Accepted answer
The limit of this technique for these molecules is reaching a point where small improvements require proportionally large investments in method development.
Proline-rich sequences are particularly problematic because the isomerisation kinetics are in the same timescale as the separation, leading to split or broadened peaks at low temperature.
Trifluoroacetic acid at 0.1 per cent is the standard ion-pairing agent because it suppresses tailing by neutralising the basic residues, but it also suppresses mass spectrometry signal.
The resolving power of a separation is quantified by the resolution parameter R, defined from the heights and widths of adjacent peaks, and pharmacopoeial methods typically demand R greater than 1.5 for a method to be considered validated.
If two labs give different numbers, the method difference is the first hypothesis, not lab quality.