So I'm going to try to explain why this was our favorite example of bad movie science from the summer: First of all, let's get a basic idea about what a spectrometer is: Wikipedia defines it as "is an instrument used to measure properties of light over a specific portion of the electromagnetic spectrum..." You can also use the word "spectroscopy" to refer to the process of using a spectrometer.
There are lots of portions of the electromagnetic spectrum that you could measure: You can have infared spectrometers, for example. Here's a basic idea of what the inside of one kind of infared spectrometer (FTIR, for those who are curious) looks like, or if you want to see more here's a video. In any case, the light that's being measured goes along that yellow arrow, which you'll notice is entirely inside the device. This thing isn't measuring anything originating from outside that little desktop-printer-sized box, so it's going to be doing absolutely nil to detect glowing cube things, whether on the roof or anywhere else.
In case you might be getting a little bored now, how about looking at a spectrometer you can hold in your hand and run around pointing at things? Things like, oh, traces of lipstick? Seriously, check out this video, doesn't that just look cool? This is one case where reality is kind of sort of vaguely like CSI, except still probably a lot slower. Anyways, I'm not gonna bore you with the details (but I will link to them for those of you who do care) but look at this. Doesn't it look so fun and high-tech? These are spectrometers that you can carry up to the roof - in fact, our heroes could've stuck one in their pocket and flown around in the Quinjet or hitched a ride with Tony Stark if height was what mattered - but these spectrometers still fail in one important factor: They can't detect gamma rays.
Gamma ray spectrometers are portable, too. Really, really portable. Portable enough to be put on the Apollo 16 mission. And a satellite or two or three. And a robot that we sent to Mars. You can hold one of these in your hand, although it looks more like a Star Trek: TOS thing than a pretty futuristic CSI thing like the last one. So, I suppose that could work, but you'd have to at least know what city the cube was in, and then deploy people to scan metal briefcases... but how strong would that radiation have to be?
