The La Trobe University Proteomics and Metabolomics research platform set out to develop an efficient practical method to teach contemporary proteomics techniques in the BIO5PRO biochemistry subject. We aimed to provide students with impactful and hands-on workflows that would teach them contemporary mass-spec-based proteomics methods. The requirements were that the practical must be "real-world", be efficiently completed in two 4-hour sessions, and be suitable for students with no proteomics experience.
Our goals were to teach the principles of preparing tryptic peptides for LC-MS/MS analysis and how to produce protein identifications using a database search on LC-MS/MS spectra. Additionally, database searches must be completed rapidly during the practical using any laptop computer and free software. These restrictions required a total re-optimisation of our bottom-up proteomics gel-band protocol, LC-MS/MS parameters, and database search workflow. We focused on streamlining the database search process to allow students to iterate through several searches to assess the impact of parameters on their results. Galaxy Australia TIaaS (Training Infrastructure as a service) was used to ensure priority queuing of student jobs and allow administrator monitoring of the class's progress. Galaxy workflows circumvented any installation of specialist software and removed the compute load on the local PC. Morpheus was used for database searching due to its speed and suitability for orbitrap mass spectra. All students toured the local proteomics mass-spectrometry facility to learn about LC-MS instrumentation and ask questions of the facility staff.
Feedback from the students was positive, with a high rate of success for the proteomics workflow. The teaching staff found the practical ran smoothly and provided a good introduction to proteomics and mass-spectrometry for the students. Consumable costs for the practical were minimal, with just a few specialist reagents required for sample preparation. The Galaxy Australia service provided via the Australian Biocommons is freely available to local researchers. The major hurdle likely for educators is access to suitable mass-spectrometry infrastructure and expertise, in this case, supplied by the local La Trobe University proteomics core facility.