I understand that to separate molecules by HPLC (or SFC) you commonly adjust the pH of the mobile phase to get preferable charges (i.e. negative charges) on the molecules - so that they interact with the column and are therefore well separated and thus give a large distinct peak.

Im not completely sure I understand what happens to switter ions like amino acids when you try to separate them. I know it can be difficult. Is it correct to think that they randomly interact with the column and thus "spread out"resulting in a chromatogram with a lot of noise? Why is it that the connected MS also has problems detecting them (should it not continuously detect the molecule)?

Example of amino acids that could be difficult to detect:

I understand that to separate molecules by HPLC (or SFC) you commonly adjust the pH of the mobile phase to get preferable charges (i.e. negative charges) on the molecules - so that they interact with the column and are therefore well separated and thus give a large distinct peak.

Im not completely sure I understand what happens to zwitterions like amino acids when you try to separate them. Is it correct to think that they randomly interact with the column and thus "spread out"resulting in a chromatogram with a lot of noise? Why is it that the connected MS also has problems detecting them (should it not continuously detect the molecule)?

Example of amino acids that could be difficult to detect: