro (Evora/PT), Stefan Clerens, Andre de Almeida (Lincoln/NZ) P034 A novel high yield protein production system based on CHO cell lysates Lena Thoring, Marlitt Stech, Srujan Dondapati, Doreen Wüstenhagen, Stefan Kubick (Potsdam/DE) P035 Proteome analysis reveals stimulation of protein biosynthesis in murine liver by non-genomic thyroid hormone signalling Janine Golchert, Vanessa Kracke, Beatrice Engelmann (Greifswald/DE), Lisbeth Harder (Lübeck/DE), Carolin Höfig (Berlin/DE), Manuela Gesell Salazar (Greifswald/DE), Jens Mittag (Lübeck/DE), Georg Homuth, Uwe Völker (Greifswald/DE) P036 A comprehensive Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions Stephan Michalik, Maren Depke, Ulrike Mäder, Tanja C. Meyer, Annette Murr, Manuela Gesell Salazar (Greifswald/DE) Ulrike Kusebauch, Samuel L. Bader, Robert L. Moritz (Seattle, WA/US), Uwe Völker, Frank Schmidt (Greifswald/DE) P037 Expression of Glutathione S-Transferases in different life stages of zebrafish: a targeted proteomics approach Alena Tierbach (Dübendorf, Lausanne/CH), Ksenia Groh (Zurich/CH), Kristin Schirmer (Dübendorf, Lausanne, Zurich/CH), Marc J.-F. Suter (Dübendorf, Zurich/CH) P038 Proteomic analysis of hemorrhage induced by the snake venom metalloproteinase HF3 and of the regeneration process in the mouse skin Amanda F. Asega, Eduardo S. Kitano (São Paulo/BR), André Zelanis (São José dos Campos/BR), Milene C. Menezes, Solange M. T. Serrano (São Paulo/BR)
Proteogenomics P100 Proteogenomic analysis of human tissues Dongxue Wang, Thomas Wieland, Mathias Wilhelm (Freising/DE), Anna Asplund, Frederik Ponten (Uppsala/SE), Mathias Uhlen (Stockholm/SE), Hannes Hahne, Bernhard Kuster (Freising/DE) Poster Sessions 33
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P101 Biodiversity research based on a combinatorial approach comprising proteomics, proteogenomics and MS/MS spectral similarity Laxmikanth Kollipara, Bernhard Blank-Landeshammer, Karsten Biß, Vera Rieder (Dortmund/DE), Marleen Stuhr (Bremen/DE), Tilman Schell (Frankfurt a. M./DE), René Peiman Zahedi (Dortmund/DE), Markus Pfenninger (Frankfurt a. M./DE), Jörg Rahnenführer (Dortmund/DE), Hildegard Westphal (Bremen/DE), Albert Sickmann (Dortmund/DE) P102 Identification of small proteins in Staphylococcus aureus strain Newman Erik Lehmann, Martin Kucklick, Ayten Mustafayeva, Tobias Ludwig, Maurice Diwo (Braunschweig/DE), Stephan Fuchs (Wernigerode/DE), Susanne Engelmann (Braunschweig/DE) P103 Identification of stress response proteins in Baikal endemic amphipods using proteogenomics Daria Bedulina (Irkutsk/RU), Stefan Kalkhof (Coburg/DE), Anton Gurkov (Irkutsk/RU), Polina Drozdova (Saint Petersburg/RU), Maxim Timofeyev (Irkutsk/RU), Till Luckenbach (Leipzig/DE)
Proteomics for Human Health I P104 Proteomics based understanding of the mechanism of Amyloid formation in novel Hemoglobins, characterization by biochemical and biophysical methods and investigating the role of Amyloids in Alzheimer’s Ravi Kant (New Delhi/IN) P105 Plasma proteomic profile of patients with inflammatory bowel disease – non invasive tool for diagnosis and coorelation with disease activity Pacint Moez, Ezzat Ali, Salah El-Din Badr El-Din, Mohamed Eid, Doaa Header (Alexandria/EG) P107 Interaction of neutrophils with Aspergillus fumigatus hyphae – a quantitative dual proteome study Iordana Shopova, Thomas Krüger, Theresia Conrad (Jena/DE), Tobias Müller, Marcus Dittrich (Würzburg/DE), Reinhard Guthke, Olaf Kniemeyer, Axel A. Brakhage (Jena/DE) P108 The proteome profile of post-surgery and post-radiotherapy recurrence in pancreatic ductal adenocarcinoma Victor Oginga Oria (Freiburg/DE), Peter Bronsert (Freiburg, Heidelberg/DE), Ulrich Wellner (Lübeck/DE), Oliver Schilling (Freiburg, Heidelberg/DE) P110 Investigations into proteomic effects in rat liver induced by28-days subacute oral nanosilver treatment Sabine Juling, Axel Oberemm, Christine Meckert, Jana Potkura, Alicia Niedzwiecka, Albert Braeuning, Alfonso Lampen (Berlin/DE) 34 Poster Sessions
P111 Proteomic differences in histopathological variants of papillary thyroid carcinoma Yasemin Ucal (Istanbul/TR), Murat Eravci (Berlin/DE), İrep Uras, Muazzez Ceren Yılmaz, Cavit Kerem Kayhan, Fatma Tokat, Mete Duren, Umit Ince, Aysel Ozpinar (Istanbul/TR) P112 Effects of Magnesium-based, biodegradable implants on the protein pattern of human mesenchymal stem cells under osteogenic differentiation Heike Helmholz (Geesthacht/DE), Maryam Omidi (Hamburg/DE), Berengere Luthringer (Geesthacht/DE), Hartmut Schlüter (Hamburg/DE), Regine Willumeit-Römer (Geesthacht/DE) P113 The huntington-chaperone HYPK & ITS multifaceted roles in Huntington’s disease Kamalika Roy Choudhury (Kolkata/IN) P114 Effects of Clostridium difficile toxins on the phosphoproteome and glucosylation degree of small GTPases Johannes Junemann, Chantal Lämmerhirt, Jelena Erdmann, Felix Polten, Ingo Just, Ralf Gerhard, Andreas Pich (Hannover/DE) P115 Toxins of Clostridium difficile reorganize the proteome of target cells Johannes Junemann, Jelena Erdmann, Alexander Wulf, Chantal Moana Lämmerhirt, Anke Schröder, Ingo Just, Ralf Gerhard, Andreas Pich (Hannover/DE) P116 Exogenous blood plasma peptides Georgij Arapidi, Maria Osetrova, Tatjana Saveleva, Polina Pavlovich, Olga Ivanova, Victoria Shender, Ivan Butenko, Nikolay Anikanov, Rustam Ziganshin, Vadim Ivanov, Vadim Govorun (Moscow/RU) P117 Evidence for immunomodulatory effects of peritoneal Alanyl-Glutamine in clinical peritoneal dialysis detected by a novel multi-omics biomarker approach Klaus Kratochwill, Rebecca Herzog, Anja Wagner, Markus Unterwurzacher, Katja Parapatics, Peter Majek, Keiryn Bennett (Vienna/AT), Seth L. Alper (Boston, MA/US), Christoph Aufricht, Andreas Vychytil (Vienna/AT)
Proteomics in Biotechnology P149 MSPEP27 – a peptide mimetic of human Interferon-beta (IFNβ) for treatment of Multiple Sclerosis Mohammad Foad Abazari (Tehran/IR), Matin Asghari (Isfahan/IR), Reza Mahmoudi (Tehran/IR), Nima Sanadgol (Zabol/IR), Seyed Shahriar Arab, Mansour Poorebrahim (Tehran/IR) P150 Cell-free systems as novel tools for directed engineering of “difficult-to-express” proteins Anne Zemella, Lena Thoring, Stefan Kubick (Potsdam/DE) Poster Sessions 35
Proteomic Forum 2017
P151 Eukaryotic cell-free systems – a novel source for functional antibodies Marlitt Stech (Potsdam/DE), Michael Hust (Braunschweig/DE), Olga Nikolaeva, Tatjana Nitzer (Berlin, Potsdam/DE), Walter F. M. Stöcklein, Lena Thoring, Doreen A. Wüstenhagen (Potsdam/DE), Stefan Dübel (Braunschweig/DE), Stefan Kubick (Potsdam/DE) P152 Analysis of PPIase FkpA from Corynebacterium glutamicum and FkpA-dependent transcriptional response and protein level changes at increased process temperature Tino Polen, Nicolai Kallscheuer, Shah Alam, Jan van Ooyen, Doris Rittmann, Aliye Mengus-Kaya, Michael Bott (Jülich/DE) P153 Investigations on the mechanism of thermo tolerancewith the aim of identifying mitigation leads against heat stress Arabinda Mahanty (Barrackpore, Kolkata/IN), Gopal K. Purohit, Sasmita Mohanty (Bhubaneswar/IN), Bimal P. Mohanty (Barrackpore, Kolkata/IN) P154 Autoimmune regulator (AIRE) regulates the expression of several nucleic acid binding and cytoskeletal proteins in spermatogonia Karthika Radhakrishnan, Kongattu Bhagya, Anil Kumar, Anandavalli Devi, Jeeva Sengottaiyan, Pradeep Kumar (Trivandrum/IN) P155 LC-MS-based proteomics for industrial applications Andre Vente (Delft/NL) P156 SILAC reveals the influence of EF-P in E. coli, an elongation factor for polyproline stretches, on the iron metabolism Simon Stephan, Mingjian Wang (Freiburg/DE), Christian Schipp, Nediljko Budisa (Berlin/DE), Veronica Dumit (Freiburg/DE) P157 Proteome characterization of nonsporulating Streptomyces asterosporus DSMZ 41452 and its AdpA mutant via SILAC Mingjian Wang (Freiburg, Berlin/DE), Songya Zhang, Andreas Bechthold Verónica Dumit (Freiburg/DE)
Standardization in Proteomics P193 Optimised peptide retention time standards for targeted proteomics Karsten Schnatbaum (Berlin/DE), Daniel P. Zolg (Freising/DE), Tobias Knaute (Berlin/DE), Mathias Wilhelm (Freising/DE), Johannes Zerweck, Holger Wenschuh (Berlin/DE), Bernhard Kuster (Freising/DE), Ulf Reimer (Berlin/DE) P194 A quality control tool for LCMS based proteomics – MQQC Henrik Zauber, Matthias Selbach (Berlin/DE) 36 Poster Sessions
P195 Biomarker screening by an improved immunoblotting technique – targeting autoantibodies against neglected proteins Christian Moritz, Juliette Svahn, Evelyne Federspiel, Jean-Philippe Camdessanché, Jean-Christophe Antoine (Saint-Étienne/FR) P196 Optimizsation of the proteomic strategies in the analysis of biological material based on MALDI-TOF/TOF mass spectrometry Joanna Hajduk, Jan Matysiak, Agata Swiatly, Zenon Kokot (Poznan/PL) Poster Sessions 37
Proteomic Forum 2017
Poster Session B – Monday, 3 April
Mass Spectrometry Technologies P050–P055 p. 37 Plant and Microbial Proteomics I P056–P063 p. 38 Post-Translational Modifications I P072–P085 p. 39 Proteomics for Human Health II P118–P132 p. 40 Quantitative Proteomics I P158–P175 p. 42 Top Down Proteomics and Macromolecular Complexes P213–P216 p. 43
