Reference
Why a peptide is a salt
A vial of peptide is not pure peptide, and the largest single reason is a counterion you were probably never told about. Where it comes from, how much of the weight it can be, and why it matters when comparing two vials.
Where the salt comes from
Peptides carry charge. Residues such as lysine and arginine are positively charged at ordinary pH; aspartic and glutamic acid are negatively charged. A charged molecule cannot be isolated on its own — it comes with an oppositely charged partner, the counterion.
Which counterion you end up with is decided by how the peptide was purified. Preparative HPLC is usually run with trifluoroacetic acid in the mobile phase, so peptides commonly come off that process as trifluoroacetate salts. That is not a choice anyone made about the product; it is a residue of the method.
TFA and acetate
The two forms you will see named are trifluoroacetate (TFA) and acetate.
Acetate is generally the preferred form, and getting it requires an extra manufacturing step — a salt exchange after purification, swapping one counterion for another. It costs money and yield, which is precisely why not every supplier does it, and why a specification that states the salt form is telling you more than one that does not.
A supplier who cannot say which salt form their material is in has probably not asked.
How much of the vial it can be
This is the part that connects to everything else. The counterion is real, weighable mass, and it is not peptide. How much depends on how many charged residues the sequence carries: a peptide with several basic residues needs several counterions, and a short chain with a lot of charge can carry a surprisingly large proportion of its weight as salt.
That is one of the main reasons a vial labelled 10 mg may hold less than 10 mg of peptide, and why net peptide content is a different figure from purity — see what each field on a certificate means.
Why purity cannot see it
An HPLC purity figure is calculated from peak areas at a wavelength where the peptide bond absorbs. The counterion produces no such peak. It is present in the vial and absent from the arithmetic, which is how a sample can be entirely genuine at 99% purity and still be materially less than 99% peptide by weight.
Nor does mass spectrometry settle it: that measures the peptide, and confirms it is the right one. Neither method is wrong. They are answering questions that do not include this one.
What to look for
- A stated salt form — TFA or acetate — rather than silence.
- A net peptide content figure, which accounts for the salt.
- Caution comparing two vials on labelled milligrams alone when neither states its salt form.
