Practical Proteomics: A training course for the BBSRC community

Proteomics, broadly speaking, is the identification and characterisation of large numbers of proteins, for the purpose of understanding biological systems by uncovering changes in protein levels and activites. Because proteomics is a relatively new field of study, there is currently a great demand amongst researchers in many areas of the biological and biochemical sciences at all professional levels for hands-on training in modern proteomic technologies. The different technologies used in proteomics are very diverse and require bioscientists to become expert in new and challenging areas with which they are not familiar. For example, the technique of mass spectrometry is absolutely central to proteomics research, but few biological scientists have any experience with it. If the research advantages that using proteomics offers to the biosciences are to be properly and fully available to British science, these techniques need to be used much more widely and effectively by biological scientists in the UK. They therefore need to be trained to use techniques like mass spectrometry and be taught how proteomics technologies can be applied to their own areas of research. The best way to provide the necessary training in proteomics technologies is to give people the opportunity to practice and learn them in the laboratory. With this kind of hands-on experience, biologists will be able to return to their own laboratories and begin to apply proteomics effectively in their own research programmes. We will meet the need for training in proteomics by providing a course to researchers in the biological sciences which will teach them the basics of proteomic technologies and give them the chance to practice the technologies themselves in the laboratory. This practical, hands-on course will be five days long, and combine class-room lectures, demonstrations, and laboratory exercises. As well as class-room lectures on the theory and practice of proteomics, participants in the course will have the opportunity to discuss the design of appropriate proteomics experiments with scientists who are experienced in proteomics. The course will be taught by experts in the technologies, who are experienced at using them routinely in their own research. The equipment and instruments that will be used by the students on the course is state-of-the-art and the best that is currently available for proteomic research. The students will learn how how to carry out a proteomic study from beginning to end, and will even be able to bring their own biological samples to analyze during the course. By students, we mean anyone interested in proteomics with at least a first degree in the biological or chemical sciences, including post-graduates, post-doctoral researchers, and research and academic staff (lecturers, readers, and professors). With the knowledge and experience gained in the course, biological scientists will be able to start using proteomic technologies in their own research.

The main objective of the work will be the provision of the York Practical Proteomics short course once per year for three years for the BBSRC community. All resources requested in this proposal are directly related to provision of the course, which will allow the course to reach an important new audience. Practical Proteomics is offered as a five-day residential course with all costs, including accommodation, meals, and course materials, included. Our highly-competitive, all-in-one pricing has proved popular and is one of the key features of the course that has made it attractive to delegates. Another attractive feature of the course is that delegates are allowed to bring their own samples, which can be carried through the entire laboratory portion of the course. Practical Proteomics covers mainly classical 2D gel-based proteomics. Despite the well-known drawbacks of this technology, it is still the 'industry standard', with 2D gels very widely used and familiar to most biologists; advances such as difference gel electrophorsis (DiGE) can increase its effectiveness. Recognizing the limitations of 2D gel electrophoresis and wanting to expose students to the full range of proteomic technologies available, we also cover bottom-up (shotgun) proteomic technologies in lectures and optional workshops. The following activities are included in the laboratory and tutorial portions of the course, in which all students get hands-on experience with their own samples: 2D gel electrophoresis: sample preparation isoelectric focusing SDS-PAGE staining scanning image analysis Mass spectrometry: spot excision in-gel tryptic digestion MALDI-MS and MS/MS electrospray-MS and MS/MS Bioinformatics: Mascot database searching de novo peptide sequencing from tandem mass spectra BLAST searching with MS-derived sequences Lectures on relevant topics always precede the laboratories and tutorials, and include the following topics: - Experimental design for proteomic studies - Protein and peptide sample-handling for proteomics - Mass spectrometric and computational techniques for protein analysis and identification - theory and practice - Interpretation of tandem mass spectra of peptides - Database searching with MS and MS/MS data - Analysis of post-translational modifications - Shotgun (HPLC-based) proteomics - Isotope labeling in proteomics, including ICAT and iTRAQ - Troubleshooting proteomics experiments