Mass Spectrometry Technologies P050 Building proteometools based on a complete synthetic human proteome Daniel Zolg, Mathias Wilhelm (Freising/DE), Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute (Berlin/DE), Bernard Delanghe (Bremen/DE), Siegfried Gessulat (Freising, Potsdam/DE), Hans-Christian Ehrlich (Potsdam/DE), Maximilian Weiniger, Peng Yu, Tobias Schmidt, Karl Kramer (Freising/DE), Judith Schlegl (Walldorf/DE), Holger Wenschuh (Berlin/DE), Thomas Moehring (Bremen/DE), Stephan Aiche (Potsdam/DE), Andreas Huhmer (San Jose, CA/US), Ulf Reimer (Berlin/DE), Bernhard Kuster (Freising/DE) P051 Proteomic substrate identification of ADAM10 in primary neurons Johanna Tüshaus (Munich, Mainz/DE), Peer-Hendrik Kuhn, Alessio Colombo, Julia Herber (Munich/DE), Dirk Montag (Magdeburg/DE), Paul Saftig (Kiel/DE), Stefan F. Lichtenthaler (Munich/DE) P052 Advances in targeted omics quantitation using a novel scanning quadrupole DIA method Gunnar Weibchen (Eschborn/DE), Christopher J Hughes, Keith Richardson, Jason Wildgoose, Martin Green, Richard Chapman, Arkadiusz Grzyb, Praveen Harapanahalli, Kirsten Craven (Wilmslow/GB) P053 Quantitation of proteomics samples using a novel scanning quadrupole DIA method Marc Kipping (Eschborn/DE), Chris Hughes, Keith Richardson, Jason Wildgoose, Lee Gethings, James Langridge, Johannes P. C. Vissers (Wilmslow/GB) P054 Accelerating data independent acquisition with microflow chromatography Dietrich Merkel (Darmstadt/DE), Christie Hunter (Redwood City, CA/US), Nick Morrice (Warrington/GB) P055 Imaging Mass Spectrometry (IMS) to discriminate neoplastic diseases Mark Kriegsmann (Heidelberg/DE), Petra Wandernoth (Trier/DE), Gustavo Baretton, Daniela Aust, Katrin Friedrich (Dresden/DE), Christine Stöhr, Arndt Hartmann (Erlangen/DE), Joerg Kriegsmann, Rita Casadonte (Trier/DE) 38 Poster Sessions
Plant and Microbial Proteomics I P056 A comprehensive protein-protein interaction map of the plant tricarboxylic acid cycle, coupled with 13C isotope labelling experiments, reveals considerable association of the constituent proteins and metabolite channeling in a subset of the reactions Youjun Zhang, Alexander Graf, Alisdair Fernie (Potsdam-Golm/DE) P057 The halophyte Cakile maritima is able to recover germination after exposure to high salinity – proteomic insights Ahmed Debez (Hammam-Lif/TN; Hannover/DE), Dagmar Lewejohann, Andreas Pich, Hans-Peter Braun (Hannover/DE) P058 How do roots of the halophyte Cakile maritima respond to long-term salt stress?: a proteomic study Ikram Belghith (Hammam-Lif/TN), Ahmed Debez (Hammam-Lif/TN, Hannover/DE), Dagmar Lewejohann, Tatjana Hildebrandt (Hannover/DE), Chedly Abdelly (Hammam-Lif/TN), Hans-Peter Braun (Hannover/DE) P059 Physiological and protein profiling response of the halophyte Cakile maritima to water deficit stress and subsequent recovery Nejia Farhat, Ikram Belghith, Sarra Hichri (Hammam-Lif/TN), Tatjana Hildebrand (Hannover/DE), Ahmed Debez (Hammam-Lif/TN), Hans-Peter Braun (Hannover/DE) P060 Evaluation of protein extraction methods for metaproteomic analysis of marine sediment Lars Wöhlbrand, Jessica Nachbaur, Bernd Blasius, Ralf Rabus, Christoph Feenders (Oldenburg/DE) P061 Characterisation of beer proteome Martina Grochalova, Hana Konecna, Karel Stejskal, David Potesil, Danuse Fridrichova, Eva Srbova, Katerina Ornerova, Zbynek Zdrahal (Brno/CZ) P062 Ecological and molecular adaptation of the active soil microbial community to climate change-induced stress Robert Starke (Leipzig/DE), Felipe Bastida, Emilio Nicolás (Murcia/ES), Nico Jehmlich (Leipzig/DE) P063 Assignment of malting barley varieties by MALDI-TOF MS profiling Ondrej Sedo (Brno/CZ), Michal Koran (Plzen/CZ), Michaela Jakesova, Renata Mikulikova, Michal Bohac, Zbynek Zdrahal (Brno/CZ) Poster Sessions 39
Proteomic Forum 2017
Post-Translational Modifications I P072 Signatures of complete glycosylphosphatidylinositol-anchored proteins in serum are correlated with (pre-)diabetic states in rats Günter Müller (Garching-Hochbrück/DE), Andreas Herling, Matthias Tschöp (Frankfurt a. M./DE) P073 Didehydrophenylalanine – a modification unique for the beta subunit of poly-galacturonase in plants Kjell Sergeant (Esch-sur-Alzette/LU), Annelie Gutsch (Esch-sur-Alzette/LU; Diepenbeek/BE) Marc Behr (Esch-sur-Alzette/LU; Louvain-la-Neuve/BE), Jenny Renaut, Jean-François Hausman (Esch-sur-Alzette/LU) P074 A simple ChaFRADIC-based method for identification of protease specificity from proteome-derived peptide libraries Minh Nguyen, Gerta Shema, René P. Zahedi (Dortmund/DE), Steven Verhelst (Dortmund/DE; Leuven/BE) P075 Characterization of the putative Radical SAM methyl transferases responsible for the unique C-methylations of Gln and Arg in the methyl-coenzyme M reductase Darja Deobald (Leipzig/DE), Michael Rother (Dresden/DE), Lorenz Adrian, Gunhild Layer (Leipzig/DE) P076 O-glycosylation analysis of human serum Adam Pap (Szeged/HU), Amol Prakash (Toronto/CA), Katalin F. Medzihradszky, Zsuzsanna Darula (Szeged/HU) P077 Transgenic Caenorhabditis elegans as model to study post-translational modifications of human transthyretin in vivo Andrea Henze, Thomas Homann, Isabelle Rohn (Nuthetal/DE), Michael Aschner (Bronx, NY/US), Christopher D. Link (Boulder, CO/US), Burkhard Kleuser, Florian J. Schweigert, Tanja Schwerdtle, Julia Bornhorst (Nuthetal/DE) P078 Multifraction, label-free quantitation of N-glycosylated proteins with Progenesis QI for proteomics Agnes Corbin, Janusz Debski (Newcastle upon Tyne/GB) P079 Role of protein thiol modifications in oxygen sensing mechanisms of the fungal pathogen Aspergillus fumigatus Elena Shekhova, Thomas Krüger, Olaf Kniemeyer, Axel A. Brakhage (Jena/DE) 40 Poster Sessions
P080 The impact of peritoneal dialysis fluid on O-GlcNAcylation of the mesothelial cell proteome and resulting changes of cell survival Rebecca Herzog, Kathrin Stampf, Anja Wagner, Christoph Aufricht, Klaus Kratochwill (Vienna/AT) P081 Increased confidence for the identification of N-linked glycopeptides using an optimised collision energy workflow Gunnar Weibchen (Eschborn/DE), Yi-Ju Chen (Taipei/TW), Lee A. Gethings (Wilmslow/GB), Alex Kuo, Yu-Ju Chen (Taipei/TW) P082 Spotlight on protein oxidation – identification of novel carbonylated amino acids in proteins from human plasma Adelina Rogowska-Wrzesinska (Odense/DK) P083 Incorporation of cell-free synthesized membrane proteins into microsomes and nanodiscs Srujan Kumar Dondapati, Doreen Wüstenhagen, Stefan Kubick (Potsdam/DE) P084 Identification of ubiquitin system components involved in the DNA damage response Matthias Ostermaier, Juanjuan Wang (Mainz/DE), Denis Dalic, Sebastian Wagner (Frankfurt a. M./DE), Petra Beli (Mainz/DE) P085 Sensitive and accurate quantitation of phosphopeptides using TMT isobaric labeling technique Pamela Saliba (Dreieich/DE), Xiaoyue Jiang (San Jose, CA/US), Ryan Bomgarden (Rockford, IL/US), Rosa Viner, Andreas Huhmer (San Jose, CA/US)
Proteomics for Human Health II P118 Impact of temperature and time-of-storage on the stability of biomarkers for a novel multiplex-protein array based serum diagnostics of pancreatic cancer Giulia Facchinetti, Timo Gemoll, Stefanie Arndt, Katja Klempt-Giessing (Lübeck/DE), Philip Lowry (Crumlin/GB), Jens Habermann (Lübeck/DE) P119 MALDI-imaging – identification of protein signatures of genomic instability in colorectal cancers Timo Gemoll (Lübeck/DE), Oliver Klein (Berlin/DE), Sarah Strohkamp, Elena Miroll, Katharina Schillo, Christoph Thorns, Jens Habermann (Lübeck/DE) P120 Protein alterations observed in sporadic colorectal cancers are distinct from those found in ulcerative colitis associated cancers and allow prognostic stratification Timo Gemoll, Sophie Kollbeck, Karl F. Karstens, Gia G. Hò (Lübeck/DE), Sonja Hartwig (Düsseldorf, Munich-Neuherberg/DE), Sarah Strohkamp, Katharina Schillo, Christoph Thorns, Martina Oberländer, Kathrin Kalies (Lübeck/DE), Stefan Lehr (Düsseldorf, Munich-Neuherberg/DE), Jens Habermann (Lübeck/DE) Poster Sessions 41
Proteomic Forum 2017
P121 Secretome signature of malignant Melanoma Vittoria Matafora, Clara Bernardelli, Angela Bachi (Milan/IT) P122 The limited effects of the major birch pollen allergen – revealing the allergenicity of Bet v 1 using HPLC-MS-based proteome analysis of stimulated dendritic cells Lisa Strasser, Jutta Horejs-Hoeck, Fatima Ferreira, Christian Huber (Salzburg/AT) P123 DNA damage-induced crosstalk between cancer cells and their microenvironment Victoria Shender, Polina Shnaider, Georgij Arapidi, Ksenia Anufrieva, Maria Lagarkova, Irin Malyants, Marat Pavlyukov, Ivan Butenko (Moscow/RU), Grigory Stepanov, Evgenij Juravlev (Novosibirsk/RU), Vadim Govorun (Moscow/RU) P124 Spatial proteomics reveals an intratumoral gradient of aggressiveness in hepatocellular carcinoma Katarzyna Buczak (Heidelberg/DE), Alessandro Ori, Joanna Kirckpatrick (Heidelberg, Jena/DE), Daniel Dauch (Tübingen/DE), Stephanie Roessler, Volker Endris, Felix Lasitschka (Heidelberg/DE), Alexander Schmidt (Basel/CH), Lars Zender (Tübingen/DE), Peter Schirmacher, Stephan Singer, Martin Beck (Heidelberg/DE) P125 Comparative analysis of porcine optic nerve head and retina subproteomes Sebastian Funke, Sascha Markowitsch, Natarajan Perumal, Norbert Pfeiffer, Franz H. Grus (Mainz/DE) P126 The proteome profile of recessive dystrophic epidermolysis bullosa driven cutaneous squamous cell carcinoma Melanie C. Föll, Matthias Fahrner, Victor Oria, Martin L. Biniossek, Oliver Schilling, Alexander Nyström, Johannes S. Kern (Freiburg/DE) P129 Differential analysis of Protein Expression Profiling (PEP) of Tannin-Treated Methicillin Resistant Staphylococcus Aureus (MRSA) using 2-D gel electrophoresis Dayang Fredalina Basri, Radhiah Khairon, Mariati Abdul Rahman (Kuala Lumpur/MY) P130 MALDI-Imaging as a tool do detect new biomarkers in prostate cancer Annette Lischka, Christoph Dumke (Lübeck/DE), Oliver Klein (Berlin/DE), Christoph Thorns (Lübeck/DE), Marie Ståhlberg, Jens K. Habermann, Alexey Chernobrovkin (Stockholm/SE), Timo Gemoll (Lübeck/DE) P132 Platelet Extracellular Vesicles are carriers of proteins. lipds and miRNA involved in vascular- and neurodegenerative diseases Fouzi El Magraoui, Christoph Bochers (Dortmund/DE), Evelyn Orso (Regensburg/DE), Helmut E. Meyer (Dortmund/DE), Gerd Schmitz (Regensburg/DE) 42 Poster Sessions
