Advances in Proteomics
11-15 April 2011
Zakopane, Poland

Organiser:

Draft Report

Summary

This workshop was aimed at increasing awareness and capabilities of researchers in mass spectrometry based proteomics leading to better designing of biological experiments. The workshop was focused on recent advancements in sample preparation
and analysis (including statistical methods in data analysis) – critical elements of a successful experiment taking advantages of mass spectrometry. The workshop was especially addressed to researchers directly involved in proteomic studies.

Advances in Proteomics workshop was organised by Prof. Michał Dadlez, Head of Mass
Spectrometry Laboratory, Institute of Biochemistry and Biophysics Polish Academy of Science in Kalatowki Hotel, Zakopane. 14 speakers from leading European Universities / Academies gave over 18 talks directed to especially young researchers involved in proteomics studies. A unique feature of this meeting was long sessions dedicated for bilateral discussions between young researchers with experienced scientists.

The outcomes so far are threefold: participants became more aware of proteomics as a
technique in modern molecular biology, its advantages and limitations. Secondly they had a chance to consult their experiments with more experienced researchers and lastly participants established new cooperation.

Scientific Content

The workshop was divided into thematic sessions: techniques for sample preparation including post translational modifications, data analysis and structural studies. The meeting was opened with a lecture of Krzysztof Skowronek, PhD, International Institute of Molecular and Cell Biology, who presented studies on protein structure analysis using mass spectrometry. Krzysztof Skowronek is especially interested in engaging cross-links technology providing structural constraints of protein complexes, that support protein structure prediction by bioinformatics tools. The lecture was followed by lecture given by Prof. Marc Bauman from Biomedicum Helsinki on clinical proteomics. Prof. Bauman works in the Institution focused in implementation of biological outcomes into hospital practice, so his lecture entitled “Clinical Proteomics: a technology to shape the future” was concerning proteomics technologies applied in the medicine. Especially interesting was presentation of microchips developed by Prof. Bauman Laboratory for diagnostics of different diseases, usually basing on body fluids analysis. Prof. Jarek Poznański, Institute of Biochemistry and Biophysics Polish Academy of Science introduced a concept of most recent developments in mass spectrometry – ion mobility separation in a lecture dedicated to Alzheimer disease and the role of Aβ peptide “Ion Mobility Separation Coupled with MS Detects Two Structural States of Alzheimer Disease Aβ 1 – 40 Peptide Oligomers”. His recent studies revealed, that signals observed on the mass spectrometers which were believed to be homogenous mixture of oligomeric forms are in fact structural conformers. Prof. Thomas Jorgensen from Southern University Denmark continued the subject of mass spectrometry based structural studies, however by application of proton deuter technology. He gave the lecture entitled “The dynamic structure of proteins probed by hydrogen / deuterium exchange monitored by mass spectrometry”, where he presented overview of the technique and focused on the problem of preventing protein scrambling (which reduces resolution of the measurement in MS/MS mode). Prof. Jacek Wisniewski from Max Planck Institute, Munich, opened a session dedicated to sample preparation techniques in a lecture entitled “Biochemical Solutions for Large Scale Proteomics”. Prof. Wisniewski talked in details on the technique he has developed, that significantly increases number of identified proteins in large scale experiments – FASP – filter aided sample preparation, together with stage tip extraction – easy and fast method of peptides fractionation, achieving around 7 000 of identified proteins. Prof. Wisniewski demonstrated also application of his methodology in analysis of post translational modifications. Lukasz Marczak from Institute of Bioorganic Chemistry PAS, continued the thread of post translational modifications and presented interesting approach towards “Analysis of N-homocysteinylated human blood proteins using mass spectrometry techniques”. Prof. Jacek Wiśniewski gave his second lecture “Quantitative Proteomics of Clinical Samples” presenting approach of proteins extraction from formalin fixed paraffin embedded tissues originating from hospital banks and further processing with FASP protocol. Such workflow appears to be not only very efficient, but also reproducible and quantitative. The lecture was followed by the second presentation of Prof. Marc Bauman “Electrophoretic techniques in modern protein chemistry and proteomics” sharing his experiences with non routine gel electrophoresis applications and technique modifications. Prof. Piotr Widłak from Institute of Oncology Maria Skłodowska - Curie Cancer Centre gave an interesting lecture of combining genetic and proteomic approaches in investigation cancer progression. Janusz Debski, from Mass Spectrometry Laboratory IBB PAS presented his recent achievements in lecture “Analysis of protein S-glycosylation” considering analysis of relatively unknown modification. Especially interesting was novel methodology of chemical derivative of such modification elaborated by Alicja Buchowiecka from Technical University of Lodz – a co-worker in this project. Aleksandra Wyslouch Cieszynska, PhD continued the topic of cystein modifications – nitrosylation by giving a talk “Synaptosomes S-Nitrosylation and Alzheimer Disease”. She managed to observe significant changes in nitrosylation profiles of Synaptosomes extracted from mouse model of Alzheimer Disease (AD). Interestingly, all of these proteins in literature expected to be involved in development of the AD, underling the outstanding performance of the method. Agata
Malinowska from Mass Spectrometry Laboratory IBB PAS, opened a data analysis session and gave a lecture “Diffprot – software for statistical analysis of differential proteomics data” addressing problem of statistical data validation in large scale proteomics studies. Diffprot appears to deal very well with fishing out differentially expressed proteins and generates less false positives, comparing to commonly used simple statistical tests, improving the results. Claire O’Donovan, from EBI introduced UniProt Database, which will became a gold standard in mass spectrometry in the lecture “UniProt and Proteomics”. She described its main features, content and opportunities of using it. Next lecture entitled “Machine Learning techniques to increase yield and assess confidence in peptide-spectrum matches for shotgun proteomics” was given by Prof. Lukas Kall from Stockholm University. Prof. Kall presented very interesting approach for estimating false discovery rate in proteomic data sets and his algorithm “Percolator”. Percolator was e.g., implemented in Mascot software (Matrix Science Ltd), which is the most commonly used software for data analysis. Closing lecture was given by Prof. Maciej Lalowski from Biomedicum Helsinki entitled “Delineating dynamic changes in the human interactome: measurements and strategies”. In his talk, Prof. Lalowski presented interactome building / predicting algorithm using multiple databases, hence giving an opportunity to detect potential interactors. Very important aspect of the meeting were special time slots reserved for interactions between participants, during which participants were conducting interesting discussions.

