DailBob on different columns

In a belated comment on Different Columns detailed, DailBob does some 'splainin that seems worth fuller exposure:


Before I start, a reminder that we don’t have an IRMS in our lab, so I’m “projecting” some of what I’ll call “GC 101” identification principles onto the IRMS. I think I’m correct in doing this, because this is essentially what the Landis team did via their retention time arguments. I also vetted my thinking with our Analytical Chem Manager, and he’s in the same place I am.

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I first want to provide some history and an example to give you some background on what’s driving my perspective. I’m old enough that I remember getting our first GC-MS in the late ‘80s. The addition of the MS was a game changer, because it added another “layer” of identification, the value of which can’t be understated. Prior to that, you could only identify by elution time, and we were sometimes wrong. Now, we’re rarely wrong. This changed the analytical chemistry world to where I think most Chemists would tell you that they require both for identification, i.e., the MS upped the bar. I’m telling you this, because not having the full mass spectra to aid in identifying something on the IRMS places all the emphasis on elution time.

A few weeks ago, we got a sample in where one of our plants thought they accidentally put glycerin in a batch instead of what was supposed to go in. To determine if this happened, we ran a glycerin standard which eluted at 2.854 minutes. We then injected the sample, where a peak eluted at 2.862 minutes (0.008 minutes or about half a second difference). The mass spectra matched the glycerin standard, so these two pieces of information, taken together, identified the material as glycerin. I’ve provided this example to demonstrate how these machines identify compounds. This is the only way they identify compounds, and the identification is pretty “black or white” – either it’s identified, or it’s not (an exception is isomers, but that’s NA here).

I think the main issue as you move a sample from the GC-MS to the IRMS is maintaining the identity of the compound for which you want to determine the CIR. I say this for a couple of reasons. First, even if the GC-MS and IRMS use the same column, the fact that the columns are two separate physical units can cause differences in elution time, or even peak swapping, if one of the columns is contaminated. Second, as I mentioned, because the IRMS cannot identify the compounds with full mass spectra, the only way of identifying it is by elution time. Consequently, I think it is absolutely paramount that it be tied directly to a known standard, because without it, you have zero “layers” of identity.

I have expressed concern about the different temperature ramps between the two machines, which you have discounted (note: Larry has uncovered information that makes it look like the difference in temperature ramps is intentional, but this doesn’t negate my point). If you look at the Landis F3 from the GC-MS, there is a peak that elutes at about 13.2 minutes. This peak seems to have disappeared in the F3 IRMS. This peak either a) contained no carbon, b) moved due to the change in temperature ramps, or c) indicates a contaminated column. I can make this argument for any peak that is in the GC-MS output that doesn’t appear in the IRMS. If I can't account for a peak, and the peak I'm interested in is not directly identified by being tied to a standard, its identity becomes suspect.

You asked me whether I think the 5aA or P could be misidentified? If you can play a mental game for a moment and adopt the perspective that the only way things are identified are by elution time (minimally) and mass spectra (ideally), I think you can see that, technically speaking (i.e., by standard separation science), they aren't identified at all. What you have done in your example is arrived at the identification by logical deduction. While your logic is excellent, logic is not science. Because of the gravity of this case on a person’s life, I have to have the identification be done by standard separation science, particularly because it's capable of doing so in an incontrovertible way, if it's done carefully and correctly.

You asked me once whether I thought the science told us whether Floyd doped, and I replied that I really couldn't tell with any surety. This is why. While I can't prove he didn't dope, this science isn't good enough, in my view, to prove that he did. When I combine this with a) generally crummy chromatography, b) poor lab practices (e.g. white-out), c) the fact that the blank urine was “positive” (for me, indicating some possible machine bias) and d) the fact that I was influenced by Amory’s testimony, I still have enough doubt that the excellence of your logic doesn't push me over the hump.