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Q&A: Jun Qin on China's PHOENIX Proteomics Center and the Chinese Human Proteome Project, Part I


By Adam Bonislawski

Name: Jun Qin
Position: Chief Technical Officer, Mass Spectrometry, Pilot Hub of Encyclopedical proteomIX, Beijing, China; Associate Professor, Biochemistry & Molecular Biology and Molecular & Cellular Biology, Baylor College of Medicine
Background: PhD, Rockefeller University

At the Human Proteome Organization's 2010 annual meeting in Sydney, Chinese researchers announced plans to expand their work on HUPO's Human Liver Proteome Project into a Chinese Human Proteome Project that would seek to characterize the proteomes of human tissues broadly, covering proteins in blood, brain, lungs, and other organs.

A centerpiece of this project is a new national laboratory in Beijing called the Pilot Hub of Encyclopedical proteomIX, or PHOENIX, center, which the government plans to fund to the tune of ¥1.2 billion ($187 million). Over half of those funds were slated for the center's new mass spectrometry facility, to be headed by Baylor College of Medicine researcher Jun Qin.

This week, at HUPO's 2011 meeting in Geneva, ProteoMonitor spoke to Qin about the PHOENIX center and how the Chinese Human Proteome Project is progressing one year after it was announced.

Below is an edited version of the interview, the first in a two-part installment. Part two can be found here.

How is work on the PHOENIX Center progressing?

I think the PHOENIX project is going as planned. The [Chinese] government has basically approved the funding, so we just finished the preliminary design for the project. The building is going to be built, and they will probably break ground at the end of this year. The preliminary design phase is really to get all the details down – what's in the building, how will it be designed, the rooms, what kind of instruments do you want to have, what functionalities are there. So that part is done.

Where is work on the CHPP going on until the PHOENIX Center is completed?

We already have the Beijing Proteome Research Center, which has been around for more than five years, so most of the [proteomics] activities in Beijing are happening in that center. We also have other activities in Shanghai and other places.

So what will the role of the BPRC be when the PHOENIX Center is up?

That hasn't been decided. But the PHOENIX Center will be totally new and an organization independent of the BPRC. But whether they are going to merge the BPRC into the PHOENIX Center or not no one knows right now.

How many mass spec instruments do you have at the BPRC right now?

I'd rather not discuss the details because the number may sound like a lot, but lots of the [BPRC] instruments are in my opinion really obsolete. So when you talk about, "Oh, you have 10 machines, 20 machines, 50 machines," people get very excited, but the lifetime of a mass spec right now is only about three to four years.

How many mass specs will the PHOENIX Center have?

There will be between 20 and 30.

What sort of instrument mix are you planning for the center in terms of discovery versus validation-type machines, hi-res versus triple-quads?

It's a national facility, so it's meant to serve the whole nation, even the world. So the design will include a variety of different instrumentation for different purposes. There are lots of mass spectrometers in China already. The total number combined is definitely much more than what we'll have in the PHOENIX project. But [some researchers] may not have the expertise, so I envision what's going to happen is that if people can't solve their problems locally, they will go to the PHOENIX Center. So when we design [the center] we have to take this into consideration. But the focus will be on [both] discovery and validation. So it will be a roughly one-to-one ratio between discovery and validation machines.

Have you started purchasing the mass specs yet?

There are strict guidelines for purchasing machines. We have to bid. So nothing has been decided. We can only decide, [for instance], that we want a discovery machine and that for this type of machine we want this resolution, this mass accuracy, this speed. So that may fit the criteria for a [Thermo Scientific] Orbitrap or an [AB Sciex] TripleTOF, but we can't say, "We're going to buy an Orbitrap." There will be a bidding process and there will be an instrument committee that decides.

So you'll provide the instrument specifications you need to do the work you plan to do, and then a separate committee will actually handle the buying process?

Right, so the design part and the purchasing part are completely separate.

Will you be aiming for some of the new machines that have been released recently like AB Sciex's TripleTOF 5600 or Thermo Fisher Scientific's Orbitrap Elite?

Definitely. You definitely want to get the best possible machines now because this field changes so fast. Actually, I have a lot of concerns about how to sustain the center.

Because mass specs purchased now could be obsolete three years down the line?

Yes, because this whole thing will take three years to build and get fully functional.

So, how do you make sure your purchases don't become obsolete, that they're useful and relevant for as long as possible?

I think it will eventually depend on, when the bidding process finishes, who will be the major supplier for our instruments. Because then we can negotiate with that company and say, for example, "Maybe we should do this step-wise. Get this number of machines this year. Get this number the next year. Get this number the third year. And if you have a new instrument coming out in the meantime, we want the option to change to those newer models."

Are vendors typically open to upgrading and accommodating on this front?

Oh yeah, vendors are very cooperative because they want to work with you. It's in their best interest.

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How many researchers will be working at the PHOENIX Center?

The final number hasn't been decided. I don't know if you know the Chinese system, but … for every institute that is funded by the government, there are positions allocated by the government. So how many exactly they haven't decided yet. But we designed this PHOENIX project for about 20 to 30 labs, all for proteomics and functional analysis. And we'll have around 10 people in a lab. So around 200 people, because that's the amount of people you'll need just to keep these machines running smoothly.

Where will you be recruiting personnel from?

It will be an open recruitment [process] for people all over the world and in China.

Does the funding in place for the PHOENIX Center also cover the research projects that are slated to go on there?

The PHOENIX project is an infrastructure project, so all the funding [provided by the government] is for building the building and buying the machines. So there is no funding to cover personnel. The funding for personnel will come with the positions [allocated by the government]. So the salaries will be covered. But then we will need to go out to get grants from the National Science Foundation or the Ministry of Science and Technology the same way as in America to support the projects. So this is just for the infrastructure.

Will the PHOENIX Center be the main site for the Chinese Human Proteome Project?

I think the CHPP will be done all over the country. A substantial amount will be done in Beijing. There are many, many mass spec groups in China. There will be more than 50 labs [around the country] participating. We will be very inclusive because it's such a huge project. Fuchu He [the president of the Chinese Human Proteome Organization] is leading the effort, and he has basically included almost [all the proteomics researchers] in the nation to do this. The CHPP will still be under his leadership, so I think it will be done in the same way.

You're leading the mass spec portion of the effort. Are there other platforms being used, like protein arrays and antibody-based methods?

There will be some, but it won't be a major part. I think the technology platform [of choice] now is clear – mass spec. A couple of years ago we were still debating, deciding how realistic it was to use mass spec for this kind of project. I don't think there is any debate anymore. I think it's pretty clear that mass spec has advanced to the stage where you can do almost everything in terms of detecting proteins.

Two or three years ago I think the issue was still sensitivity and throughput. Now I don't think people have those issues anymore. I think that for detecting and measuring proteins, 90 percent of the task can be done with mass spec now. There's still that ten percent, which is why there are still some specialized techniques within the project for when mass spec isn't the best method.

Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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