Apr 232008
Our 500, that is. As I related in previous posts, our 500 MHz spectrometer was hamstrung by the signal from a local HDTV broadcast and subsequently had to be moved to a space in the basement of one of our research buildings. This process took about a year, because that space first had to be renovated, and in fact the last upgrades to the space won’t be finished for several days yet. But the 500 has moved into its new digs, (hopefully) finished quenching, and is ready to work. So yesterday I finally was able to collect an HSQC on it for the first time in many months.

So, here’s the spectrum I got:

For comparison, here is the last HSQC taken before we stopped using it. Obviously, this is of a different protein, but both spectra were taken using the same probe on samples with the same concentration, at the same temperature. I countoured them identically. The only difference here is that the protein in the spectrum below has much better relaxation characteristics than that in the spectrum above. In theory, this should produce much better signal to noise. Oh, and also that when I took this spectrum I was also receiving data about cubic zirconium.

This is really good news for a couple of reasons. The first is simply that we have another magnet, and that allows us more flexibility in scheduling. No more fighting when people want 9 days of NMR time next week. The second thing is that, for a variety of reasons, some experiments just work better on a lower-field magnet. In particular, I have some experiments that are sensitive to chemical shift anisotropy and REX; using a lower-field magnet attenuates both these problems.

Mar 272008
In one of the very first posts on this blog I related the story of how television ruined our 500 MHz spectrometer, at least when it came to pesky things like low-sensitivity spectra of biomolecules. That’s right, folks. Television not only rots your brain, it bricks your enormously expensive magnetic resonance spectrometer, at least if your proton Larmor frequency overlaps the broadcast band of the home shopping network. It turns out that this problem is actually rather difficult to fix: blocking out the television signal well enough to actually get reasonable spectra would have required lining the room with a considerable quantity of copper, an expensive proposition and one unlikely to be supported given that there are plans to tear that building down anyway. Instead it was proposed that we move the spectrometer to a room lined with a significant quantity of rock, i.e. the basement.

Unfortunately, the particular basement in question already had a spectrometer and rather a lot of other equipment and was anyway in need of some serious remodeling. The school managed to gather up the money for this, and just a few days ago the 500 was brought down from field and moved. Here (courtesy of Sara) is a picture of the old 500 in its new digs. This week was spent getting it down there and getting it back on its legs (obviously, they were removed for the trip). Tomorrow and Friday will be spent bringing it up to field. This will probably entail a quench.

For those of you who are not familiar with NMR spectrometers, these instruments have a superconducting coil to produce the magnetic field, and like most superconductors this must be kept extremely cold by some cryogen, in this case liquid helium. The liquid helium, in turn, is kept cold by being surrounded by liquid nitrogen. And the liquid nitrogen is insulated by a vacuum, just as in a thermos. When something goes wrong and the superconductivity is lost, an enormous amount of heat gets dumped into these cryogens and all that liquid gas turns into normal gaseous gas and emerges from the magnet with a sound resembling a freight train running over your ear. This video of a much smaller magnet quenching under controlled conditions should give you an idea of what’s to come.

A quench is dangerous, especially in a small space, because all this extra nitrogen and helium can lower the percentage of oxygen in the local area to below what can be tolerated by human beings. Because the particular basement room in question is so enormous this will likely not be a serious problem. Anyway, our 500 apparently has a history of quenching when it is brought to field, so it will likely be several more days before we are actually back to using it again. Or at least, we will once we get through with the referencing, calibrations, etc. that are necessary to actually get anything to work.

UPDATE: The magnet quenched on the afternoon of 3/31. Regrettably there wasn’t time to get the lab downstairs for a “Wizard of Oz” re-enactment.


 boo, equipment problem, nmr  Comments Off on HDTV
Aug 142007
This story begins back in March, when I got an amazingly crappy hetNOE spectrum from our 500 MHz spectrometer. The hetNOE is always a low-sensitivity spectrum, but for a 1 mM sample the signal I got was simply unacceptable. At first, I didn’t think much of this, for the simple reason that I thought the HX probe was in, and I’m used to getting poor signal-to-noise from that thing.

Except… except that everyone else was getting low-quality spectra too, no matter what probe was in. Finally one day Chris and Janice got almost no signal at all from an HSQC of a 1 mM monomeric protein, and that was the end. We had Sara test the magnet, and she found we had a four-fold reduction in signal to noise. To put things into perspective, we would have to take 16 times as many scans as before in order to achieve the same signal under these conditions. For a 1-hour HSQC, this is marginally acceptable. For a 2-day triple-resonance sequence, it is not. The new noise, strangely enough, came and went at odd times.

Al, because he knows all, immediately suspected a television signal, which he attributed to a rogue broadcaster somewhere out on Bear Hill. You see, an NMR spectrometer is really two things. It is a giant magnet, yes. But it is also a radiofrequency transmitter and receiver. The RF pulses induce a signal that the transmitter/receiver coil picks up. For our 500 MHz spectrometer, the primary signal we pick up is the proton signal at 499.75 MHz. This frequency is in a TV band.

Al was deflated, however, when Wlad tried to check the spectral band on his TV and found nothing. The search for the cause continued, with suspects ranging from the Brandeis student radio station to the construction crew radios to various parts of the magnet to secret government transmissions.

In the end, Al turned out to be right, and Wlad turned out to have a cheap TV. There was a channel broadcasting in this frequency range, but it was HDTV channel 18, a signal Wlad’s cheap TV cannot decode. Our spectrometer can’t decode it either, but we can sure see it. It knocks our signal down to an unrecoverable level. You can lose 75% of your signal for a small molecule and still be OK, but with proteins it’s a different story. The spectrometer is essentially useless to us in this condition.

And the worst part, the very worst part about this is that it’s a terrible channel! WMFP digital channel 18, broadcasting in the 494-500 MHz band, airs infomercials and “Gems TV”! Yes, that’s right, our scientific research has been derailed by a display of cubic zirconium jewelry in glorious high definition. Their antenna is located just south of us and we’re right in one of their strongest broadcast regions. Natural cures and cash-at-closing real estate ads are screwing us badly.

Hopefully, we’ll be able to boost the spectrometer’s frequency out of the channel 18 broadcast band to something like 500.13 MHz. However, there’s a Channel 19 (WGBH) broadcasting in the 500-506 MHz band as well; the spectrum analyzer shows a little gap between them that we can hopefully hit, and the WGBH signal is only half as strong as WMFP. Still, we may be screwed even if we boost the frequency. And there’s no way to shield the magnet, except maybe in the basement, but we’ll need to renovate the basement area in order to do that. So basically, we are screwed.