Quantitative Proteomics I P158 iST – sample preparation for high throughput clinical proteomics – a novel, fast, sensitive and reproducible sample preparation for MS-based proteomics Garwin Pichler, Nils Kulak, Matthias Mann (Martinsried/DE) P159 Thermal proteome profiling for drug discovery Isabelle Becher (Heidelberg/DE) P160 Characterisation of cerebrospinal fluid via data-independent acquisition mass spectrometry Katalin Barkovits, Andreas Linden, Sara Galozzi, Julian Uszkoreit (Bochum/DE), Brit Mollenhauer (Kassel/DE), Katrin Marcus (Bochum/DE) P161 Evaluation of a pulsed SILAC-TMT multiplexing strategy for measurement of proteome dynamics Jana Zecha (Freising, Munich, Heidelberg/DE), Chen Meng, Mathias Wilhelm (Freising/DE), Bernhard Kuster (Freising, Munich, Heidelberg/DE) P162 Proteomic differences between fetal and adult blood stem and progentor cells Maria Jassinskaja, Trine Kristiansen, Hugo Åkerstand, Karin Olsson, Kristoffer Sjöholm, Simon Hauri, Johan Malmström, Joan Yuan, Jenny Hansson (Lund/SE) P163 Comparative evaluation of relative label-free quantitation methods for “shotgun” proteomics Julia Bubis, Mark Ivanov, Lev Levitsky, Irina Tarasova, Mikhail Gorshkov (Moscow/RU) P164 Hit-Gel – streamlining in-gel protein digestion for high-throughput proteomics experiments Corné Swart, Silvia Martinez Jaime, Michal Gorka, Kerstin Zander, Alexander Graf (Potsdam-Golm/DE) P165 Quantitative proteome analysis of carcinoma associated fibroblasts and normal human fibroblasts in 2D and 3D cell culture reveals changes induced by 3D culture conditions Regine Tölle (Fribourg/CH; Freiburg/DE), Julia Donauer (Freiburg/DE), Jörn Dengjel (Fribourg/CH; Freiburg/DE) P166 Qualitative and quantitative characterization of a novel DIA Method for omics analysis and its application to biomedical analyses Marc Kipping (Eschborn/DE), Arthur M. Moseley (Durham, NC/US), Chris Hughes (Wilmslow/GB), Erik Soderblom, Will Thompson (Durham, NC/US), Nick Tomczyk, Johannes P. C. Vissers, Keith Richardson, Jason Wildgoose, James Langridge (Wilmslow/GB) P167 High precision retention time indexing (iRT) improves coverage and reproducibility in the targeted analysis of DIA data using Spectronaut Roland Bruderer, Oliver M. Bernhardt, Tejas Gandhi, Lukas Reiter (Schlieren/CH) Poster Sessions 43
Proteomic Forum 2017
P168 Absolute quantification of the human plasma proteome by using stable-isotope-standard peptides in data-independent-acquisition analysis Sebastian Müller, Jan Muntel, Lukas Reiter (Schlieren/CH) P169 Quantitative proteome analysis of plasma microparticles for characterization of HCV-induced hepatocellular carcinoma Raghda Taleb (Bochum/DE; Alexandria/EG), Pacint Moez, Doreen Younan (Alexandria/EG), Thilo Bracht, Barbara Sitek (Bochum/DE) P170 Higher multiplexing with NeuCode SILAC metabolic labeling Ryan D. Bomgarden (Rockford, IL/US), Katherine A. Overmyer, Elyse C. Freiberger, Alexander S. Hebert, Michael S. Westphall (Madison, WI/US), Juergen H. Cox (Martinsried/DE), Joshua J. Coon (Madison, WI/US), John C. Rogers (Rockford, IL/US), André C. Müller (Vienna/AT) P171 Targeted data-independent-acquisition data analysis in super complex samples Roland Bruderer, Lukas Reiter (Schlieren/CH) P172 A new method for label-free quantification in the proteome discoverer framework Claire Dauly (Courtaboeuf/FR), Torsten Ueckert, Kai Fritzemeier, Katja Tham, Carmen Paschke, (Bremen/DE), Joseph Brown (San Jose, CA/US), Bernard Delanghe (Bremen/DE) P173 Comprehensive proteomic analysis of ibrutinib mediated changes on protein levels and PTMs in human B cells Reinhild Rösler, Angelina Dangel, Sebastian Wiese (Ulm/DE) P174 Dynamic range test of QqTOF (Impact II) proteomics platform Kamil Mikulášek, David Potěšil, Zbyněk Zdráhal, Jan Havliš (Brno/CZ) P175 A simplified approach to fast and accurate, high throughput targeted MS2 quantitation using internal standards Sonja Radau (Dreieich/DE), Romain Huguet, Graeme McAlister, Vlad Zabrouskov, Michael Blank, Shannon Eliuk (San Jose, CA/US)
Top Down Proteomics and Macromolecular Complexes P213 Hydrophobic interaction chromatography for bottom-up proteomics analysis of single proteins and protein complexes Michal Rackiewicz (Fribourg/CH), Adrew J. Alpert (Columbia, SC/US), Mostafa Zarei (Basel/CH), Jörn Dengjel (Fribourg/CH) 44 Poster Sessions
P214 Venom analysis of the transcaucasian nose-horned Viper (Vipera ammodytes transcaucasiana) by mass spectrometry and bioactivity screening Benjamin-Florian Hempel (Berlin/DE), Ayse Nalbantsoy (Izmir/TR), Daniel Petras (San Diego, CA/US), Bayram Gocmen, Mert Karıs, Mehmet Anıl Oğuz (Izmir/TR), Roderich D. Süssmuth (Berlin/DE) P215 Potential effects on the variation of the venom for species of the viperidae family caused by environmental influences Robert Sroka, Benjamin-Florian Hempel (Berlin/DE), Ayse Nalbantsoy, Bayram Gocmen (Izmir/TR), Daniel Petras (San Diego, CA/US), Mert Karis, Mehment Anil Oguz (Izmir/TR), Roderich Süßmuth (Berlin/DE) P216 The study of intact casein as a model system for the separation of intact phosphorylated proteins by Capillary Electrospray Ionization (CESI) Stephen Lock (Warrington/GB), Christopher Lößner (Darmstadt/DE) Poster Sessions 45
Proteomic Forum 2017
Poster Session C – Tuesday, 4 April
Integrated OMICs/Systems Biology P040–P049 p. 45 Plant and Microbial Proteomics II P064–P071 p. 46 Post-Translational Modifications II P086–P098 p. 47 Proteomics for Human Health III P133–P148 p. 48 Quantitative Proteomics II P176–P192, P217 p. 50 Structural Proteomics P197–P202 p. 52 Subcellular Proteomics P203–P212 p. 53
Integrated OMICs/Systems Biology P040 Protein synthesis and secretion provides insight into signaling pathways: the case of BRAF-V600E in melanocytes Gertjan Kramer, Jeroen Krijgsveld (Heidelberg/DE) P041 Metaproteomics reveals significant changes in the community structure and the functional composition of the intestinal microbiota after gastric bypass surgery Sven Haange, Nico Jehmlich, Constantin Hintschich, Mohammed Hankir, Florian Seyfried, Wiebke Fenske, Martin von Bergen (Leipzig/DE) P042 IMS-DIA-MS characterisation and IMS-MRM QconCAT quantitation of the Lipidome and Apolipoprotein complements of obesity and diabetes cohorts Marc Kipping (Eschborn/DE), Lee A. Gethings, Johannes P. C. Vissers (Wilmslow/GB), Jose Castro-Perez (Milford, CT/US), Yvonne Woolerton, Lynn McLean, Robert Beynon (Liverpool/GB), James Langridge (Wilmslow/GB) P043 Of Cancer and chaos – onco-omics view on how a single mutation alters the cellular landscape Mohamed ali Jarboui, Layal Dernayka (Tübingen/DE), Susan Kennedy, Cinzia Raso (Dublin/IE), Kenneth Bryan (Adelaide/AU), Sascha Dammeier, Jörg Schlotterbeck, Franziska Klose, Nicola Horn, Michael Lämmerhofer (Tübingen/DE), David Lynn (Adelaide/AU),Walter Kolch (Dublin/IE), Marius Ueffing, Karsten Boldt (Tübingen/DE) P044 Proteome changes influence the functional decline of the intestinal epithelium during aging Nadja Gebert, Joanna Kirkpatrick, Jerome Korzelius (Jena/DE), Henry Jasper (Jena/DE; Novato, CA/US), Alessandro Ori (Jena/DE) P045 Identification of the “success” factors of Mycobacterium Tuberculosis Beijing B0/W148 cluster strains by using OMICs methods Julia Bespyatykh, Egor Shitikov, Ivan Butenko (Moscow/RU), Nataliya Melnikova, Viacheslav Zhuravlev,Igor Mokrousov (St. Petersburg/RU), Elena Ilina (Moscow/RU) 46 Poster Sessions
P046 Structural and functional insights into the ruminal microbiome by using a combination of different Omics techniques Jana Seifert, Simon Deusch, Amélia Camarinha-Silva, Jürgen Conrad, Markus Rodehutscord (Stuttgart/DE) P047 Characterisation of novel protein-coding genes in the human testis using next generation proteomics and sequencing Melaine Nathalie (Rennes cedex/FR), Joerg Dojahn (Darmstadt/DE), Laetitia Cloarec, Emmanuelle Com (Rennes/FR), Nick Morrice (Warrington/GB), Régis Lavigne, Mélanie Lagarrigue (Rennes/FR), Dietrich Merkel (Darmstadt/DE), Charles Pineau (Rennes/FR) P048 Analyzing quantitative proteomics drug toxicity data at the level of biological networks Gal Barel (Berlin/DE), Nathalie Selevsek (Zurich/CH), Olivia Clayton, Sally Deeb, Hans Gmuender, Adrian Roth (Basel/CH), Ralph Schlapbach (Zurich/CH), Ralf Herwig (Berlin/DE) P049 Qantifying the dynamics of protein synthesis and degradation in defence response Phillip Ihmor, Wilhelm Gruissem, Mark Robinson, Katja Baerenfaller (Zurich/CH)
Plant and Microbial Proteomics II P064 Large scale SILAC based quantitative analysis of electron acceptor stressed Azospira Suillum PS using retention and drift time profiling Marc Kipping (Eschborn/DE), Anthony Iavarone, Matthew Youngblut, Emilie Gios (Berkeley, CA/US), Michael Daly (Pleasanton, CA/US), Hans Carlson, Ulla Andersen (Berkeley, CA/US), Johannes P. C. Vissers (Wilmslow/GB), John Coates (Berkeley, CA/US) P065 Somehow Similar but Different – how MALDI-TOF/TOF and LC-MS/MS data complement each other – a study of the cell wall proteome of medicago sativa stems in response to Cd exposure Annelie Gutsch (Esch-sur-Alzette/LU; Hasselt/BE), Kjell Sergeant, Jean-François Hausman, Jenny Renaut (Esch-sur-Alzette/LU), Ann Cuypers (Hasselt/BE) P066 Arabidopsis proteome and phosphoproteome experience dynamic changes to fulfil diurnal adaptation and in response to light transitions Sira Echevarría-Zomeño, R. Glen Uhrig, Jonas Grossmann, Bernd Roschitzki, Wilhelm Gruissem (Zurich/CH) P067 The mitochondrial complexome of Arabidopsis thaliana Jennifer Senkler, Michael Senkler, Holger Eubel, Tatjana Hildebrandt, Christian Lengwenus, Peter Schertl (Hannover/DE), Markus Schwarzländer, Stephan Wagner (Bonn/DE), Ilka Wittig (Frankfurt/DE), Hans-Peter Braun (Hannover/DE) Poster Sessions 47
Proteomic Forum 2017
