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APRS Symposium and Late Summer Meeting, 26-28 August 2015

The 13th annual Austrian Proteomic Research Symposium (APRS) will take place on the campus of the Institute of Science and Technology Austria (IST Austria) in Klosterneuburg and is organized in collaboration with the Austrian Proteomics Association (AuPA) and the Late Summer Meeting IMP/IMBA/GMI/CSF.

The purpose of the symposium is to present the latest technologies and applications to scientists coming from Europe. Top experts will be invited to speak, and a number of participants will also be selected to give a short talk and present their posters during formal poster sessions.


Follow the #APR2015 symposium on Twitter.

Program

Program

Flash Talks Time Table

26.08.2015

André Müller
Maksym Danchenko
Barbara Darnhofer
Johannes Doblmann
Juan Antonio Fafian Labora
Katarina Fritz
Florian Füssl
Johannes Griss
Richard Kandasamy
Dominique Kreutz
Juraj Lenco
Lev Levitsky

28.08.2015

Laura Liesinger
Peter Májek
Shane Austin
Christof Regl
Iskra Sainova
Matthias Schittmayer
Tamaj Şeker
Fernando Sialana
Peter Socha
Karel Stejskal
Lisa Strasser
Tamara Tomin
Dijana Vitko

Program

26.08.2015

08.00 – 08.30Symposium shuttle leaves from Wien Heiligenstadt, stopping at Parkhotel around 08:15
08.30 – 09.00Registration
09.00 – 09.45Andrea Sinz, “Chances and Pitfalls of Chemical Cross-Linking/Mass Spectrometry for structural Proteomics”
09.45 – 10.15Rebecca Beveridge, “A mass spectrometry-based framework to investigate (un)structural characteristics of p27”
10.15 – 10.30Coffee Break
10.30 – 11.00Christoph Lenz, “Crosslinking, SILAC, SWATH – Implementation and Applications of a TripleTOF Mass Spectrometry System in a Proteomics Core Facility”
11.00 – 12.15Flash talks
12.00 – 14.00Lunch at Redlinger Hütte
14.00 – 17.30Practical workshops (coffee break from 15:30 to 15:50)
17.30 – 18.00Wine and cheese with SaxoFun
18.00Symposium shuttle going back to Parkhotel and Wien Heiligenstadt
18.00 – 19.45General Council of the Austrian Proteomics Society (for members of AuPA)
19.45Shuttle to speakers and AuPA dinner leaves in front of Lecture Hall
20.00Speakers dinner at Aigner-Krauthahn
22.00Special shuttle going back to IST, Parkhotel and Wien Heiligenstadt

27.08.2015

08.15Symposium shuttle leaves from Wien Heiligenstadt (Parkhotel 08:30)
09.00 – 09.45Christian Huber, “Nanotoxicity-Screening by Means of Proteome and Metabolome Analysis”
09.45 – 10.15Stefan Helm, “Quantitative multiplex MS analysis (MSE) as effective tool to trace chloroplast development”
10.15 – 10.30Coffee Break
10.30 – 11.00Christoph Borchers, “Short range photoactivatable cross linkers and HDX/middle down by LC/MS/MS at -20C using ETD for structural characterization of proteins”
11.00 – 12.00Poster session
12.00 – 14.00Lunch at Redlinger Hütte
14.00 – 18.00Practical workshops (coffee break from 15:45 to 16:05)
18.00 – 23.00Conference Party with BBQ and live music by Big Yellow Taxi Quartett
21.00First symposium shuttle going back to Parkhotel and Wien Heiligenstadt
23.00Second symposium shuttle going back to Parkhotel and Wien Heiligenstadt

28.08.2015

08.15Symposium shuttle leaves from Wien Heiligenstadt (Parkhotel 08:30)
09.00 – 09.45Andreas Pichlmair, “The proteome under viral attack”
09.45 – 10.15Herbert Schiller, “Proteomics of the extracellular niche in lung injury, repair and fibrosis”
10.15 – 10.30Coffee Break
10.30 – 11.00Wolfram Weckwerth, “Complex Integration of Metabolomics, Proteomics and Phosphoproteomics with Metabolic Modelling in Plant and Animal Signalling Networks”
11.00 – 11.20Florian Meier, “Very deep proteome coverage using a high resolution quadrupole time-of-flight instrument”
11.20 – 12.40Flash Talks
12.40 – 13.00Awards and prices for best flash talk and best poster
13.30End of conference
Symposium shuttle going back to Parkhotel and Wien Heiligenstadt

Abstract Guidelines for Flash Talks and Posters

Abstracts should be submitted via the registration form only. Please do not send in an abstract more than once. 


