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[iito] Business Intelligence. (9/29/11). "[iito]view – E-mail Interview with Pierre Legrain, Vice President of HUPO". Bremen.
|Organisation||HUPO (Human Proteome Organisation)|
|Organisation 2||[iito] Business Intelligence|
|Product 2||mass spectrometry (MS)|
|Person||Legrain, Pierre (HUPO 201109 Vice President HUPO)|
|Person 2||Lippold, Marcus ([iito] Business Intelligence 2002– + Board Member of Life Sciences Bremen 200903–201106)|
[iito]view, an exclusive e-mail interview with Pierre Legrain, Vice President, HUPO
[iito]: The Human Proteome, What Is It Made Of?
Which set of proteins would you consider as the "human proteome"? All proteins within a human body (or any organism, for that) at one moment in time?; in a specified period?; in the whole of a lifetime? Only proteins produced by the human body itself?; only functional proteins? Or what else?
Pierre Legrain: ALL! Any protein made from the human genome, at any time...
ALL! Any protein made from the human genome, at any time, any amount, any cell. From you or from me! Or from any other person. This is why the project is very exciting, and very complicated. We will start on a modest level, with characterization of proteins made from a reference genome and already described variants of it. And the most abundant will be easier to identify than others. In principle, we will annotate all of them, but it will take time. And we hope to relate these identifications with function.
[iito]: What is a Gene and How Is It Related to a Protein?
Some time ago genomic science called the larger part of DNA in the chromosomes "junk". As an economist, without any deeper biological knowledge, I already asked myself back then, why should god & the evolution leave so much "junk" after so many millions of years in our body, if it is really "junk" without any meaning/function?
Would you consider it today more appropriate to see DNA sequences as coding for building blocks to build proteins and that these "building blocks" are open to as much free and unforeseeable combinations than to determined ones? In other words, are DNA sequencences in our chromosomes not determining but only making possible the production of proteins by the organism?
Pierre Legrain: Very little of the human sequence codes for proteins
Very little of the human sequence codes for proteins. We count roughly 20,000 genes encoding proteins, totalling probably under 2% of the human genome sequence. However, the remainder of the sequence is not junk! It's related to the regulation of the expression of protein genes. And also probably to other functions ignored by us as far as now.
My personal view is that we ignore a lot about biology. We do not know how a new individual emerges from his/her parents (a newborn!), what does he/she inherit from them as genetic sequences and how much reflects his/her personal history... or the history of his/her parents! A lot will be understood from future research on proteomics, including with systems biology approaches.
[iito]: Is Bioinformatics a Blessing, a Curse, or Simply a Necessity?
As DNA sequencing and the sequencing and structural analysis of proteins produce data over data, do we simply drown in data and calculate or way through disaster without seeing nothing (or everything) at all?
I suppose that if you have so much data, surely something will correlate, and someone will publish this correlation, but this does not have to say anything at all. A correlation is a correlation is a correlation. Is there a way to go beyond the data, when it is simply impossible for a researcher to individually take a look at each data point in his data set and put it into perspective without software, simple because there are millions to billions or even trillions of data points to go through?
To me it seems a little bit like having a lot of notes and let the computer and the software write the song, while actually the most important songs have only a few chords and not too many different notes. Possibly to write the most famous of these songs took only some beers or other drugs (at least in the times before mass-spec based forensics and drugs-of-abuse testing) and a few minutes. What about putting some alcohol into the reasearcher instead of one more software programme?
Pierre Legrain: Some tasks will require talented and creative scientists and beers
I like your comparison with music and notes. Not to say beers and drugs!
In a sense we have first to clean out our possible notes. Current data are not all clean, we need guidelines and quality control to improve the general value of datasets. The open comparison of these datasets will help the scientific community in establishing a reference dataset on human proteins. These are the proteomics "musical" notes.
Do you realize that it took probably tens of thousands years for humans to create reference musical datasets (we do not have the same in western or Asian countries but we do have rules)? Then some of us (in the past, and still today) have been able to communicate with others creating musical sounds and languages.