P068 Disclosing novel Arabidopsis MPK substrates and interaction partners Nicola Huck, Franz Leissing (Aachen/DE), Lan Huang (Irvine, IL/US), Wolfgang Hoehenwarter (Halle/DE), Uwe Conrath, Gerold J. M. Beckers (Aachen/DE) P069 Selenoproteins analysis in plants by high resolution mass spectrometry Anna Łuciuk, Anna Konopka, Eliza Kurek, Julio Torres, Ewa Bulska (Warsaw/PL) P070 Proteomic analysis of aluminum stress response in alfalfa plant (Medicago sativa L.) Kim Dong-Hyun (Jinju/KR), Rahman Md. Atikur (Jinju, Suwon/KR), Kim Yong-Goo, Lee Joon-Woo, Lee Byung-Hyun (Jinju/KR) P071 A proteomic approach to identify immunogenic proteins from Brachyspira pilosicoli and B. hyodysenteriae Vanessa Casas, Arantza Rodríguez-Asiain, Roberto Pinto-Llorente, Joaquin Abian, Montserrat Carrascal (Barcelona/ES)
Post-Translational Modifications II P086 High pH reversed-phase sample fractionation for phosphoproteomic and glycoproteomic workflows Patrick Pankert (Dreieich/DE; Rockford, IL/US), Sergei Snovida, Jae Choi, Ryan Bomgarden (Rockford, IL/US), Julian Saba, Rosa Viner (San Jose, CA/US), John Rogers (Rockford, IL/US) P087 Information on extracellular PTMs ‘hiding’ in plain sight Eva Klement, Katalin F. Medzihradszky (Szeged/HU) P088 Comprehensive phosphoproteome analysis of activated and inhibitedhedgehog signaling in human medulloblastoma cells Tamara Scheidt (Salzburg/AT), Humberto Gonczarowska-Jorge (Dortmund/DE), Wolfgang Gruber (Salzburg/AT), Margherita Dell’Aica, René P. Zahedi (Dortmund/DE), Fritz Aberger, Christian G. Huber (Salzburg/AT) P089 Mass spectrometry-based quantitative proteomics for redox cysteine modifications Ruzanna Mnatsakanyan, Stavroula Markoutsa, Albert Sickmann, Steven Verhelst, René P. Zahedi (Dortmund/DE) P090 Subtilisin for large scale (phospho)proteomics – The beginning of a wonderful love story? Humberto Gonczarowska-Jorge (Dortmund/DE; Brasília/BR), Stefan Loroch, Margherita Dell Aica, René P. Zahedi (Dortmund/DE) 48 Poster Sessions
P091 The O-Carbamoyl-transferase Alb15 Is responsible for the modification of Albicidin Benjamin-Florian Hempel (Berlin/DE), Daniel Petras (San Diego, CA/US), Dennis Kerwat, Alexander Pesic, Siamak Semsari, Leonard von Eckardstein (Berlin/DE), Julie Arastè, Mélanie Marguerettaz, Monique Royer, Stéphane Cociancich (Montpellier/FR) Roderich D. Süssmuth (Berlin/DE) P092 Simple, scalable and sensitive tip-based enrichment of N-terminal peptides allows studying dynamic proteolytic processes Gerta Shema, Minh Nguyen, Saskia Venne (Dortmund/DE), Steven Verhelst (Dortmund/DE; Leuven/BE), René P. Zahedi (Dortmund/DE) P093 Analysing the role of ubiquitination for cowpox virus infection using mass spectrometry Marica Grossegesse, Joerg Doellinger, Annemarie Fritsch, Janett Piesker, Andreas Nitsche (Berlin/DE) P094 In silico predictions on various markers/proteins from different sites and its role in molecular evolution Saleem Muhammad, Rabia Arif, Tazeen Jamil (Lahore/PK) P095 Challenges in the identification and quantification of acetylation sites from leaf of Arabidopsis thaliana Ines Lassowskat (Cologne/DE), Jonas Giese, Iris Finkemeier (Münster/DE) P096 Insertional Mutagenesis of Mannosidase I and Xylosyltransferase A Modifies the N-Glycan Composition of Chlamydomonas reinhardtii Anne Oltmanns, Stefan Schulze, Nick Machnik (Münster/DE), Gai Liu, Kaiyao Huang (Wuhan/CN), Michael Hippler (Münster/DE) P097 SugarPy facilitates the discovery-driven analysis of intact N-glycopeptides from diverse complex samples Stefan Schulze, Christian Fufezan, Julia Krägenbring, Nick Machnik, Anne Oltmanns, Eugen Urzica, Michael Mormann, Michael Hippler (Münster/DE) P098 A large-scale filter-aided sample preparation method (LFASP) for the analysis of the ubiquitinome Albert Casanovas, Roberto Pinto-Llorente, Montserrat Carrascal (Barcelona/ES), Joaquin Abian (Barcelona, Bellaterra/ES)
Proteomics for Human Health III P133 Olink – a precision proteomics solution for targeted human protein biomarker discovery L. Pollack (Uppsala/SE) Poster Sessions 49
Proteomic Forum 2017
P134 The proteomic landscape of patient-derived CD4+ T-cells in recent-onset type 1 diabetes Marlen Lepper (Munich, Neuherberg/DE), Uli Ohmayer, Christine von Toerne, Anette-Gabriele Ziegler (Munich/DE), Stefanie Hauck (Munich, Neuherberg/DE) P135 Comparative proteome profiling of endothelial cells in challenging experimental setups Eric Witt (Greifswald/DE), Mario Lorenz (Berlin/DE), Florian Lorenz, Manuela Gesell Salazar, Vishnu Dhople, Martin Bahls (Greifswald/DE), Verena Stangl (Berlin/DE), Uwe Völker, Elke Hammer (Greifswald/DE) P136 Multi-OMICS analyses of an experimental human thyrotoxicosis model Beatrice Engelmann, Maik Pietzner, Tim Kacprowski (Greifswald/DE), Anne-Luise Dirk (Lübeck/DE), Janine Golchert, Elke Hammer, Matthias Nauck, Henri Wallaschofski (Greifswald/DE), Thomas Münte (Lübeck/DE), Nele Friedrich (Greifswald/DE), Georg Brabant (Lübeck/DE), Uwe Völker, Georg Homuth (Greifswald/DE) P137 Community proteomics offers new insights into the dynamics of supragingivale plaque under treatment Alexander Rabe, Manuela Gesell Salazar (Greifswald/DE), Stephan Fuchs (Wernigerode/DE), Maral Memarzadeh Zahedani, Harald Below, Alexander Welk, Uwe Völker (Greifswald/DE) P138 Targeted and untargeted proteomics in the ovarian cancer characterisation Agata Swiatly, Agnieszka Horala, Jan Matysiak, Joanna Hajduk, Ewa Nowak-Markwitz, Zenon J. Kokot (Poznan/PL) P139 Proteomic analysis of honeybee venom allergy markers Jan Matysiak, Eliza Matuszewska, Agata Swiatly, Joanna Hajduk (Poznan/PL), Joanna Matysiak, (Kalisz/PL), Anna Bręborowicz, Katarzyna Olejniczak, Zenon J. Kokot (Poznan/PL) P140 Proteomic characteristic of indicators of asthma in children Jan Matysiak, Olga Szklanny, Agata Swiatly, Joanna Hajduk (Poznan/PL), Joanna Matysiak (Kalisz/PL), Anna Bręborowicz, Katarzyna Olejniczak, Zenon J. Kokot (Poznan/PL) P141 Influence of different blood sample collection methods on clinical biomarker discovery Maria Ilies (Cluj-Napoca/RO; Greifswald/DE), Cristina Adela Iuga, Felicia Loghin (Cluj-Napoca/RO), Vishnu Mukund Dhople, Uwe Völker, Elke Hammer (Greifswald/DE) P142 Angiogenic factor profiling in patients with stage I non-small cell lung cancer using a bead-based multiplex immunoassay Agnieszka Klupczynska, Paweł Dereziński, Jan Matysiak, Wojciech Dyszkiewicz, Mariusz Kasprzyk, Zenon J. Kokot (Poznan/PL) 50 Poster Sessions
P143 Invasive Aspergillus fumigatus protein patterns in bronchoalveolar lavage and urin Roland Lehmann, Silke Machata, Mario Müller, Hortense Slevogt, Ilse Jacobsen (Jena/DE) P144 RNA binding Proteins (RBPs) in Alzheimer disease Neelam Younas, Saima Zafar (Göttingen/DE), Isidre Ferrer (Barcelona/ES), Olivier Andreoletti (Toulouse/FR), Markus Glatzel (Hamburg/DE), Inga Zerr (Göttingen/DE) P145 Systems biology of the unfolded protein response in glioma Chi Nguyen (Dortmund/DE), Himanshu Soni (Heidelberg/DE), Sascha Steltgens (Düsseldorf/DE), Stefan Reich (Regensburg/DE), Grischa Tödt, Björn Tews (Heidelberg/DE), Christiane Knobbe-Thomsen (Düsseldorf/DE), Jan Medenbach (Regensburg/DE), Robert Ahrends (Dortmund/DE) P146 Investigation of Q-TOF instruments advantages for label-free proteome analysis Stephanie Kaspar-Schoenefeld, Markus Lubeck, Andreas Jakob, Annette Michalski (Bremen/DE), Pierre-Olivier Schmit (Wissembourg/FR) P147 Profiling of intact proteins in the CSF of Alzheimer´s disease patients Jerome Vialaret, Sylvain Lehmann, Audrey Gabelle (Montpellier/FR), Pierre-Olivier Schmit (Wissembourg/FR), Christophe Hirtz (Montpellier/FR) P148 Imaging endogenous peptides in paraffin sections of formaldehyde fixed human tissues by mass spectrometry histochemistry – discrimination between healthy and cancer cells Peter Verhaert (Herentals/BE), Tiffany Porta (Maastricht/NL), Marthe Verhaert (Leuven/BE), Ron Heeren (Maastricht/NL), Marc Ramael (Herentals, Hasselt/BE)
Quantitative Proteomics II P176 Data-independent acquisition analysis of the mitochondrial proteome to identify quantitative, disease-specific signatures Craig Mageean, Karsten Boldt, Marius Ueffing, Christian Johannes Gloeckner (Tübingen/DE) P177 Quantitative profiling of membrane-associated proteins in Melioribacter roseus P3M-2 grown under fermentative and aerobic resperatory conditions Alexander Smolyakov, Ilya Altukhov (Dolgoprudny/RU), Sergey Gavrilov, Ivan Butenko, Olga Pobeguts, Ilya Kublanov (Moscow/RU), Dmitry Alexeev (Dolgoprudny/RU) P178 Revealing cellular functions of the prokaryotic serine/threonine kinase PknB from Staphylococcus aureus by combined proteome, phosphoproteome, interactome and sectretome analysis Mirco Steger, Marcel Jarick, Knut Ohlsen, Andreas Schlosser (Würzburg/DE) Poster Sessions 51