PLEASE NOTE
Only abstracts submitted by registered participants will be accepted. It is the responsibility of the presenting author to ascertain whether all authors are aware of the content of the abstract before submission. Abstracts have to be submitted until August, 7th, 2015.

For any further information please contact mechtler@imp.ac.at; 


INSTRUCTIONS FOR ABSTRACT SUBMISSION:
Only papers whose abstracts have been reviewed and approved by the Scientific Committee will be presented as flash talk.

The body of the abstract must not exceed 2300 characters, spaces included.
Only 1 abstract per participant will be accepted. 


GENERAL REQUIREMENTS
The text must be clear, concise, and written in proper English. The content must not have been previously published in academic journals or subject to peer review. 
Significant technical information must not be withheld. Abstracts must absolutely contain results. Statements such as “results will be discussed” are not acceptable and will lead to rejection. 


STRUCTURE OF THE ABSTRACT
Abstracts should be structured and must include: 
BACKGROUND: a brief introduction stating the purpose of the investigation and its relevance to laboratory medicine; 
METHODS: a description of the methodology used; 
RESULTS: to be supported by statistical or other evidence to show their validity; 
CONCLUSIONS 


GENERAL INFORMATION
Confirmation of receipt of the abstract will be acknowledged by e-mail immediately after submission.


HOW TO PREPARE AND SUBMIT AN ABSTRACT
It is important to carefully follow the instructions below. Incorrectly prepared abstracts will be rejected.
Abstracts should be prepared off-line in advance;
– Prepare your abstract on a word processor (such as Microsoft Word);
– Do not include title, authors’ names and affiliations in the abstract file;

– When abbreviations are used, spell out the full word at first mention in the text followed by the abbreviation in parentheses. Thereafter, use the abbreviation throughout.
– When the on-line system requires the abstract to be entered, copy and paste your text. Abstracts are limited to 2300 characters, spaces included (title, authors’ names and affiliations excluded).

Confirmed Speakers

Univ. Prof. Mag. Dr. Christian Huber
“Nanotoxicity-Screening by Means of Proteome and Metabolome Analysis”Department of Molecular Biology, Division of Chemistry and Bioanalytics,University of Salzburg, Salzburg, Austria
Prof. Dr. Andrea Sinz
“Chances and Pitfalls of Chemical Cross-Linking/Mass Spectrometry for structural Proteomics”Institute of Pharmacy, Halle (Saale), Germany
Dr. Andreas Pichlmair
“The proteome under viral attack”Max Planck Institute of Biochemistry, Martinsried, Germany
Dr. Herbert Schiller
“Proteomics of the extracellular niche in lung injury, repair and fibrosis”Max Planck Institute of Biochemistry, Martinsried, Germany
Dr. Christof Lenz
“Crosslinking, SILAC, SWATH – Implementation and Applications of a TripleTOF Mass Spectrometry System in a Proteomics Core Facility”Max Planck Institute for Biophysical Chemistry, Proteomics Service Facility,Universitätsmedizin Göttingen, Germany 
Stefan Helm, M.Sc. (cand. Dr. rer. nat.)
“Quantitative multiplex MS analysis (MSE) as effective tool to trace chloroplast development”Martin-Luther-Universität Halle-Wittenberg, Abt. Pflanzenbiochemie, Germany
Rebecca Beveridge, B.Sc.
“A mass spectrometry-based framework to investigate (un)structural characteristics of p27″University of Manchester, UK
Univ.-Prof. Dr. Wolfram Weckwerth
“Complex Integration of Metabolomics, Proteomics and Phosphoproteomics with Metabolic Modelling in Plant and Animal Signalling Networks”Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Christoph Borchers, Ph.D.
“Short range photoactivatable cross linkers and HDX/middle down by LC/MS/MS at -20C using ETD for structural characterization of proteins”UVic Genome BC Proteomics Centre, Canada
Florian Meier, MSc
“Very deep proteome coverage using a high resolution quadrupole time-of-flight instrument”Max Planck Institute of Biochemistry, Munich, Germany

Practical Workshops

Spoiler title

“High-Efficiency and High Peak Capacity Single- and Multidimensional Chromatographic Separation Methods for Proteome Analysis”

