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NAME: Peter Hains

POSITION: Director of mass spectrometry facility, Australian Proteome Analysis Facility, Sydney

What mass spectrometers do you have in your lab?

A Micromass TOFSPEC 2E MALDI-TOF, PerSeptive Biosystems Voyager DE STR MALDI-TOF, a Micromass Q-TOF, and a Micromass [email protected] MALDI-TOF.


How do you use the instruments in your lab?

Primarily the TOFSPEC is used for the high throughput work. If we’ve got a couple hundred samples to run, we’ll put that on the TOFSPEC, and that’s primarily because the automation on it is much better than on the Voyager instrument. We’re also using the [email protected] for that as well, but we’ve had some issues with the [email protected] so we’re still relying primarily on the TOFSPEC. The Voyager is used basically if you want to run a couple samples, and we get the students on that as well. It’s a very good instrument. It’s got better resolution and sensitivity than the TOFSPEC but in terms of automation it just doesn’t work as well. We tend to use the Voyager for the manual sample analysis, whereas the TOFSPEC is for the automated sample analysis. That’s the basic breakdown.

In terms of the Q-TOF, the vast majority of the work is manual MS/MS analysis. We do have a Waters CapLC, and we use that for LC/MS/MS, but most of the time we’re using it manually for MS/MS—that’s with a nanospray source on it.


Why not always connect up the CapLC?

We really need another MS/MS instrument to have a dedicated LC/MS/MS, and then a manual MS/MS, which we’re looking at doing. But the reason we don’t run the LC all the time is because a lot of the work we get is for new sequences that aren’t in the databases, so we need to go in and manually call the sequence. The LC isn’t useful in that case [because you can’t manually pick the collision energy]. Thus the data is a lot better when you’re doing it manually.


What’s your philosophy on choosing an instrument?

Well, when we got the instruments I unfortunately wasn’t here. But I’m literally going through that process now, and I’ve got a three page list of what’s important to me and basically it’s going to come down to things like—obviously—resolution, sensitivity, ease of use, reliability, maintenance contract, software, how well the database searching works, and how well integrated all that kind of thing is. It’s bascially the whole package: how well does it work to serve our needs, rather than just the best mass spec. We may not buy the best spec; we’ll buy the mass spec that will best suit our needs, and that may not be the one that’s got the best resolution or the highest sensitivity.


Do you need to have an instrument suitable for those with little mass spectrometry experience?

Yes, absolutely, especially with the [MALDI-TOFs]. With the Q-TOF, we tend to leave that to three or four key operators, but with the [MALDI-TOFs] people who have virtually no experience do get on them. That is certainly a factor for us. It needs to be a machine that’s usable, rather than [one] that’s just so esoteric in its setup that you need someone who’s been learning for 10 years how to use it. Not quite open access, but we want something that’s easy to use.


Would it make sense for you to buy a mass spec packaged with separation equipment?

In terms of getting an LC with the mass spec, yes, that makes sense. In terms of the whole proteomics packages that some of the companies are selling, where they sell the 2D gel, the whole shebang, along with the spot cutters and the zip tip robots—for us that wouldn’t make any sense because we’ve already got the various components. But I guess for someone setting up a new lab that might be the way to go. The problem with that is you’re not going to get the best of everythingo one company is going to make the best of everything. For someone who’s new, yes, it might be worthwhile, but for us, we wouldn’t get the whole package. [But] if someone’s offering a mass spec plus an LC that’s something we’d look at.


What mass spec looks particularly promising at the moment?

Probably the TOF/TOF. That’d be nice to get a look at. They’re very expensive, which is a factor, but they look like they could have some really nice promise to give some information that we can’t get with our current machines. Either that, or one of the MALDI Q-TOFs are what we’re looking at buying next.


Do you get the impression that one TOF/TOF — the Bruker or the ABI — is better than the other?

I can’t say at the moment. I haven’t actually seen it. According to the companies, yes, but I’d be surprised if there’s much difference. When it’s all said and done, I’d really be surprised if there’s a significant difference between the two machines. Time will tell on that one.


What about a hybrid machine, such as an ion trap-TOF or a triple quad combined with an ion trap?

I think the mass spec companies have gone hybrid crazy to be perfectly honest. It’s like, ‘What hybrid can we make next?’ It may make sense for some people, but I can’t give you a good feel for that one; I’m not sure myself what the advantages are of having an ion trap with a TOF. I mean, you get better resolution with a TOF than you would with a trap, but overall whether it’s going to be a superior instrument to what is already out there, [the mass spec companies] may not even know themselves. It’s just a case of playing around at the moment. I’m certainly interested to see what comes out of it. I really couldn’t say one way or the other whether it’s going to be worth their time doing.


How much are you planning to spend on new instruments?

We’ve got it pretty much sorted out. We want to get two or three mass specs. Real money—as in your dollars—we’re probably looking at $800,000 to $1.5 million. That would be for a TOF/TOF and a new MALDI-TOF. We need to update our MALDIs as they’re getting a bit long in the tooth. And maybe an ion trap. It’s under consideration but I’m not sure yet.

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