Me and the IRMS: A Magnetic Tale

I have spent the last 2 weeks here in Kuopio dancing attendance upon an analytical machine by the name of a GC-IRMS.  This stands for Gas Chromatograph Isotope Ratio Mass Spectrometer.  I’m just gonna call it the IRMS from here on out.  The IRMS is the machine that analyzes the isotopic signature of various compounds, and it does this thanks to a really big, really fancy magnet.

IRMS from the topA little background on stable isotopes.  These are really cool, I promise!  So all elements are made up of three sub-elements: a nucleus consisting of 1) protons and 2) neutrons, all orbited by 3) electrons.  Elements (all the different boxes in the periodic table), are defined by the number of protons and electrons in the element, also known as the ‘atomic number’.  Any element on the planet that has 8 protons is Oxygen.  Any element with 19 protons is Potassium.  Any element with 47 protons is Gold.  And so on, and so forth.  So the actual definition of an element is the number of protons in the nucleus.

Periodic Table of the ElementsIn contrast, elements have a semi-flexible number of neutrons.  When the number of neutrons changes, but the protons and electrons stay the same, that is an isotopeExample: the element carbon (C) is defined by having 6 protons.  The most common form of carbon has 6 protons and 6 neutrons, for a total atomic mass of 12 [atomic mass = number of protons + number of neutrons], and written as 12C.  If a carbon has an extra neutron, its atomic mass becomes 13, and we denote this by writing it as 13C.  But it is still carbon, because the number of protons hasn’t changed.  If it has two extra neutrons, its atomic mass becomes 14, and it’s written as 14C, but it’s still carbon.

If we use hydrogen (H) as another example, here’s a graphic showing how the three different isotopes of hydrogen are defined:

H isotopesProtium is what we think of as ‘normal’ hydrogen, with an atomic number of 1, and an atomic mass of 1.  Add a neutron and you now have an atomic mass of 2, but it’s still hydrogen, because there is still only one proton.  You can also have hydrogen with 2 neutrons, taking the atomic mass to 3, but it’s still hydrogen.  Why?  Because there’s still only one proton!!  Scientists have assigned fancy-sounding names to the different hydrogen isotopes, but they’re all still the element hydrogen.

Neutrons appear to be rather faithless sub-atomic particles, so there are a whole bevy of isotopes littering the periodic table.  The distinction between ‘stable’ and ‘radioactive’ isotopes is also important, and refers to if the nucleus is emitting energy or not.  A radioactive isotope has a nucleus that is emitting energy (aka: radiation), and thus is in a process of ‘decay’.  This could mean lots of things, but it always means that the elemental form is in transition.  In contrast, a stable isotope is not emitting any radiation (NOT decaying), and will stay in its present form indefinitely.  Here’s a graphic that really helps me think about isotopes, as you can see how protons and neutrons interact within each element (check out the axes, and the 8 isotopes of carbon):

Nuclides ChartSo back to my IRMS tale.  The brilliantly simple physics behind being able to measure stable isotopes was developed in large part by the American physicist Alfred Nier.  Damn that Manhattan Project, and its double-edge of innovation!  Anyway, Nier worked on being able to separate isotopes, and the IRMS works by physically separating different isotopes.  Remember that isotopes of the same element all have a neutron-weight’s difference in their masses, which affects that isotopes ‘mass-to-charge’ ratio (abbreviated as ‘m/z’).  An IRMS uses a magnet and the natural variation in the mass-to-charge ratio to slingshot different isotopes towards different detectors:

IRMS physicsThis is so simple it almost hurts my brain.  The heavier isotopes (the ones carrying around extra neutrons) will be bent less by the magnet when they’re being flung through the detection chamber.  Lighter is easier to throw, easier to manipulate.  Like pushing against a solid object – you can push a domino over with a tiny finger shove, but try to push a book over with the same tiny finger shove, and you’ll move it much less.  So apply the same magnetic force to all the isotopes, and the flight paths of the heavier ones will be bent less, and so fly off in a trajectory that’s different than its lighter brethren.  Then all you have to do is physically place detectors in the different trajectories, and voila!  You can measure the amounts of the different isotopes!

If you waded through the post on my stable isotope experiment here in Kuopio, more power to you!  If not, the highlight is that I use the two stable isotopes of carbon to measure the rates of a pair of microbial processes: methane production and anaerobic methane consumption.  This is possible because of the unavoidable: life is hard!  It might not sound like much, but those extra-neutron forms of elements are heavier, so they move slower, and take more energy to use.  If presented with both stable isotopes of carbon, life will choose to use the lighter form (12C) – this is called ‘discrimination’ (not kidding), and the exact amount of discrimination is different for each cellular process.  So thanks to the predictable nature of this isotope discrimination, you can determine what microbes are doing with their carbon.  :)

Moral of the story: My experiment is finished, and now I’m analyzing my stable isotope samples to determine the ratio of 12C to 13C for both CH4 and CO2 molecules.  The IRMS here in Kuopio does not have a technician, so I must run my own samples.  This is perfectly fine, as long as the machine is working properly, but IRMSes are notoriously mercurial and delicate. I was hoping that my 14-day time slot for the machine, combined with my relatively straightforward samples would mean that I could escape the black hole of an IRMS tantrum, but boy, was I wrong!

An IRMS can be configured into multiple modes, both for which element you’re measuring, and the method for preparing the sample prior to the ionic slingshot portion of the analysis.  [I use a gas chromatograph for my sample prep mode – the GC part of the GC-IRMS.]  Once through the sample prep portion, a sample enters the “ion source chamber”, where the sample is ionized and then exposed to a high voltage in order to make an “ion beam”, which is shot forward into the magnet chamber, and eventually on to the detector cups for the different isotope masses.

IRMS mass spec detailI mention this again because this is the portion of the IRMS that broke down on me.  It started with the slow failure of the ionizing filament, and graduated quickly into the total failure of the magnet.  Yeah, I thought I’d broken a magnet!  I honestly hadn’t even known that was possible (turns out it’s really not).  Long story, short: the ionizing filament needed to be replaced, and some electrical issues needed to be resolved to remind the magnet that it wasn’t actually broken.  With the indispensable help of two of my fellow PhD students, we had to ‘crack the chest’ of the IRMS and essentially replace its heart (the filament).  What follows is a photographic journey of the filament being changed.

Here’s a shot of the whole IRMS room, where I’ve pointed out some of the instrumentation (sorry for all the acronyms).

UEF IRMS roomThe real meat of the IRMS fits on a single shelf, and is the triple threat of the ionization chamber, the magnet and the detection chamber, the configuration of which has been shown in the two IRMS schematics shown earlier in this post.

IRMS explanationOkay, so the first step in filament replacement: open the ionization chamber, closed with 8 extremely tight clamp screws.

Ionization ChamberNext: carefully remove the filament housing, without touching it to the chamber walls.  You end up with the ‘heart’ of the IRMS in your hands, or rather, Simo’s hands.

IRMS's metal heartHere’s a closer shot of the filament housing unit, containing a LOT of wiring and protective casing for the actual filament, which is tucked into the area amongst all the metal coils, and surrounded by white plastic on the left side of the picture.

IRMS filament housingThis is the part that was replaced.  The filament is a 1cm-long wire the size of a single strand of hair, held within the metal box with the circle view cutout on the farthest right side of the part.  You can see that the hair-sized filament is worn down so that there is a break in what should be a continuous strand of metal.

broken filamentWhile a colleague placed a new filament unit into the casing, I cleaned out the ionization chamber, which gets microscopically dirty over time.  This was like a really high-pressure game of ‘Operation’, because I had to use metal tweezers and an ethanol-soaked cloth to reach all the way to the back of the chamber to clean the ion beam inlet (around 10 inches deep), all while not touching the metal tweezers to any surface.  The inside of the chamber is polished metal, and any scratches or imperfections on the surface will affect the ionization.  Hence, the extremely high-stakes game of ‘Operation’.  Here’s a shot of the inside of the chamber.  The small slit in the back surrounded by darker, burned-looking marks is the ion beam inlet, so this is where the beam of ions created by the filament is focused and propelled through to the magnet and detectors.

Inside the ionization chamberNew filament installed, we carefully re-inserted the filament housing unit into the ionization chamber, tightly re-screwed it all shut, and started the 3-7 day process of re-calibrating the machine for use.  So I might not have finished running my samples prior to this hiccup, meaning I’m now holding up the sample queue while the instrument calibrates.  I may have spent an entire day conversing with a very nice Italian gentleman tasked with helping me service the instrument.  I also might not have been able to troubleshoot this all myself, thereby sucking additional people into the fix-the-IRMS black hole.  But it turns out I didn’t break the magnet, so that’s something!  :)

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