Column No longer Elutes Ammonia

I have a few questions about a column combination that we have been using here on site for around 20 years (Porapak QS 100/120 connected to a chromasorb 103 100/120). The columns were replaced earlier this month with an identical replacement and now no longer elutes the 20% ammonia that is contained in the sample. It will elute the other contaminants (Hydrogen, methane, ethane, etc.) with no issue. I have checked my samples against another GC with the same column, so I know that the ammonia is in the sample.   

I am suspicious that my predecessors used a deactivating compound such as hexamethyldisilazane (HMDS) or trimethylchlorosilane (TMCS) to allow ammonia to pass through the column, but did not record this step in the procedure. Could this have been the case?

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