Assessment of the results & impact of the event on the future direction of the field

The workshop set two main goals - to create a friendly environment for exchange of ideas, discussions and to enhance collaboration between workshop participants, and to familiarise young scientists with most recent innovations in the field of proteomics. This is why, the main emphasis of the workshop was allocated to practical aspects of the experiments, rather than presenting particular projects. During the bilateral discussions they had a unique opportunity to consult their experiments with more experienced colleagues. As a result, Mass Spectrometry Laboratory begun cooperation with Biomedicum Helsinki. One publication is at the moment under preparation, and they plan to submit in September a joint proposal. Also Prof. Jacek Wisniewski from Max Plank Institute start to cooperate with Prof. Marc Bauman from Biomedicum Helsinki. At the end of the workshop it was suggested to organise an event with the same formula next year in another country, to attract other local young scientific communities.

Programme
Monday, 11th April 2011
16:45 Welcome and short introduction
17:00 Marc Baumann - Clinical Proteomics: a technology to shape the future?
19:00 Krzysztof Skowronek - Mass spectrometry in protein structure modelling.
20:00 Relax a bit and get together

Tuesday, 12th April 2011
08:00 Breakfast
09:00 Discussions and interactions
14:00 Lunch
15:00 Jarek Poznański - Ion Mobility Separation Coupled with MS Detects Two Structural States of
Alzheimer's Disease Ab1-40 Peptide Oligomers.
16:00 Thomas Jorgensen - The dynamic structure of proteins probed by hydrogen/deuterium
exchange monitored by mass spectrometry.
17:00 Coffee break
17:15 Jacek Wiśniewski - Biochemical Solutions for Large Scale Proteomics
18:15 Agata Malinowska - Diffprot – software for statistical analysis of differential proteomics data.
19:00 Lukasz Marczak - Analysis of N-homocysteinylated human blood proteins using mass spectrometry techniques.
19:45 Dinner

Wednesday, 13th April 2011
08:00 Breakfast
09:00 Discussions and interactions
14:00 Lunch
15:00 Jacek Wiśniewski - Quantitative Proteomics of Clinical Samples.
16:00 Marc Baumann - Electrophoretic techniques in modern protein chemistry and proteomics.
17:00 Coffee
17:15 Piotr Widlak
18:15 Janusz Debski - Analysis of S-glycosylation.
19:30 Dinner

Thursday, 14th April 2011
08:00 Breakfast
09:00 Discussions and interactions
13:30 Lunch
14:30 Aleksandra Wyslouch Cieszynska - Synaptosomes S-nitrosylation and Alzheimer disease.
15:30 Claire O'Donovan - UniProt and Proteomics.
16:30 Coffee
16:45 Lukas Kall - Machine learning techniques to increase yield and assess confidence in peptidespectrum
matches for shotgun proteomics.
17:45 Maciej Łałowski - Delineating dynamic changes in the human interactome: measurement and validation strategies.
18:45 End of the meeting
19:00 Bonfire or farewell dinner