pH will affect the retention (short or long) and it is depending on pH. You showed that pH less than 2, you will have H3PO4 which is not ionized (no negative property), so it will not be retained on the stationary phase, and it will be eluted at the solvent front. At pH >12, it will be more negative than at pH 2-7.2 and it will be retained the most. Therefore, the peak shape will be different and will affect the chromatographic property. At any specific pH, the phosphate in sample will behave the same way as phosphate in standard; therefore, the concentration will be the same (using response factor). Of course, the peak shape/retention time will be different at that specific pH.
You will measure whatever the molecule will be at that specific pH. Remember, it is not absolute but interchangeable between two forms. At the pKa value of the analyte, it will be 50% for each form. The pH 2-7 is a wide range and you did not tell me what pH you want to work on. It is reproducible if you have the pH that your analyte is stable in one form or another, not both. Like a surfboard, you want a good balance so you will stay on it longer. I don't know if you have two forms in the sample and you may have two peaks. You may have to do it experimentally by injecting the same sample at a different pH and see how it goes. Dionex run IC with 20 mM KOH and that means you have phosphate in one form as PO4-3 and it will give you a better reproducible peak shape and response (only one form present).
https://appslab.thermofisher.com/App/2863/assay-for-citrate-phosphate-pharmaceutical-formulations-using-a-compact-ic-system
Obviously pH affects chromatographic measurements. Ususally pH 3 to 8 is recommended for chromatographic measurements to avoid too acidic and too basic conditions which can hamper column packing.
As far as your problem is concerned variation molecule will vary retention time Rt. So, only one form may be quantified.
Column from Dionex (AS-4A or AS-11) is made with polymer beads and it has a wide pH operation range (1-12) and will not be affected like the silica column.
Independent from the eluent pH, you will get the total amount of phosphate in the sample. This is due to the fact that the protonation equilibrium of the different phospagte species is so fast that no separation of the phosphate species can be achieved.
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