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P179 MS1 based quantification optimization on DIA methods on a quadrupole-Orbitrap mass spectrometer Yue Xuan (Bremen/DE), Roland M. Bruderer, Oliver M. Bernhardt, Tejas Gadhi (Zurich-Schlieren/CH), Claire Dauly (Courtaboeuf/FR), Lukas Reiter (Zurich-Schlieren/CH), Thomas Moehring (Bremen/DE), Ken Miller (San Jose, CA/US) P180 Quantitative proteomic analysis in shoots of wheat varieties under copper and iron nanoparticles exposure Yasmeen Farhat, Naveed Raja, Setsuko Komatsu (Rawalpindi/PK) P181 Subunit specificity of the CCT chaperonin towards its substrates Michal Nadler-Holly, Matthias Selbach (Berlin/DE) P182 Extending the depth of coverage in SWATH® acquisition with deeper ionlibraries Zuzana Demianova, Joerg Dojahn, Nick Morrice, Christie Hunter (Redwood Shores, CA/US) P183 Proteomics as part of a multi-omics systems toxicological assessment of a mentholated candidate modified risk tobacco product Ulrike Kogel, Bjoern Titz (Neuchatel/CH), Walter K. Schlage (Bergisch Gladbach/DE), Catherine Nury, Florian Martin (Neuchatel/CH), Alberto Oviedo (Singapore/SG), Stephane Lebrun, Ashraf Elamin, Emmanuel Guedj, Keyur Trivedi, Nikolai V. Ivanov, Patrick Vanscheeuwijck, Manuel C. Peitsch, Julia Hoeng (Neuchatel/CH) P184 A comprehensive Proteomic Investigation of EBF1 Heterozygosity in pro B lymphocytes utilizing Data Independent Acquisition (DIA) and Data Dependent Acquisition (DDA) Approaches Yaarub Musa, Soeren Boller, Rudolf Grosschedl, Gerhard Mittler (Freiburg/DE) P185 Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX) – a combinatorial multimolecular omics approach for systems biology Cristina Coman, Christin Lorenz, Fiorella Andrea Solari, Andreas Hentschel (Dortmund/DE) Albert Sickmann (Dortmund/DE, Aberdeen/GB), René P. Zahedi, Robert Ahrends (Dortmund/DE) P186 Comparison of label free quantification of an artificial protein spiked into a complex matrix in data-dependent acquisition (DDA) and data-independent acquisition (DIA) mode Uli Ohmayer, Marlen Lepper, Marcel Blindert, Stefanie M. Hauck (Munich/DE) P187 Dissecting the inhibitory cAMP/PKA and cGMP/PKG signalling networks in human platelets to identify novel targets for antiplatelet treatment Oliver Pagel (Dortmund/DE), Elena Walter (Mainz/DE), Humberto Gonczarowska-Jorge (Dortmund/DE), Ulrich Walter, Kerstin Jurk (Mainz/DE), René P. Zahedi (Dortmund/DE) 52 Poster Sessions
P188 Time-resolved elucidation of type I and II interferome by label-free quantitative proteome analysis Dominik Andre Megger (Bochum/DE), Vu Thuy Khanh Le-Trilling (Essen/DE), Jos Philipp, Barbara Sitek (Bochum/DE), Mirko Trilling (Essen/DE) P190 Improving speed and robustness of DIA Quantitation using longer microLC columns Joerg Dojahn (Darmstadt/DE), Remco Van Soest, Christie Hunter (Redwood City, CA/US) P191 Novel gsalpha-dependent protein Kinase A phosphorylation targets identified in platelets Frauke Swieringa (Dortmund/DE; Maastricht/NL), Fiorella A. Solari (Dortmund/DE), Marion A. H. Feijge, Nadine J. A. Mattheij (Maastricht/NL), Oliver Pagel, Florian Beck (Dortmund/DE), Connie T. R. M. Stumpel (Maastricht/NL), Joachim Pohlenz, Jörg Faber, Alexandra Russo (Mainz/DE), Otfried Schwab, Barbara Zieger (Freiburg/DE), Kerstin Jurk (Mainz/DE), Albert Sickmann (Dortmund/DE), Paola E. J. van der Meijden, Irene M. L. W. Körver-Keularts (Maastricht/NL), René P. Zahedi (Dortmund/DE), Johan W. M. Heemskerk (Maastricht/NL) P192 Turning up the volume – extension of the tandem mass tag reagents for 11plex protein quantitation Matthias Tremmel (Rockford, IL/US) P217 MRM and PRM Assay Development for a Panel of >3000 Proteins from 20 Mouse Tissues Sarah Michaud, Nicholas Sinclair (Victoria/CA), Ingo Feldmann (Dortmund/DE), Yassene Mohammed (Victoria/CA; Leiden/NL), Derek Smith (Victoria/CA), Albert Sickmann (Dortmund/DE), Christoph Borchers (Victoria/CA)
Structural Proteomics P197 Physical modeling of structure formation of the histone dimers H2A, H2B, H3 and H4 Kirill Kulikov, Tetiana Koshlan (St. Petersburg/RU) P198 Detection of transient disulfide bridges using disulfide permutation databases Florian Richter, Heiko Giese, Ina Koch, Ilka Wittig (Frankfurt a. M./DE) P199 Disturbing TCEP-induced side-reaction Eva Hunyadi-Gulyas (Szeged/HU), Tamas Lango Gábor Tusnády (Budapest/HU), Katalin Medzihradszky F. (Szeged/HU) P200 Optimization of crosslinked peptide analysis on an Orbitrap Fusion Lumos mass spectrometer Marc Guender (Reinach/CH), Ryan Bomgarden, Erum Raja Chris Etienne (Rockford, IL/US), Fan Liu, Albert Heck (Utrecht/NL) Mathias Mueller (Bremen/DE), Rosa Viner (San Jose, CA/US) Poster Sessions 53
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P201 Proteome-wide identification of protein-protein interactions by in vivo chemical crosslinking and mass spectrometry Elena Rudashevskaya, Tomáš Ječmen (Dortmund/DE), Karl Makepeace, Evgeniy Petrotchenko (Victoria/CA), Kerstin Jurk (Mainz/DE), Chris Meisinger (Freiburg/DE), René P. Zahedi, Albert Sickmann, Christoph Borchers (Victoria/CA) P202 Structural aspects of Bcy1, the regulatory subunit of protein kinase A from Saccharomyces cerevisiae approached by proteomic methods Silvia Moreno, Enzo Tofolon, Pia Valacco, Ricardo Neme Tauil, Germán Fernández, Silvia Rossi (Buenos Aires/AR)
Subcellular Proteomics P203 Degradation of protein translation machinery by amino acid starvation-induced macroautophagy Stephanie Kaeser-Pebernard (Fribourg/CH), Christine Gretzmeier (Freiburg/DE), Gregory R. Johnson (Pittsburgh, PA/US), Robert F. Murphy (Freiburg/DE; Pittsburgh, PA/US), Jörn Dengjel (Fribourg/CH; Freiburg/DE) P204 Mass spectrometry based characterization of the intracellular domain (ICD) of NG2 proteoglycan Tanmoyita Nayak (Mainz/DE) P205 Quantitative secretome analysis of activated jurkat cells using click chemistry-based enrichment of secreted glycoproteins Kathrin Elisabeth Witzke, Kristin Rosowski, Christian Müller, Maike Ahrens, Martin Eisenacher, Dominik Andre Megger, Jürgen Knobloch, Andrea Koch, Thilo Bracht, Barbara Sitek (Bochum/DE) P206 Two sides of the same coin – decoding polarized protein organization on epithelial surfaces Anika Kötemann (Zurich/CH) P207 Ultrasensitive pSILAC-SP3 reveals cue-specific signatures in the newly synthesized proteome of axons Christian Frese (Heidelberg/DE), Roberta Cagnetta, Toshiaki Shigeoka, Christine Holt (Cambridge/GB), Jeroen Krijgsveld (Heidelberg/DE) P208 Comparative proteomic analysis of integral membrane proteins in different larval tissues from the poplar leaf beetle Chrysomela populi Natalie Wielsch, Lydia Schmidt, Ding Wang, Aleš Svatoš, Antje Burse (Jena/DE) P209 AHA p-c uncover mitochondrial protein degradation of excess complex subunits Henrik Zauber, Erik McShane, Matthias Selbach (Berlin/DE) 54 Poster Sessions
P210 Improved qualitative and quantitative analysis of the human mitochondrial proteome by hybrid acquisition Scott Geromanos (Milford, CT/US), Alexander Muck (Eschborn/DE), Johannes Vissers, Christopher Hughes (Wilmslow/GB), Brad Williams (Milford/US), Maurizio Ronzi, Enrico Cilio, Andrea Urbani (Rome/IT), Steven Ciavarini, Curt Devlin (Milford, CT/US) P211 Differential regulation of synaptic phosphoproteomes after appetitive and aversive motivation in an auditory learning paradigm in mice Sandra Richter, Angela Breme, Karl-Heinz Smalla, Frank Ohl, Constanze Seidenbecher, Wolfgang Tischmeyer, Eckart Gundelfinger, Michael Naumann, Thilo Kähne (Magdeburg/DE) P212 Proteome wide analysis of granular protein complexes evoked by differential heat stress stringency in Saccharomyces cerevisiae Silvia Moreno, Carla Barraza, Pia Valacco, Germán Fernández, Paula Portela (Buenos Aires/AR) 55
Proteomic Forum 2017
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Lecture Abstracts* DGPF Young Investigator Session Tuesday, 4 April 2017 16:30 –18:00
*45 Participants took part in the competition – 6 are invited for the Young Investigator Session 56 Lecture Abstracts of Young Investigator Award Session
Facts of Protein-Protein Interaction Research YIA1 Y. Gao1 1Beijing Normal University (Beijing/CN)
The fact one of current protein-protein interaction research is that tagging is widely used. Tagging is a good way to track or see the protein. We assume that tagging does not change the structure and function of the protein too much. This is probably not true for many proteins. The fact two is that overexpression is widely used too. To put in anexogenous tagged protein, overexpression is the most common way. We assume that overexpression is not interfering its location and interaction of the protein. This is probably not true for many proteins either.The fact three is that we believe that we wash the protein complex gentle enough so that the weak interactions remain intact and we wash hard enough so that no new false positive interaction can form and stay. This is probably not true in most of cases either.The fact four is that many protein interactions were identified in a condition other than their original environment. They were forced to express and interact in test tube in an artificial solution, in other cells, in nucleus, on membrane or on the pili of an phage.The fact five is that many massive studies that are widely referred were done with the methods with one or more of these flaws. When an interaction was found by two independent studies, it was believed to be the fact. There is actually a way to find the facts of protein interactions. Fast Fixation is necessary to study real-time protein-protein interactions under physiological conditions. Fast formaldehyde cross-linking can fix transient and weak protein interactions. Immunoaffinity purification can Fish out complexes that include particular target proteins. Since the complex is covalently bond, it can be washed as hard as the antibody-antigen reaction can stand. The weak interactions will remain. Even if the nonspecific binding can stay on the beads or antibody, they will be eliminated by the next step. To Filter out these complexes, SDS-PAGE is used to disrupt non-covalent bonds, the gel can then be sliced base on molecular weight without staining. All the protein complexes can be identified at the sensitivity of mass spectrometry rather than the sensitivity of the staining method. This strategy was originally name 4F-acts before the reviewer changed it to 4F (for fail)(1).The advantages are: 1) it does not use tag; 2) it does not overexpress; 3) the weak interaction can be detected because the complexes can be washed as hard as the antigen-antibody reaction can stand since the complexes are crosslinked covalently. No new covalent bond can be formed as false positive; 4) the formaldehyde crosslinking can be done in cell, tissue or organ level fast enough so that the protein complexes were fixed in situ in real time.A massive study should be done with this strategy to give us the facts of true protein interactions in situ in real time.
