Apparently, Navalny’s biomaterials were flown to Moscow's Nii Sklif lab which didn't find any traces of the poison. But they used an American Agilent Technologies GC-MS [1], while Bundeswehr toxicology lab reportedly used an order of magnitude more sensitive, and more expensive, Bruker's apex-Qe FTMS (no official source for this as "Bundeswehr didn’t disclose the details of their work") which successfully detected novichok.

How did German scientists outplay their Russian counterparts in this case and could it be attributed to simply using a more sensitive equipment with perhaps a better MS method?

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    $\begingroup$ And why would a Russian lab want to find evidence for the Russian state poisoning somebody? $\endgroup$ – Jon Custer Sep 4 '20 at 14:21
  • $\begingroup$ @JonCuster It equally may be speculated if / which part(s) of the analysis and therapy disclosed (when) to a / the public, too. Recalling the dioxine case of Victor Yushchenko, maybe was an exception (2009Lancet1179 or 2011TocicolSci310). $\endgroup$ – Buttonwood Sep 4 '20 at 15:04
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    $\begingroup$ @JonCuster, had they found it, they wouldn't have released him, and they might not even disclose the results. But instead they were so openly certain he was clean of any traces as to allow him to be transported to the scrutiny of German labs. So the question is should they upgrade their hardware. $\endgroup$ – rych Sep 4 '20 at 15:22
  • $\begingroup$ @rych Equally plausible speculation, given the scale of research (e.g., entry in wikipedia including details like the yields e.g., in the Polish edition): #1 hardware is not the problem (in Russia), #2 neither is it the know-how, likely including ADME data (in Russia), #3 Mr Nawalny was permitted to leave Russia when the chance to identify the substance (and / or) its origin by a non Russian lab was assumed to be insignificant. Because of #3, #4 someone else is now sweating bullets. $\endgroup$ – Buttonwood Sep 4 '20 at 15:51
  • $\begingroup$ Related: Differences in Novichok agent mass spectra $\endgroup$ – user7951 Sep 4 '20 at 20:37

Lacking additional information, answers likely will be speculation-based only. To mention a few factors to consider:

Stating GC-MS analysis only states, that there is technique to separate compounds by different rate of retention over a stationary phase (gas chromatography, GC) combined (a.k.a. hyphenated) with an other technique to analyze fractions sorting at different times by mass spectroscopy (MS). Mass spectroscopy typically shatters the molecules into charged fragments which, by their mass/charge ratio, behave differently in electromagnetic fields. However, depending on the setup, the separation of the fractions by GC may be better, or worse. On the side of mass spectroscopy, there are multiple methods to ionize and fragment molecules and to record these. It is a problem that the parameters of running a mass spectroscopy may alter the shape of mass spectra quite a lot; signals may vary in their relative intensity, or sometimes be below the detection limit altogether. It need not be the engineering advantage among corporations, of Agilent's technology over the by Bruker (if there is?).

In the line of smaller benchtop mass spectrometers typically mounted behind a GC, larger sector field mass spectrometers, and Fourier mass spectrometers, there is a significant increase of resolution to record tiny differences in the masses of the fragments the experiment of mass spectroscopy generates. This may help to attribute the signals to the correct analyte, especially if there already is a suspicion to search for a selection of compounds only.

Routine GC-MS used for forensics and IOC doping screenings, for example compare the mass spectra recorded for a sample against previously recorded trustful references. (Different to IOC doping screening, it is not evident if the Russian government shares / shared such standards here, though.) Depending on the compound to identify, though, the analysis does not need to stop at the level of a GC-MS. Both other types of chromatography may have been used now (e.g., HPLC) to separate the compounds; or multiple mass spectrometers coupled into a tandem (MS/MS) to observe not only the initial fragments obtained by mass spectroscopy, but equally their further fragmented «daughter radicals», too which equally rises the chance to identify your compound in question.

Maybe the Germans did not trace the poison itself, but metabolites judged as sufficient evidence for earlier reported, related compounds. Especially with small amounts of sample material, the success of an analysis equally depends on every step of sample preparation; here likely (incomplete listing): what was the delay between Nawalny's intake of compound X and obtaining a sample by him (metabolism), the nature of the sample (tissue, blood, hair, etc.), delay and conditions of storage of the specimen to get it to the lab (unwanted sample decomposition), concentration and digestion protocols in the lab to eventually submit the sample to the mass spectrometer; the people's experience and availability reference data / techniques.


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