I asked the question, “How many biological replicates do I need?”
“Enough!” was the succinct answer, given with a wry smile, from my friend and colleague, Philippe Bogard, at the COST Action FA1002 Farm Animal Proteomics Spring Meeting 2011 held in Glasgow.
We had the final, 19th slot, to give a presentation. We could have used this time to present our technology, but decided to deal with what we see as the biggest challenge in proteomics – building reproducibility into experimental design.
We anticipated (correctly!) that the audience would be quite tired by 6pm, so we decided to do something a little different – a double act.
I played the part of a researcher, setting up their first proteomics experiment with very little knowledge. I had prepared a few questions in advance.
Philippe played himself — an experienced proteomics consultant giving advice on how to avoid common pitfalls in proteomics experiment design.
Philippe gave his customary humorous and honest replies, based upon his extensive experience.
Here are the questions and Philippe’s condensed replies:
1 Where do I start? Which technique is best?
We talked about pros and cons of electrophoresis and mass spectrometry, Philippe concluding that they are complementary and are both needed.
Nobody disputed this.
2 How many biological replicates do I need?
You can then calculate the number of biological replicates you will need.
3 What about technical replicates? What should I be doing about them?
You need to be sure that your system is reproducible. Philippe mentioned the importance of running standards and same:same experiments. He mentioned how Progenesis can help you handle technical replicates.
Once you have good reproducibility, it is far better to run more biological replicates than keep running unnecessary technical replicates
4 How can I be sure I have the right answer?
On your own, you can’t! The only way to be absolutely sure is to be able to repeat the experiment in a different lab and get the same result.
I think the delegates, despite being tired, were quite surprised and refreshed by our presentation. There was a lot of scribbling going on (especially when Philippe mentioned The Fixing Proteomics campaign) and the feedback afterwards was very positive.
We went to the conference dinner at The Bothy feeling pleased we had been so well received. The next day, people came to our stand and told us how useful the presentation had been. It was very relevant to this meeting, as quite a few delegates were just starting out in proteomics.
So a Merci beaucoup to Philippe who shared his knowledge in such an interesting and fun way with all of us.
Nonlinear Dynamics is committed to building reproducibility into all our technology. If you would like to explore our technology further, please don’t hesitate; click here.