Where do deletion sequences in a synthetic peptide come from?

I have both a purity figure and a content figure, which is why the discrepancy is visible.

I suspect the usual explanation for this is wrong, or at least incomplete.

I am aware this may have a boring answer. I would still like the boring answer stated clearly.

So what is the mechanism, and how well established is it?

The method matters more than the vial, which is why specifying a method buys you far more than changing suppliers does.

Gradient slope controls resolution, and gentler slopes resolve co-eluting impurities into separate peaks — so the better method reports the worse purity number.

On the detail: mobile phase additive choice affects ionisation and peak shape — TFA gives sharp peaks but suppresses mass spectrometry signal, formic acid gives worse peaks but preserves signal.

Worth noting that method standardisation is poor in the research-grade space compared to pharmaceutical work, so identical-looking methods can produce different results.

If you are ranking vendors, specify a method and have all samples tested at the same place.

The single most important distinction is between what purity measures — the fraction of detected material that is your target — and what you actually want to know — how much of the material in the vial is your target.

Buffer versus acid in the mobile phase changes the ionisation state of basic and acidic residues, shifting retention and selectivity — same vial, potentially different separation.

Mass on column affects detector linearity and peak overlap — overloading broadens peaks and hides neighbours, while underloading improves resolution but loses sensitivity.

The limitation is that single-digit micro-impurities become invisible at typical reporting thresholds, so "no impurities detected" means "none above one in two thousand."

Compare purity within a single laboratory on the same method, never across laboratories.

Purity is a method-dependent figure, and that is not a limitation of the measurement, it is a property of what the measurement actually answers.

Retention time is sequence-specific and method-specific, so comparing your result to a supplier value using a different method is meaningless without method documentation.

On the detail: tailing factor measures peak shape, and a badly tailing peak spreads into the region where small impurities live, forcing tangent-skim integration that assigns tail area to the main peak.

I would be careful about over-reading a single measurement — treat it as a data point, not as ground truth.

The practical summary: ask for the chromatogram and the method, and ignore the headline number until you have both.

More usefully, the short answer is that two competent laboratories on identical material will disagree, and the disagreement is almost always explainable by method differences.

Column pore size affects mass transfer — a 100 Angstrom packing on a 5 kDa peptide restricts diffusion, broadening the peak and potentially hiding small impurities in the shoulders.

If you are ranking vendors, specify a method and have all samples tested at the same place.

Put another way, understanding purity requires separating the chemistry from the method from the reporting convention, and the three are not independent.

Temperature affects the dynamics of molecular conformation, and if a peptide has proline residues that interconvert on the chromatographic timescale, the peak will split or shoulder at low temperature and collapse at high temperature.

Inter-laboratory studies on identical peptide material routinely find half-a-per-cent to a full-per-cent spreads in reported purity on the same sample.

Compare purity within a single laboratory on the same method, never across laboratories.