Christian Huber – Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Salzburg, Austria

Details:

Proteomics stands as a synonym for the comprehensive analysis of large numbers of proteins that are believed to adequately describe the state and dynamics of biological systems. It is hoped that the enormous amount of data generated will help to understand the mechanisms of aging, disease, drug effects, or environmental stresses, and hence, offering insights for diagnosis and therapy. Although advances in mass spectrometry technology have enormously promoted the feasibility of large-scale analysis of biological samples, separation before mass spectrometric investigation becomes crucial in the face of the considerably high complexity of biological samples. In this workshop we will therefore recapitulate the achievements and challenges of separation technology based on chromatographic principles both for proteins and peptides. Although single-stage separation systems offer high selectivity and separation power, two or more separation stages often have to be combined into multidimensional separations in order to provide sufficient peak capacity. An overview of the different separation modes is given. The combination of different separation principles, including ion-exchange chromatography, chromatofocusing, or ion-pair reversed-phase chromatography into two-dimensional separation systems is discussed in terms of their total peak capacity, reproducibility, and yield of peptide or protein identifications. Different stationary phase configurations, including non-porous, superficially porous, or monolithic support materials, have been proven to circumvent the problem of slow diffusional mass transfer with biopolymers. Due to its high separation efficiency, reversed-phase chromatography both at the peptide and the intact protein level is shown to be a real alternative to ion-exchange chromatography or chromatofocusing for first-dimension separations of complex peptide- or protein mixtures. We also discuss the new trends of ultrahigh- pressure chromatography or monolithic separation media, which have facilitated a significant increase in separation performance and speed of analysis. Finally, some selected examples of application including top-down or bottom-up proteome analyses, differential proteome analysis in toxicity profiling or the characterization of cancer stem cells are presented in order to shed light on the potential and the limitations of (multidimensional) separations for “proteomics” analyses.

“Chances and Pitfalls of Chemical Cross-Linking/Mass Spectrometry for structural Proteomics”

Andrea Sinz – Institute of Pharmacy, Halle (Saale), Germany

Details:

During the last 15 years, chemical cross-linking combined with mass spectrometry (MS) and computational modeling has advanced from investigating three-dimensional structures of isolated proteins to deciphering protein interaction networks. As the chemical cross-linking/MS approach allows to the capture of transient and weak interactions it has the potential to become a routine technique for unraveling protein interaction networks in their natural cellular environment. In this workshop, we will give practical advice on the use of different cross-linkers (amine-reactive linkers, photo-activatable amino acids) and data analysis with the StavroX software (http://www.stavrox.com).

“Label free quantification with Progenesis QI for Proteomics – A practical hands on experience”

Martin Wells – Nonlinear Dynamics (a Waters company), UK

Details:

Please bring your laptop.

This workshop covers the hands on practical analysis of a supplied dataset using the very latest v2 version of Progenesis QI for Proteomics for label free comparative quantification.
Participants can download the evaluation software in advance which they will have to take with them after the workshop. The session will cover the complete Quantify then Identify workflow from the unique co-detection technology in Progenesis, the new Quality Control metrics, peptide identification through to protein inference and multivariate statistics. There will also be a demonstration of on the impact Ion Mobility has on the separation, quantification and identification of co-eluting and or isobaric ions.
The workshop will then look at the downstream integration of data into workflows including integration with Pathways tools, importing additional data from third party programs and exporting data. This is an ideal opportunity to experience for yourself this intuitive, easy to use program in action.

“Is QTOF technology ready to play a role in quantitative proteomics?”

Annette Michalski – Bruker, Germany

Details:

During the last decades quadrupole time-of-flight mass spectrometry (QTOF) has evolved into a versatile high performance technology. Today we can achieve mass accuracies of < 1 ppm and resolving powers up to 80,000 opening a wealth of analytical options. QTOF technology can deliver large ion populations per scan thus providing a unique statistical base to accurately measure isotope patterns. Very high acquisition speed further makes QTOF technology very suitable for quantitative proteomics strategies. This workshop will cover insights into the technology as well as important features and developments for data analysis.

“Novel hardware and software workflows for glyco proteomics”

Ulrike Schweiger-Hufnagel – Bruker, Germany

Details:

In most naturally occurring glycoproteins, pools of glycans are attached to one or more glycosylation sites. For proteins with multiple sites of glycosylation, the site specific analysis of each individual glycan attachment site becomes a challenging task. Reverse phase (RP) liquid chromatography separation in combination with quadrupole TOF mass spectrometric detection is highly suited for the analysis of glycopeptides due to its high mass accuracy, fast duty cycles and high m/z range. In this workshop we present novel software and hardware workflows and practical guidance to the analysis of glyco proteomics samples.