Reference: ZHU Lisi, LI, Menglin, WEI Lilong, et al. Fast fixing and comprehensive identification to help improve real-time ligands discovery based on formaldehyde crosslinking, immunoprecipitation and SDS-PAGE separation. Proteome Science 2014, 12:6 Lecture Abstracts of Young Investigator Award Session 57
Proteomic Forum 2017
Dynamics of protein synthesis and degradation YIA2 in FLG22-stimulated arbidopsis P. Ihmor1, W. Gruissem1, M. Robinson2, K. Baerenfaller1 1ETH Zurich (Zurich/CH) 2Universität Zurich (Zurich/CH)
Gene expression regulation is a multi-step process that shapes the most central aspects of a cell. At its core, it determines protein levels by regulating transcription, translation and protein degradation yet the relative contributions of these regulatory mechanisms are not well resolved on a systems-wide level, especially in plants. We quantified four aspects of gene expression on a time-resolved, genome-wide scale using RNA sequencing (RNA-Seq, transcription), ribosome footprint profiling (Ribo-Seq, translation), quantitative common-reference SILAC MS (protein abundance) and dynamic SILAC MS (protein degradation). All datasets were obtained from the same Arabidopsis cell cultures under control conditions or after stimulation with flg22, the elicitor-active epitope of bacterial flagellin. Analyzing the four datasets individually and in combination let us to the conclusion that the transcriptional and translational level showed the largest response to flg22 stimulation. Only few genes show divergences in translation compared to the transcriptional response. The protein data indicated that many but not all protein abundances followed the transcriptional and translational regulation. For the 123 proteins that maintained constant abundances despite transcriptional and translational upregulation, we could determine a coordinated increase in protein degradation, counteracting the upregulation in protein synthesis. Downregulated gene expression, in contrast, is mostly determined by a gradual reduction in transcription, which slowly affects the protein abundances. The speed in which the protein level respond to the transcriptional downregulation depends on the turnover rate of the individual protein. In conclusion, our data shows that protein levels are mostly determined by transcriptional regulation and to a lesser degree by protein degradation regulation. 58 Lecture Abstracts of Young Investigator Award Session
Optimized de novo peptide sequencing and proteogenomics YIA3 workflows to refine ab initio gene prediction B. Blank-Landeshammer1, L. Kollipara1, K. Biß1, T. Schell2, R. Zahedi1, M. Pfenninger2, A. Sickmann1 1Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Protein Dynamics, (Dortmund/DE) 2Biodiversity and Climate Research Centre (BiK-F), (Frankfurt a. M./DE)
Recently, the costs of whole-genome sequencing have steadily decreased and thus it is readily employed in many research areas, from clinics to biodiversity research. The growing availability of raw genomic sequences gathered from hundreds of different species demands accurate gene annotation methods. While commonly used gene prediction pipelines are sensitive, their findings require profound empirical validation. Proteome-level data can add valuable information not only by confirming the presence of predicted genes, but also in refining the protein-coding regions as well as in the discovery of priorly unpredicted gene products. Here, the pond snail Radix auricularia was chosen as model organism. Genomic data was obtained by shotgun sequencing and assembly of the reads as well as ab initio gene prediction (MAKER pipeline) were performed, serving as basis for further proteogenomics workflows. Sample preparation for LC-MS/MS was based mainly on FASP protocol. Samples were digested with various proteases and subjected to high-/low-pH RP-RP LC separation prior to MS/MS analysis. Additionally, N-terminal peptides were enriched by charge-based fractional diagonal chromatography (ChaFRADIC). Two different search approaches were employed: Firstly, conventional database search against the predicted protein database. Non-matching spectra were further subjected to a two-step reductive search approach against the assembled genome. Secondly, an independent combinatorial de novo peptide sequencing workflow was developed in order to identify peptides independent of genomic data. This workflow was thoroughly quality-controlled and leads to a threefold increase of peptide hits at 5% FDR compared to a single algorithm approach. Thus, a comprehensive dataset of R. auricularia was generated. A total of 184,689 peptides could be identified as directly matching to predicted protein sequences, thereby confirming 50% of the annotated genes. Remarkably, another 26,015 peptides (1% FDR) were found to match regions of the genome not initially accounted for by gene prediction, while 28,328 peptides (5% FDR) were identified by de novo sequencing only. By introducing our novel combinatorial search approach for proteogenomics studies, this work provides a first refinement of the draft proteome of R. auricularia. Lecture Abstracts of Young Investigator Award Session 59
Proteomic Forum 2017
Deciphering acute cellular response to X-ray-, proton- and carbon ion YIA4 irradiation via quantitative proteomics and phosphoproteomics M. Winter1,2, I. Dokic2, R. Mayer1, U. Warnken1, A. Abdollahi2, M. Schnölzer1 1German Cancer Research Center (DKFZ), Functional Proteome Analysis, Heidelberg, Germany 2German Cancer Research Center (DKFZ), Translational Radiation Oncology, Heidelberg, Germany
Question: Radiotherapy is a major field in cancer research. Recently particle radiotherapy came into focus. Contrary to X-rays, particles deposit most of their energy to a small region within tissue, the so-called Bragg peak. This enables dose escalation in the tumor while sparing healthy tissue. Differences between these radiation qualities at the molecular level are largely unknown or controversial. In order to improve this knowledge we applied mass spectrometry- based quantitative proteomics and phosphoproteomics. Methods: Human lung carcinoma cells were irradiated with 2 Gy carbon ions, 3.5 Gy protons and 6 Gy X-rays (representing biological equivalent doses) and harvested 2 h after irradiation to uncover acute cell response. For accurate quantification, cells were metabolically labeled using SILAC. GeLC-MS/MS was applied for protein expression analysis and IMAC/TiO2 affinity enrichment for analysis of the phosphorylation status. For validation of the obtained results and for functional studies synthetic isotope labeled phosphopeptides were used in a spike-in as well as in pull-down experiments. Results: We quantified 2634 proteins and 2818 phosphorylation sites in the irradiated samples. Negligible changes occur at protein expression level 2 h after irradiation. As phosphorylation is a much faster event than synthesis or depletion of proteins, we identified 181 radiation regulated phosphorylation sites. Interestingly, 55 of these show differential regulation between radiation qualities indicating for the first time differential signaling triggered by different sources of radiation. For validation of these results, 28 phosphopeptides were selected to be confirmed in a targeted spike-in approach using synthetic isotope labeled peptides. With this experiment we were able to confirm the selected candidates by checking co-elution of endogenous and synthetic peptides as well as their corresponding fragmentation pattern. For functional interpretation of these results we are currently establishing a synthetic phosphopeptide pull- down strategy to profile direct and phospho-specific binders of the selected phosphorylation sites. In a pilot experiment we successfully identified the direct binding of MDC1 and 53BP1 to the DNA double-strand break marker γH2AX confirming recently published results (Kleiner et al. 2015). 60 Lecture Abstracts of Young Investigator Award Session
Conclusions: We established a robust and efficient workflow for the investigation and validation of phosphorylation changes in response to radiation. We show for the first time, that X-ray and particle based irradiations induce differential signaling events. With this we provide an initial study to better understand molecular effects induced by different radiation qualities and offer potential drug targets for radiotherapy modulation.
Figure 1 Experimental design of the proteome and phosphoproteome analysis to elucidate acute radiation response
Lecture Abstracts of Young Investigator Award Session 61
Proteomic Forum 2017
Impact of gene overdosage in the Hippocampus and cerebellum YIA5 proteome and phosphoroproteome M. Ortega1, I. De Toma2,3, E. Sabidó2,1,3, M. Dierssen2,3 1Centre for Genomic Regulation, CRG, CRG/UPF Proteomics Unit (Barcelona/ES) 2Centre for Genomic Regulation, CRG (Barcelona/ES) 3Universitat Pompeu Fabra (Barcelona/ES)
Trisomy of human chromosome 21 results in Down syndrome (DS), the most complex and common genetic perturbation leading to intellectual disability. A plausible candidate gene to explain DS phenotypic abnormalities is the dual-specificity tyrosine (Y)-phosphorylation kinase 1A (Dyrk1A), which regulates fundamental cellular functions and which overdosage recapitulates DS phenotypic alterations in transgenic mice (TgDyrk1A). Its normalisation through inhibition of DYRK1A kinase activity could be sufficient to rescue the cognitive and the neuronal phenotype. This could explain that epigallocatechin-3-gallate (EGCG), a green tea flavonol, which has DYRK1A inhibitory properties, improves the cognitive phenotype in trisomic Ts65Dn mice, as well as in DS humans. However, EGCG is a multi-targeted drug and thus, the molecular mechanisms of its beneficial effect remain elusive. We investigated the molecular effects induced by in vivo overexpression of Dyrk1A on the proteome and phosphoproteome of the hippocampus and the cerebellum of wild type and TgDyrk1A mice and the effect of EGCG. Quantitative proteomics data reveal that in vivo overexpression of Dyrk1A significantly alters cell functions such as mitochondrial regulation and cytoskeletal proteins, dysfunctions also found in DS patients. We also observed that EGCG can partially rescue DS-related protein abundance deficits in both tissues. Interestingly, increased Dyrk1A dosage in the cerebellum compared to the hippocampus causes major changes in transcriptional regulation affecting the proteome. The laboratory of M.D. is supported by DIUE de la Generalitat de Catalunya (Grups consolidats SGR 2014/1125). Supported by MINECO (SAF2013-49129-C2-1-R) and EU (Era Net Neuron PCIN-2013-060). The CRG is a Center of Excellence Severo Ochoa SEV-2012-0208. The CIBER of Rare Diseases is an initiative of the ISCIII. The CRG/UPF Proteomics Unit is part of the Plataforma de Recursos Biomoleculares y Bioinformáticos (ProteoRed) supported by grant PT13/0001 of ISCIII and Spanish Ministry of Economy and Competitiveness. We acknowledge support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (2014SGR678). 62 Lecture Abstracts of Young Investigator Award Session
Protein complex identification using combination of fractionation YIA6 methods and label-free quantification of complexome changes M. Górka1, A. Graf1, S. Streb2 1Max Planck Institute for Molecular Plant Physiology, Metabolic Networks (Potsdam/DE) 2ETH Zurich (Zurich/CH)
Is it possible to identify and quantify protein complexes in high-throughput manner? In this project we aimed to establish a map of protein complexes which can be reliably detected in the model organism – Arabidopsis thaliana. We used size exclusion chromatography (SEC), clear-native PAGE (CN-PAGE), blue-native PAGE (BN-PAGE) and analytical ultracentrifugation (AUC) for the fractionation of protein complexes. Fractions were prepared for mass spectrometry analysis and measurements were performed by nanoHPLC-MS/MS. The key point of our study was to invent an effective method for identification of protein complexes. We developed a platform which enabled us to perform such study in a high- throughput manner. The majority of quantified proteins were detected in size ranges indicating complex formation regardless of the employed separation technique. Based on these results, we aimed to identify potential interaction proteins using the fact that each subunit/protein of a protein complex should behave as integral entity during the fractionation and presumably display similar elution profiles. Following the deconvolution of protein profiles into isolated peaks we therefore calculated for each dataset the Euclidean distance for all combinations of deconvoluted peaks. To illustrate the trade-off in identification of interactions misclassified as positive (false positive rate) versus the proteins correctly classified as positive (true positive rate) the receiver-operator characteristic curve (ROC curve) for Euclidean distance was generated. To further validate our strategy, we examined the elution profiles of proteasome which is consequently used as a reference protein complex to test the quality of data sets. Preservation of protein-protein interaction (PPI) during complex separation allowed us to discover hierarchical organization of protein complexes and enables to perform quantitative comparison study between the complexomes in different environmental conditions or genetic backgrounds that led to better understanding of mechanisms underlying cell regulation. Our approach can be applied to any biological system. Lecture Abstracts of Young Investigator Award Session 63
Proteomic Forum 2017
Figure 1 Schematic overview of the experimental workflow.
