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I have read a few articles where it is stated that samples containing water are detrimental for a GC experimental results and equipment.

For example, in the paper Identification of essential oil components by gas chromatography/mass spectrometry, ed. 4.1 by Robert P. Adams, it is written: "Oxygen and water can severely affect the mass spectrometer both in the quality of spectra obtained and in permanent damage to components such as the filament."

But why is it so damaging with water in a GC machine? What happens with the filament, and how is the column damaged?

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    $\begingroup$ I assume searching for water damage GC MS column brings a lot of valuable hits. $\endgroup$
    – Poutnik
    Nov 21, 2021 at 20:33
  • $\begingroup$ yes, that is true, "The myth about water GC incompatibility is historical and comes from the old column technology, which were coated and not chemically bonded. " , from phenomenex.blog/2018/01/30/inject-water-gc. So if I check that I have a compatible column, there should be no problems? Still in papers from 2017 and forward, they claim water is a serious problem... $\endgroup$
    – John
    Nov 21, 2021 at 20:45
  • $\begingroup$ In depends what stationary phase is used. Polar phases would not be happy about water. MS part is another topic. Water may affect MS sample input preparation and ioniation chamber, but I am not expert here. $\endgroup$
    – Poutnik
    Nov 21, 2021 at 20:49
  • $\begingroup$ It depends on the temperature and the polarity of the column, Apolar capillary columns contains usually polyethylene or similar polymer. They are not sensitive to water, Polar columns may be made of heavy esters. When working around 100°C, water has no effect. But at about 300°C, the risk of hydrolysis is not negligible. It depends of course of the nature of the stationary phase. $\endgroup$
    – Maurice
    Nov 21, 2021 at 21:16
  • $\begingroup$ Obviously, I'm a novice... The sample is a water-based solution containing volatile components, such as aldehydes, esters, and an unknown pesticide. The column is of the apolar capillary type and the detector is built around a TCD design, the carrier gas is nitrogen, and the temperature is set to 120 C. Will I see a water peak? Or will the water just be diluted in the mobile phase and look like a drifting baseline? $\endgroup$
    – John
    Nov 22, 2021 at 14:41

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This is a very specific case that you quote about GC-MS. Many mass spectrometers are used daily with water (called electrospray ionization MS), the issue is that of a particular gas chromatography-electron impact mass spectrometer.

First of all many GC columns have been invented that are meant to analyze water in solvents. We are talking about parts per million levels of water. However water is a low molecular weight compound and MS detector with electron impact ionization is not a good choice. So, the GC instrument itself with detectors such as barrier discharge ionization detectors are compatabile with water (of course very tiny amounts).

The issue is that GC temperature is pretty high (> 150-250 Celcius), and the filaments in mass spectrometers are made of tungsten/rhenium and other fancy metals/alloys. Heated water vapor is corrosive to metals. These metals are not totally inert and they are sitting at high temperature. They too react with the analytes slowly including hydrocarbons. Halogenated compounds are quite reactive too. Even organic solvents can damage them. Presence of water may accelerate corrosion.

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