“Next Generation of SWATH™ – New features and workflows”

Christian Baumann – Sciex, Germany

Details:

This workshop covers new features in the SWATH™ workflow – ID and quantitation of all peptides detectable in a sample with the ability of retrospective analysis without the need of re-running the sample. Now the workflow can also be used for isotopically labeled workflows such as SILAC to benefit from the better and cleaner MRM-like quantitation on the MS2 level.
The session will include an overview of the MS instrument and the new workflow from acquisition, library building to data processing and data alignment as well as statistical analysis using ProteinPilot®, Peakview™ and Markerview™ Software, as well as an outlook of the potential for future applications.

“Capillary electrophoresis based proteomics”

Anthonius Heemskrerk – Sciex, UK

Details:

This workshop covers the fundamentals and developments in CESI-MS for peptide and bottom-up proteomics analysis. Where CE-MS used to be a cumbersome and insensitive technique it is now a highly sensitive and robust technique through the use of the CESI Opti-MS spray interface which merges the separation and electrospray sections into one seamless apparatus.

The session will include a thorough explanation of fundamentals of the coupling of the CE to mass spectrometry through CESI. This is followed by a discussion of all the aspects that are necessary in the development of an analytical method using CESI.
Finally, a run through of a number of applications to provide a frame of reference of the performance of CESI-MS in the fields of bottom-up proteomic and peptide analysis.

“Identify and quantify with Q Exactive(s): a set of tips and tricks to get the best of your instrument in Data Dependent and Data Independent modes”

Sega Ndiaye – Thermo Fisher Scientific, France

Yue Xuan – Thermo Fisher Scientific, Germany

Details:

In this workshop we will give you guidelines to perform optimum data dependant and independent experiments with the different Q Exactive™ models. Data acquisition and processing will be discussed.

“TMT labeling for multiplexing experiments and accurate quantification of peptides and PTMs: from method set-up to data processing”

Sonja Radau – Thermo Fisher Scientific, Germany

Samy Memmi – Thermo Fisher Scientific, Belgium

Details:

In this workshop we will describe LC-MS set-up for TMT experiments, introduce specific features of the Orbitrap Fusion™ Tribrid™ mass spectrometer and present Proteome Discoverer 2.1 as an optimized software tool for data processing of TMT experiments. We will also highlight the use of TMT reagents for PTM identification and quantification.

26.08.2015

W1“Changes and Pitfalls of Chemical Cross-Linking/Mass Spectrometry for structural Proteomics”
W2“Label free quantification with Progenesis QI for Proteomics – A practical hands on experience”
W3“Novel hardware and software workflows for glyco proteomics”
W4“Identify and quantify with a Q Exactive: a set of tips and tricks to get the best of your instrument in Data Dependent and Data Independent modes”
W5“Capillary electrophoresis based proteomics”

27.08.2015

W1“High-Efficiency and High Peak Capacity Single- and Multidimensional Chromatographic Separation Methods for Proteome Analysis”
W2“Is QTOF technology ready to play a role in quantitative proteomics?”
W3“TMT labeling for multiplexing experiments and accurate quantification of biomolecules: from method set-up to data processing”
W4“Next Generation of SWATH™ – New features and workflows”

Travel Grants

Travel grants are available from EUPA and AuPA.

Sponsors

Organizing Committee

Academic:
Michael Sixt, michael.sixt[AT]ist.ac.at
Karl Mechtler, mechtler[AT]imp.ac.at

Organizational:
Marie Trappl, marie.trappl[AT]ist.ac.at

Institute of Science and Technology Austria
Am Campus 1
A – 3400 Klosterneuburg
Phone: +43 (0)2243 9000
Fax: +43 (0)2243 9000 2000

Past Conferences

APRS 2014 – Salzburg:
http://www.aprs2014.sbg.ac.at/abstract.html

APRS 2013 – Innsbruck:
http://biocenter.i-med.ac.at/index.php?option=com_content&view=article&id=85

APRS 2012 – Graz:
http://aprs2012.tugraz.at/

APRS 2011 – Vienna:
http://www.meduniwien.ac.at/orgs/index.php?id=3665