Figure 2 Graphical display of influence of combination different experiments and fractionation methods on the prediction power. The shape of the symbols indicates the number of data sets that were combined while the color of the symbols shows how many different methods are involved. 64 Lunch Workshops Monday, 3 April
12:45–13:45 Thermo Fisher Scientific GmbH High-Throughput Multiplexed Quantitative Proteomics Room H 01 When combined with multiplexing capabilities, quantitative proteomics provides a deep and comprehensive understanding of the molecular mechanisms underlying biological processes and disease states. Thermo Scientific™ TMT™ isobaric mass tag labeling combined with Orbitrap high resolution accurate mass (HRAM) mass spectrometry (MS) enable greater multiplexing capacity, resulting in increased depth of quantitative proteomic analysis across larger numbers of samples. An improved workflow for phosphopeptide quantification based on TMT-MS3 methodology will be presented. 12:45 Sensitive and Accurate Quantitation of Phosphopeptides using TMT isobaric labeling technique Patrick Pankert (Dreieich/DE) 13:05 Stability proteomics for unbiased assessment of protein state and function in live cells Mikhail Savitsky (Heidelberg/DE) 12:45–13:45 Bruker Daltonik GmbH Glycosylations, Proteoforms and Spatial Distribution: Driving Biomarker Discovery to the Next Level Room H 02 Glycoproteomics of Plasma Glycoproteins Manfred Wuhrer (Leiden/NL) Innovative Top-Down and Glyco-proteomics in Translational Healthcare Alain Van Gool (Nijmegen/NL) rapifleX TissueTyper MALDI Imaging Corinna Henkel (Bremen/DE) 12:45–13:45 Waters GmbH WATERS Mass Spec Technologies Room S 18 Overview about Waters MS Innovations Eric van Beelen (Saint-Quentin/FR) SONAR – a Novel Scanning Quadrupole DIA Method for Shot-Gun Analysis in OMICS Research Marc Kipping (Eschborn/DE) Lunch Workshops • Tuesday, 4 April 65
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12:45–13:45 Thermo Fisher Scientific GmbH Protein Structure Analysis with Cross-Linking Mass Spectrometry Room H 02 Chemical cross-linking combined with mass spectrometry (CX-MS) is a powerful method to probe the structure of proteins, complexes and interactions. The high resolution and mass accuracy of Orbitrap technology, in combination with enhanced fragmentation modes (e.g., HCD, ETD, EtHCD) and MSn modalities, allow completely unique and effective methods to probe protein structure. New reagents and software facilitate sample preparation and data interpretation to make these capabilities available to all labs. 12:45 Novel Data Acquisition and Analysis Strategies for High Confident Cross-link Identification Using Orbitrap Mass Spectrometers Sonja Radau (Dreieich/DE) 13:05 Applications and perspectives of protein cross-linking combined with MS Henning Urlaub (Göttingen/DE) 12:45–13:45 Biognosys AG Recent advancements in Next Generation Proteomics Room S 16 LC-MS based proteomics has become the method of choice for the identification and quantification of a large number of proteins over a large number of samples across different samples types. Recently, targeted analysis of data independent acquisition (DIA) data (also SWATH) has emerged as a powerful technology for quantitative, label free proteome profiling, providing excellent proteome coverage, reproducibility and quantitative precision. In this lunch symposium we will learn about the recent advancements in the next generation proteomics approaches and how they compare against traditional workflows based on data dependent acquisition (DDA or shotgun). 12:45 High precision iRT for a more reproducible and comprehensive proteome profiling using Spectronaut Lukas Reiter (Zurich/CH) 13:15 Benchmarking precision, linearity, and analytical depth of LFQ of a complex sample in Data-independent acquisition (DIA) and Data-dependent acquisition (DDA) mode Uli Ohmayer (Munich/DE) 66 Lunch Workshops Tuesday, 4 April
12:45–13:45 SCIEX
Room S 18 Robert Graham Ph.D. will present “There are a myriad of issues within the field of biomarker discovery, we will focus on our experience of working with clinical serum samples from biobanks. We will present a few recent stuies we carried out on the identification of early detection ovarian cancer (OC) biomarkers. OC has the highest mortality of all gynaecological cancers. Early diagnosis offers an approach to achieving better outcomes for patients. Using mass spectrometry and immunoassays we conducted a blinded-evaluation of prospectively collected preclinical serum from participants in the multimodal group of the UK Collaborative Trial of Ovarian Cancer Screening.”
Dr. Christopher Lößner will present “CESI is the integration of capillary electrophoresis (CE) and electrospray ionization (ESI) into a single dynamic process within the same device. CESI-MS operates at low nL/min flow rates, offering advantages over LC-MS which include increased ionization efficiency and low sample consumption. CESI-MS is orthogonal to LC-MS, separating analytes by their charge and size, which has advantages for analysis of certain PTMs and intact proteins. In this presentation, we will show examples of peptide, phosphoprotein, protein isoform as well as monoclonal antibody separation.” 12:45 Biomarkers for the early detection of ovarian cancer Robert Graham (Manchester/GB) 13:15 CESI-MS for top-down, middle-down and bottom-up Proteomics Christopher Lößner (Darmstadt/DE) Lunch Workshops • Wednesday, 5 April 67
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12:45–13:45 Doctor’s Office: Serva Electrophoresis GmbH Room H 02 Chair Kai Stühler (Düsseldorf/DE), Günter Theßeling (Heidelberg/DE) 12:45 Protein or peptide – that is the question Katrin Marcus (Bochum/DE) 13:05 Absolute Quantification Dörte Becher (Greifswald/DE) 13:25 Serological proteome analyses of the antibody response of patients with invasive mycoses Olaf Kniemeyer (Jena/DE) 68 General Information
General Information 68 Speakers’ Ready Room 69 Requirements for Poster 69 Poster Sessions 70 Awards and Prizes 71
Registration Thank you for your interest in the Proteomic Forum 2017 to be held from 2–5 April in Potsdam (Germany). Registration for the congress is required. Please register online at www.proteomic-forum.de.
Registration Fees Congress Day ticket Member DGPF or EuPA* 500 EUR 200 EUR Non-member 600 EUR 250 EUR Member, student 300 EUR 100 EUR Non-member, student 400 EUR 150 EUR HUPO Workshop 100 EUR Congress party 40 EUR * Please have your EuPA membership number at hand.
Payment and Confirmation of Payment An invoice or confirmation of registration will be sent to you via postal or electronic mail within 14 days. This invoice is a valid invoice which may be submitted to the local tax and revenue office. All fees are due upon receipt of invoice/registration confirmation. Payment transfers must include participant’s name and invoice number. Payment is also accepted by credit card (Master-/Eurocard, American Express, VISA). In case you have transferred the registration fee shortly before the start of the congress, (up to 10 days prior to congress opening), we ask you to please present your transfer remittance slip onsite.
General Terms and Conditions Please find our General Terms and Conditions at www.proteomic-forum.de. General Information 69
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General Hints for Authors and Presenters Submitting your Presentation/Technical Information The presentation should be prepared as PDF, MS Office PowerPoint 2007, 2010 for Windows or Keynote for Macintosh DVD in format 4:3. A presentation notebook with a PDF reader and MS Office PowerPoint 2016 will be provided. The use of personal notebooks is possible upon agreement. However, it may interrupt the flow of the program in the lecture hall. Please provide an adapter for VGA if necessary. A notebook, presenter and laser pointer are available at the speaker’s podium in the lecture hall. A technical supervisor can help you. Please visit our speakers’ ready room. Should you wish to use non-digital equipment, please contact us. We can be reached at [email protected].
Speakers’ Ready Room The speakers’ ready room is located on the first floor in room S 13. For submission, please use a USB flash drive, CD or DVD disc that is not protected with software. You may view and/or edit your presentation. Please note, that different codes for video and audio files can result in problems. So we ask you to visit our speakers preview area in time – at least 2 hours before the presentation should begin.
Requirements for Poster The size of your poster has to be in accordance to DIN portrait format A0 (84,1 cm width x 118,9 cm height) and should not be laminated. Poster pinboards are 120 cm x 150 cm and mounting material will be supplied on site. No other material should be used. The posters should be mounted on the respective day until 09:00 (except Sunday until 17:00) and must be removed by Tuesday, 4 April until 17:00. Please note that all posters which have not been removed cannot be stored or sent back to the authors. 70 General Information
Poster Sessions Poster Session A – Sunday, 2 April • 19:00–20:30 Affinity Proteomics P002–P008 p. 29 Bioinformatics P011–P031 p. 30 Free Topics P032–P038 p. 32 Proteogenomics P100–P103 p. 32 Proteomics for Human Health I P104–P117 p. 33 Proteomics in Biotechnology P149–P157 p. 34 Standardization in Proteomics P193–P196 p. 35
Poster Session B – Monday, 3 April • 15:00–16:30 Mass spectrometry Technologies P050–P055 p. 37 Plant and Microbial Proteomics I P056–P063 p. 38 Post-Translational Modifications I P072–P085 p. 39 Proteomics for Human Health II P118–P132 p. 40 Quantitative Proteomics I P158–P175 p. 42 Top Down Proteomics and Macromolecular Complexes P213–P216 p. 43
Poster Session C – Tuesday, 4 April • 15:00–16:30 Integrated OMICs/Systems Biology P040–P049 p. 45 Plant and Microbial Proteomics II P064–P071 p. 46 Post-Translational Modifications II P086–P098 p. 47 Proteomics for Human Health III P133–P148 p. 48 Quantitative Proteomics II P176–P192, P217 p. 50 Structural Proteomics P197–P202 p. 52 Subcellular Proteomics P203–P212 p. 53 General Information 71
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Abstracts All abstracts are provided within the abstract book that can be downloaded online via www.proteomic-forum.de.
Awards and Prizes Poster Prizes of the German Society of Proteome Research 1st Prize 1,000 EUR 2nd Prize 500 EUR
The evaluation will take place on-site by the organizers. Poster prize candidates will be informed about the status of their poster on-site and are kindly asked to attend the award ceremony on Wednesday, 5 April from 15:15–15:30.
Young Investigator Award Scientists participating at the Proteomic Forum 2017 and being younger than 33 years are invited to apply for this year´s Young Investigator Award of the German Society for Proteome Research. There are 3 prizes: 1,000, 500 and 250 EUR. In addition, all selected presenters are invited to the Speakers’ Dinner at Schloss Glienicke. A senior scientist evaluation committee has invited 6 selected applicants to present their results during the YIA Session on Tuesday, 4 April, from 16:30–18:00. The winners are determined by voting directly by the audience after the last presentation.
Promotion Prize The promotion of young scientists is one of the main tasks of the German Society for Proteome Research (DGPF e.V.). For this purpose, the DGPF has inaugurated the Promotion Prize donated with 2,500 EUR which will be awarded for the second time to an outstanding dissertation in the field of proteomics which was finished during the last 2 years. Here, the originality as well as the duration of work and a conceivably high degree of independency will be the basis for awarding the Promotion Prize.
All winners will be announced at the Award Ceremony on Wednesday, 5 April, 15:15–15:30. 72 General Information
Opening Hours Sunday Monday Tuesday Wednesday Industrial exhibition 15:30–21:00 10:30–16:30 10:30–16:30 10:30–15:30 Poster exhibition 17:00–21:00 08:00–18:00 08:00–17:00 Check-in 08:00–19:00 08:00–18:00 08:00–18:00 08:00–16:00 Speakers’ ready room 08:00–19:00 08:00–18:00 08:00–18:00 08:00–15:00 Cloakroom 08:00–21:00 08:00–19:00 08:00–18:30 08:00–17:00
Internet Wireless internet will be available. Wifi-codes are available at the check-in. If your university provides eduroam, please use your login at the University of Potsdam.
Parking You can use several parking spaces which are located near the venue: Train station “Griebnitzsee” behind the university library (coming from Prof.-Dr.-Helmert-Strasse) Parking space next to Haus 1 of the University of Potsdam (coming from August-Bebel-Straße/Am Klubhaus (Babelsberg))
Name Badge Please wear your name badge during all conference events, including the networking activities. Admission to scientific sessions and to the industrial exhibition is restricted to participants wearing their badge. Participants will receive their name badge when collecting their conference documents at the check-in desk. If you have pre-registered and paid your conference fee, please use the self check-in at the conference venue.
Catering Coffee will be provided and lunch will be available at industry lunch symposia or catering stations within the exhibition.
Accommodation We reserved a contingent of rooms at special rates in different categories. Please quote the special conference booking code “DGPF 2017” when booking to benefit from the special conference rates. Conventus acts as an intermediary for hotel reservations and therefore assumes no liability for reservations. Changes and cancellations have to be addressed to the according hotels directly. The cancellation terms of the individual hotels apply. Further information on accommodation is provided at www.proteomic-forum.de. General Information 73
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City Map Castle Glienicke University Potsdam Bridge Campus Griebnitzsee Glienicker rain Station New Garden Main T City centre chapel © terra press GmbH 74 Social Program
Get-together and Poster Session A Join the Get-together and meet all exhibitors and supporters of the Proteomic Forum 2017 within the industrial and poster exhibition area in the foyers of the ground and first floor of the University Potsdam. All participants are cordially invited free of charge.