The same is true with proteomics. Let's describe what the molecular building blocks are. Some of their meaning will appear easily, but some other will require talented and creative scienctists to offer a good representation of the functioning of human (and other) living systems.
[iito]: The Role of Mass Spectrometry in Proteomics: Growing? Competing? Complementary?
Mass Spectrometry is becoming more and more prominent in the area of proteomics. What are the particular strengths of mass spec in proteomics? Which particular mass spec technologies and features are of special importance in this area? And finally, is mass spectrometry a competing or a complementary technology for older technologies used in the proteomics field?
Pierre Legrain: May be a breakthrough will happen that will change our minds
Mass spec gives us the opportunity to qualify datasets on proteins with pretty good accuracy, specificity and sensitivity. And it will still improve. Some argue that mass spec will not allow us to detect minor proteins in complex fluids or extracts. Or to differentiate between two very closely related proteins. We'll see. I believe that subtle combinations of existing technologies and methodologies will push away a lot of the present limitations. But may be a breakthrough will happen that will change our minds, such as in affinity-based proteomics (ie new reagents, more sensitive and specific than classical antibodies).
[iito]: The Scientist and the Industry? Buying Complete Solutions vs. Each Device as I Like It?
All major mass spec producers are heavily investing into being able to offer complete solutions in the mass spec field, from sample preparation to the mass spectrometer and finally the data analysis and documentation.
When you look at analytical laboratories in the commercial field, there is clearly a strong need for ready- & easy-to-use, automated, standardised, integrated and validated systems and respective analytical methods. So this may drive this development. Especially when you look at the mass spec producers trying to enter the clincial laboratory markets, this seems to be one of the utmost challenges.
Accordingly, the big MS players spend a whole lot of money and time buying companies that offer complementary technologies. I think of special note is for example the acquisition of two liquid chromatography companies by Thermo and acquisitions of LC firms by AB Sciex and Bruker.
While for commercial labs complete solutions probably will more and more dominate the market, for the scientific researcher the situation might look different. Will she be trapped by one supplier, making it more difficult to get the instrument she wants for the problems at hand? Will research be easier by handing over day-to-day service and support to the manufacturer and concentrating on research? Will third party multiple-vendor services offer an alternative (GE and AB Sciex recently announced a respective collaboration)? Will budget constraints in science funding will leave researchers no option other than to work more closely with one or two major suppliers of complete packages?
Pierre Legrain: Complete packages will be attractive if cost-effective
Complete packages will be attractive if cost-effective. Researchers prefer customized solutions, to which they contribute (more or less efficiently!)+. Cost will be a major issue, but my personal view is that the general trend will be given while answering the question of mass spec as part of a routine medical diagnostic/prognostic process. If this were to happen (as the DNA sequence is almost part of a genetic medical answer to patients needs), the competition would be wild for a huge market. And scientists and basic research will benefit from this acceleration.
Pierre Legrain, THANK YOU VERY MUCH!
We would also like to thank Kate Whelan from Notch Communications for helping to arrange this [iito]view!
[iito]view – The EXCLUSIVE E-Mail Interview
welcome to our first [iito]view ever, the premier issue of our exclusive series of e-mail interviews with high-level thought leaders in the field of life sciences.
In the aftermath of the HUPO 2011 meeting we have asked some questions about proteomics and mass spectrometry to Pierre Legrain, the Vice President of HUPO. My thanks go to him for answering them all and well!
Future [iito]views will be published from time to time and will be announced via our [iito] twitter channel and our [gs] Newsletter.
We are open for your proposals for this new interview series about which persons and/or topics to include, just let me know.
Actually, we wanted this to be a little bit different: personal, entertaining, interesting to read and professional! Thanks to Pierre Legrain, I think this premier [iito]view issues is, and I hope you enjoy it!
Thanks for reading, back soon!
Record changed: 2012-06-04
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