Inteview with HPP- SAB Chair Professor Ruedi Aebersold

30 Aug 2019 3:50 PM | Anonymous member (Administrator)

Vera Ignjatovic,University of Melbourne, Australia

Q: Can you please tell us about when did you first become involved in HUPO activities?
Ruedi Aebersold: I got involved with HUPO pretty early. One of the early activities was the formation of what is today the PSI working group. Around 2000 it was pretty clear to us that as proteomics researchers we would run into problems if the computational analysis of MS and MS/MS data could not become more transparent and better benchmarked. We developed in our group at ISB in Seattle some tools that we presented at HUPO meetings, I believe first in Montreal. These included a data representation scheme in xml format (mzXML) developed by Patrick Pedrioli and statistical models developed by Alexey Nesvizhskii and Andy Keller to assign probabilities to peptide identifications (PeptideProphet) and inferred protein identifications (ProteinProphet). Out of these developments and the perceived need to discuss and benchmark these and other tools came the PSI.With Albert Heck and Anne-Claude Gavin I was a co-organizer of the Amsterdam meeting and was subsequently heavily involved in the HPP, specifically the B/D part of the project.

Q: What major achievements over the past 10 years have contributed to the success of HUPO?
Ruedi Aebersold: I think the major success of HUPO overall is that it provides a worldwide forum for proteomic scientists and a face of proteomics to the other fields of science. As specific achievements I would name the successful annual congresses, the initiatives which have had a large effect on how proteomic experiments are planned, carried out and reported and the support of young scientists. All these have contributed to increasing the visibility of proteomics.

Q: What made you interested in becoming the HPP-SAB Chair?
Ruedi Aebersold:I was for a while chair of the B/D-HPP project before I had to step down due to obligations at my home institution. It is therefore very interesting for me to become involved in the project again in another role. I look forward to catching up on what has happened and to work with the SAB members and the project leaders to further develop the project.

Q: Where do you see the HPP heading both in the short and the long-term?
Ruedi Aebersold: I think in the short term and long term the HPP should continue to help making proteomics a mainstream technology for the life sciences including clinical research. The HPP has already accomplished a lot in that direction with providing results, techniques, resources and knowledge towards the exploration of the (human) proteome. Importantly, this has been accomplished in the spirit of international cooperation. I would like to see a convergence of the two HPP directions towards that goal.

Q: What do you think that the SAB can/may deliver in the short and long term?
Ruedi Aebersold: I hope that that the SAB can be an effective sounding board, provide feedback on the HPP plans and activities developed by the project leaders and provide suggestions as to how the project could develop. In my opinion, it is important that the roles of the project leadership and the SAB are clearly defined and separate. SAB’s in general should be advisory and not become operationally active or intrusive.

Q: Could you please list three practical steps that all proteomics researchers can take in improving the visibility of proteomics globally?
Ruedi Aebersold: Unfortunately, in many circles proteomics still has the reputation of being complicated, slow, expensive and to only work in few places. This is distinctively not the case anymore (if it was ever the case). I think proteomics researchers could and should take steps to counter these wrong impressions. They could do this by: i) conveying the capabilities of the field and the excitement to colleagues in different fields, ii) by collaborating on interesting projects, iii) by focusing the conversations and communication on what is possible as opposed to what is not (yet) possible, i.e. focus communication on solutions and not problems.

Q: What are the major hurdles that proteomics faces on the way to it's integration into daily clinical practice?
Ruedi Aebersold: There are of course technical hurdles that need to be overcome. However, I think the main hurdles that hamper integration of proteomics into daily clinical practice (and for that matter into basic life science as well) are access and perception (as explained above).

Q: Last but not least....What advice would you give to Early Career "proteomics practitioners" to best set up themselves for a long and prosperous career?
Ruedi Aebersold: The amazing advances in instrumentation and techniques realized over the past few years make the measurement of proteomes routine compared to the situation some years ago and provide data of high quality. To best set themselves up for a successful career in proteomics I would recommend to young scientists to learn as much as possible about experimental design and computational analysis of large datasets, and to learn about the important biological and clinical questions where proteomics can make a unique contribution and then to go for it.

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