Date Sunday, 2 April Time 19:30–20:30 Place Industrial exhibition Fee free of charge (for congress delegates)
Congress Party Date Tuesday, 4 April Time from 19:30 Place Mensa in the University Potsdam (congress venue) Fee 40 EUR Sponsors and Exhibitors 75
Proteomic Forum 2017
Sponsors We would like to thank the following sponsors for their great support.
Gold Sponsor
Thermo Fisher Scientific GmbH (Dreieich/DE)
Silver Sponsors
SCIEX (Darmstadt/DE)
Bruker Daltonik GmbH (Bremen/DE)
Waters GmbH (Eschborn/DE)
Serva Electrophoresis GmbH (Heidelberg/DE)
Bronze Sponsor
Biognosys AG (Schlieren/CH)
State at printing 76 Sponsors and Exhibitors
Exhibitors The following exhibitors are looking forward to greeting you and to present you their comprehensive range of innovative products:
Booth no. Company 1 SCIEX 2 JPT Peptide Technologies GmbH 3 Bruker Daltonik GmbH 4 Gilson International 5 Waters GmbH 6 Matrix Science 7 EURISO-TOP 8 Shimadzu Deutschland GmbH 9 Promega GmbH 10 I&L Biosystems GmbH 11 Thermo Fisher Scientific GmbH 12 Wako Chemicals GmbH 13 Serva Electrophoresis GmbH 14 Decodon GmbH 15 Proteogenix 16 Intavis AG 17 glyconet Berlin Brandenburg e. V. 18 HUPO 19 MRM Proteomics Inc. 20 Luminex 21 NH DyeAGNOSTICS GmbH Room Overview 77
Proteomic Forum 2017 State at printing Rooms S16, S18 and the poster exhibition are located on the first floor. Catering Cloakroom Mensa/Conference Party Check-In & Self Plenary Hall Workshops Industry 78 Author List (Presenting Authors)
Name Page ID Abazari, M. F. 34 P149 Aebersold, R. 21 IS20 Allshire, R. 28 IS32 Arapidi, G. 13 HUPO7 Arapidi, G. 34 P116 Baerenfaller, K. 46 P049 Basri, D. F. 41 P129 Becher, I. 42 P159 Bedulina, D. 33 P103 Belghith, I. 38 P058 Bespyatykh, J. 45 P045 Blank-Landeshammer, B. 58 YIA3 Brakhage, A. A. 20 IS13 Bruderer, R. 43 P171 Bubis, J. 42 P163 Buczak, K. 41 P124 Buettner, F. 20 O07 Buzas, E. 20 IS15 Byung-Hyun, L. 47 P070 Caprioli, R. 16 IS04 Carrascal, M. 47 P071 Casadonte, R. 37 P055 Casanovas, A. 48 P098 Choudhury, K. R. 34 P113 Corbin, A. 39 P078 Cottrell, J. 14 NC03 Cristea, I. M. 21 IS19 Daily, C. 43 P172 Darula, Z. 39 P076 de Almeida, A. 32 P033 Author List (presenting Authors) 79
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Debez, A. 38 P057 Debski, J. 30 P021 Dell Aica, M. 27 O20 Demianova, Z. 14, 51 NC04, P182 Demmers, J. 27 O19 Deobald, D. 39 P075 Dijkstra, T. 30 P020 Distler, U. 14 NC01 Dojahn, J. 46, 52 P047, P189 Dondapati, S. K. 40 P083 Echevarría-Zomeño, S. 46 P066 El Magraoui, F. 41 P132 Emirbayer, P. E. 13 HUPO4 Engelmann, B. 49 P136 Facchinetti, G. 40 P118 Farhat, N. 38 P059 Farhat, Y. 51 P180 Ferro, M. 30 P016 Föll, M. C. 41 P126 Frese, C. 53 P207 Funke, S. 41 P125 Gao, Y. . 56 YIA1 Gastaldello, A. 30 P017 Gemoll, T. 40 P119, P120 Giese, H. 52 P198 Gingras, A.-C. 16 IS02 Goeminne, L. 15 NC12 Golchert, J. 32 P035 Gonczarowska-Jorge, H. 47 P090 Górka, M. 25, 62 YIA6 Grossegesse, M. 48 P093 80 Author List (Presenting Authors)
Guender, M. 52 P200 Gutsch, A. 46 P065 Haange, S. 45 P041 Hahne, H. 22 O12 Hajduk, J. 36 P196 Hanf, B. 15 NC11 Hartkopf, F. 14 NC02 Hauck, N. 47 P068 Helmholz, H. 34 P112 Hempel, B.-F. 44, 48 P214, P091 Henze, A. 39 P077 Herwig, R. 46 P048 Herzog, R. 40 P080 Heyer, R. 14 NC07 Hicks, L. 23 O09 Hippler, M. 23 IS21 Hoehenwarter, W. 19 O05 Hollenstein, D. 31 P026 Huber, C. 17 IS06 Hunyadi-Gulyas, E. 52 P199 Ihmor, P. 25, 57 YIA2 Ilies, M. 49 P141 Ivanov, M. V. 15 NC09 Jakob, A. 50 P146 Jarboui, M. A. 45 P043 Jassinskaja, M. 42 P162
Ječmen, T. 53 P201 Junemann, J. 34 P114 Junker, S. 15 NC08 Kaderali, L. 26 IS23 Kaeser-Pebernard, S. 53 P203 Author List (presenting Authors) 81
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Kant, R. 33 P104 Kelleher, N. 17 IS07 Kipping, M. 37, 42, 45, 46 P053, P166, P042, P064 Klement, E. 47 P087 Kniemeyer, O. 23 O10 Kokot, Z. J. 49 P142 Kollipara, L. 33 P101 Koshlan, T. 31 P031 Kötemann, A. 53 P206 Kramer, G. 45 P040 Kratochwill, K. 34 P117 Krijgsveld, J. 28 IS31 Krüger, T. 33 P107 Kubiniok, P. 29 P006 Kuhring, M. 31 P027 Kulikov, K. 30, 31, 52 P012, P031, P197 Larsen, M. 21 IS18 Lassowskat, I. 48 P095 Lehmann, E. 33 P102 Lehmann, R. 50 P143 Lepper, M. 49 P134 Levitsky, L. 30 P019 Lichtenthaler, S. 28 O22 Lischka, A. 41 P130 Liu, F. 27 IS27 Lorenz, C. 51 P185 Lößner, C. 44 P216 Łuciuk, A. 47 P069 MacCoss, M. 17 IS08 Mackmull, M.-T. 22 O11 Mageean, C. 50 P176 82 Author List (Presenting Authors)
Mahanty, A. 35 P153 Marcus, K. 42 P160 Martens, L. 26 IS24 Martinez Jaime, S. 19 O06 Marty, F. 14 NC05 Matafora, V. 41 P121 Matysiak, J. 49 P139, P140 Mayr, M. 13 HUPO6 Mechref, Y. 27 IS30 Megger, D. A. 52 P188 Meissner, F. 22 O14 Merkel, D. 37 P054 Meyer, K. 29 P008 Michalik, S. 32 P036 Michaud, S. 52 P217 Mikulášek, K. 43 P174 Millar, H. 26 IS25 Mnatsakanyan, R. 47 P089 Moez, P. 33 P105 Møller, I. M. 19 IS10 Moreno, S. 53, 54 P202, P212 Moritz, C. 36 P195 Muck, A. 54 P210 Muhammad, S. 48 P094 Müller, G. 39 P072 Müller, S. 43 P168 Müller, A. C. 43 P170 Musa, Y. 51 P184 Muth, T. 30 P015 Nadler-Holly, M. 51 P181 Nayak, T. 53 P204 Author List (presenting Authors) 83
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Nesvizhskii, A. I. 17 IS09 Netz, E. 30 P013 Nguyen, M. 39 P074 Nguyen, C. 50 P145 Niedzwiecka, A. 29, 33 P002, P110 Nilse, L. 31 P025 Nilsson, P. 22 O13 Novo, P. 14 NC06 Nury, C. 51 P183 Obermann, J. 29 P007 Ohmayer, U. 51 P186 Oltmanns, A. 48 P096 Ori, A. 45 P044 Oria, V. O. 33 P108 Ortega, M. 25, 61 YIA5 Osetrova, M. 31 P030 Ostermaier, M. 40 P084 Pagel, O. 51 P187 Paneru, T. 32 P032 Pankert, P. 47 P086 Pfeuffer, J. 17 O04 Pich, A. 34 P115 Pichler, G. 42 P158 Polen, T. 35 P152 Pollack, L. . 48 P133 Poorebrahim, M. 34 P149 Rabe, A. 49 P137 Rackiewicz, M. 43 P213 Radau, S. 43 P175 Radhakrishnan, K. 35 P154 Rajendran, L. 20 IS16 84 Author List (Presenting Authors)
Rees, J. 27 O17 Reinecke, M. 29 P004 Reiter, L. 42 P167 Renard, B. Y. 30 P011 Rhode, H. 22 O15 Richter, F. 27, 52 O18, P198 Richter, S. 54 P211 Rogowska-Wrzesinska, A. 40 P082 Rudashevskaya, E. 53 P201 Russell, R. 26 IS26 Sachsenberg, T. 31 P022 Saliba, P. 40 P085 Schallert, K. 30 P018 Scheidt, T. 47 P088 Schilling, O. 13 HUPO3 Schlüter, H. 15 NC10 Schmit, P.-O. 50 P147 Schmitz, G. 14 HUPO8 Schnatbaum, K. 35 P193 Schroda, M. 23 IS22 Schulze, S. 48 P097 Schwämmle, V. 28 O21 Sedo, O. 38 P063 Seidel, K. 17 O01 Seifert, J. 46 P046 Senkler, J. 46 P067 Sergeant, K. 39 P073 Serrano, S. M. T. 32 P038 Shekhova, E. 39 P079 Shema, G. 48 P092 Shender, V. 41 P123 Author List (presenting Authors) 85
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Smolyakov, A. 50 P177 Spengler, B. 16 IS05 Sroka, R. 44 P215 Starke, R. 38 P062 Stech, M. 35 P151 Steger, M. 50 P178 Stephan, S. 35 P156 Sticker, A. 17 O03 Stoehr, G. 29 P005 Strasser, L. 41 P122 Swart, C. 42 P164 Swiatly, A. 49 P138 Swieringa, F. 52 P190 Taleb, R. 43 P169 Thelen, J. 19 IS11 Thoring, L. 32 P034 Tierbach, A. 32 P037 Tölle, R. 42 P165 Tremmel, M. 52 P192 Trost, M. 20 O08 Turewicz, M. 31 P023 Tüshaus, J. 37 P051 Ucan, Y. 34 P111 Uszkoreit, J. 31 P024 van Eyk, J. 15 IS01 Vente, A. 35 P155 Verhaert, P. 50 P148 von Kriegsheim, A. 16 IS03 von Törne, C. 23 O16 Wang, D. 32 P100 Wang, M. 35 P157 86 Author List (Presenting Authors)
Weibchen, G. 37, 40 P052, P081 Wielsch, N. 53 P208 Wiese, S. 43 P173 Wilmanns, M. 27 IS28 Wilmes, P. 20 IS14 Wilson, D. N. 20 IS12 Winter, M. 25, 59 YIA4 Witt, E. 49 P135 Witzke, K. E. 53 P205 Wöhlbrand, L. 38 P060 Wuhrer, M. 27 IS29 Xi, L. 31 P029 Xuan, Y. 51 P179 Younas, N. 50 P144 Zauber, H. 35, 53 P194, P209 Zdrahal, Z. 38 P061 Zecha, J. 42 P161 Zemella, A. 34 P150 Zhang, Y. 38 P056 Zheng, R. 25 YIA1 Zolg, D. 37 P050 Did you know?
Conventus is the Professional Congress Organizer of the of the Proteomic Forum 2017 www.proteomic-forum.de
Proteomic Forum 2019 Spring 2019 Berlin/Germany
Hosting Society German Society for Proteome Research c/o ISAS Bunsen-Kirchhoff-Straße 11 44139 Dortmund (DE) www.dgpf.org
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