Organisers

Lennart Martens, EBI, Hinxton, Cambridge, UK
Henning Hermjakob, EBI, Hinxton, Cambridge, UK

Introduction

The proteomics community has only recently begun to adopt quality control of the different steps in the complex workflows employed when analysing a sample. As a result, efforts towards QC are currently specific to individual laboratories, resulting in widely divergent and incomparable strategies to verify the operational status of the instrumentation and analysis steps. At the same time, educational initiatives such as the Fixing Proteomics Campaign, and academic organisations such as the Association of Biomolecular Research Facilities (ABRF) are trying to raise the awareness of the community with regards to the importance of QC. Furthermore, the Human Proteome Organisation (HUPO) has recently constructed a 20 protein equimolar test sample to provide a baseline QC test for entire proteomics workflows. These efforts on the QC front can be compared to the early days of proteomics data standardization, which then led to the successful formation of the HUPO Proteomics Standards Initiative (PSI).

The main objective of the workshop is to assemble a critical mass of representatives from the academic community, from industry (pharma, biotech start-ups, and consumables vendors), and from key scientific journals. The workshop will take a practical focus, by analysing proteomics workflows and identifying areas where QC strategies are available or where they are not. Additionally, the implementation of QC in standard laboratory practice requires readily available and reasonably priced
consumables (e.g. protein or peptide standards) as well as informatics tools that can automate relevant data acquisition and evaluation during analysis run time. Based on this core evaluation, a whitepaper will be written that outlines the current status of the field and that identifies specific areas where progress must be made. In order to ensure follow up on the whitepaper recommendations, a Proteomics Quality Control Consortium with broad participation from the workshop participants will be
created. The core objective of this Consortium will be to establish core funding to create the appropriate laboratory standards, tools and procedures, along with educational materials and future wet-lab tutorial workshops. The Consortium will also work with the scientific journals to help draft unified QC-oriented guidelines for authors.

The whitepaper that will be written after the workshop will provide the required foundation for the creation of a new international Consortium with broad participation in the field of proteomics that will be dedicated to the standardisation and implementation of quality control in proteomics laboratories. To this end, the first tasks of the newly formed Consortium will consist of identifying relevant funding sources, and establishing prioritised task lists based on the analysis given in the whitepaper. The long- term objectives for this Consortium will be: (i) the creation best practices for quality control in
proteomics experiments, (ii) the provision of educational resources and workshops to aid implementation, (iii) the availability of wet-lab standards, and (iv) the development of free, open source software tools to automate QC steps.

Preliminary Programme

Day 1
09:00 -09:35 Experiences from the HUPO Test Sample efforts
09:35 -10:10 Experiences of the ABRF Proteomics Research
10:10 -10:45 Experiences of the Fixing Proteomics Campaign
10:45 -11:15 Coffee break
11:15 -11:50 A view from industry
11:50 -12:25 Quality control in the biotech start-up
12:25 -13:25 Lunch
13:25 -14:00 Quality control in a clinical setting
14:00 – 14:25 Delineation of key areas of proteomics experiments affected by quality control
Tentatively: sample extraction, sample separation, sample processing, mass spectrometry
14:25 -15:25 Breakout sessions according to the key areas delineated in the previous session
15:25 -15:45 Coffee break
15:45 -16:45 Breakout sessions continued
16:45 -17:30 Progress reports from each breakout session
18:00 -20:00 Dinner and discussions

Day 2
09:00 -09:35 Creating standards for the proteomics community: the HUPO Test Sample
09:35 -10:10 Creating standards for the proteomics community: the ABRF UPS-1 Test Sample
10:10 -10:45 Vendor Quality Control standards for mass spectrometry
10:45 -11:15 Coffee break
11:15 -11:50 Providing software for quality control
11:50 -12:25 Quality control practices in core facilities
12:25 -13:25 Lunch
13:25 -15:25 Breakout sessions (continued from Day 1)
15:25 -15:45 Coffee break
15:45 -16:45 Breakout sessions (continued)
16:45 -17:30 Progress reports from each breakout session
18:00 -20:00 Dinner and discussions

Day 3
09:00 -09:35 Quality control and journals
09:35 -10:10 Quality control and funding opportunities
10:10 -10:45 Quality control and minimal reporting requirements
10:45 -11:15 Coffee break
11:15 -11:45 White paper outline and division of writing tasks by breakout session
11:45 -12:25 Breakout sessions: write-up of white paper contribution
12:25 -13:25 Lunch
13:25 -14:45 Breakout sessions: write-up of white paper contribution
14:45 -15:15 Coffee break
15:15 -15:45 Creation of the Proteomics Quality Control Consortium
15:45 -16:30 Overall discussion
16:30 Meeting end

List of Speakers

Prof. Dr. Karl Mechtler, IMP, Vienna, Austria
Prof. Dr. Kathryn Lilley, Cambridge University, Cambridge, UK
Prof. Dr. Bruno Domon, ETHZ, Zurich, Switzerland
Prof. Dr. Albert Sickmann, ISAS, Dortmund, Germany
Marc Vaudel, ISAS, Dortmund, Germany
Dr. Sara Ten Have, University of Dundee, UK
Prof. Dr. Lennart Martens, UGent/VIB, Ghent, Belgium
Dr. Chris Taylor, EMBL-EBI, Cambridge, UK
Dr. Matthieu Visser, Philips Research, Eindhoven, The Netherlands
Dr. Hans Vissers, Waters Corporation, UK
Dr. Will Dracup, Nonlinear Dynamics, United Kingdom
Dr. Ola Forsstrom-Olsen, Ludesi, Sweden
Dr. Pierre-Alain Binz, SIB, Geneva, Switzerland
Dr. John Cottrell, Matrix Science Ltd, UK
Dr. Cathleen Verleysen, Pronota, Belgium
Dr. Sarah Robinson, Thermo Fischer Scientific, UK
Dr. Matthew Cook, Sigma-Aldrich, UK
Prof. Dr. Roz Banks, University of Leeds, UK, Wiley journals Proteomics and Proteomics Clinical Applications (PCA)
Dr. Michael Smith, RSC journal Molecular BioSystems, UK
Prof. Dr. Gert Lubec, Medical University of Vienna, Austria, Springer journal Amino Acids

Venue

The meeting will be hosted at the European Bioinformatics Institute.

Registration

Registration is closed.