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Counter-ions and salt forms
Synthetic peptides are almost always isolated as salts. The counter-ion carries mass, and it is the single most common reason a certificate’s stated mass looks wrong to somebody checking it against a reference value.
- Trifluoroacetate, TFA
- Routine after reverse-phase purification. Each trifluoroacetate adds roughly 114 g/mol, and basic residues — lysine, arginine, histidine — each tend to carry one. A peptide with three basic residues can legitimately come in about 342 heavier than its free-base mass.
- Acetate
- Roughly 60 g/mol per acetate, used where trifluoroacetate is unwanted. Same arithmetic, smaller increment.
- Free base
- The peptide alone, with no counter-ion. This is the figure a reference database reports, and the figure a sequence calculation returns.
- Average against monoisotopic
- A second, separate source of confusion. The average mass uses the natural isotope distribution; the monoisotopic mass uses the lightest isotope of each element. On BPC-157 that is 1419.5 against 1418.70 — a gap large enough to look like an error and small enough to be missed.
A worked example
BPC-157 has a free-base average mass of 1419.5 g/mol. A certificate stating 1533.5 is not wrong: that is the free base plus one trifluoroacetate. A certificate stating 1418.7 is not wrong either: that is the monoisotopic mass. A certificate stating 1200 is wrong, and no salt form or isotope convention accounts for it.
This is why a checklist that asks “does the certificate include a mass?” catches nothing. Our certificate check does the arithmetic for all three cases, and will compute the expected mass from a sequence if you have one.
What to ask
Which salt form, how many counter-ions, and whether the quoted weight is gross or net of them. The answers change the mass, the net content, and the price per milligram of actual peptide — see net peptide content.