Carbonate and bicarbonate can be determined in natural water samples using pH and alkalinity.  The balance between carbonate and bicarbonate is pH dependent.

But with small samples (mg) or more complex samples (peptides), one can determine carbonate directly using ion exclusion chromatography.  The chromatogram of a peptide sample spiked with carbonate below was conducted on a Dionex system.  The ICE-AS6 column uses 1.6 mM heptafluorobutyric acid as an eluent with suppressed conductivity detection.

In ion exclusion chromatography, the anions of strong acids (like Cl^-) are not retained, eluting in the void volume.  Anions of weak acids are retained.  This technique can also be used for determining borate.

Dionex Ion Chromatograph

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Formerly West Coast Analytical Service (WCAS) and Bodycote Testing Group