Two Small Modifications That Move the Mass
Look at a sequence written out with no trailing NH2 and no leading Ac-. By convention that string denotes a free acid with a free amine at the other end. The trouble is that the convention is not universally observed, so a bare sequence sometimes means the free forms and sometimes means nobody bothered with the notation. Which is why, on a certificate, the calculated mass is worth more than the way the name is spelled.
Notation, and where it stops helping
The marks themselves are simple. A trailing NH2 after the final residue records amidation. An Ac- in front of the first records acetylation. Written properly, the string is unambiguous.
Trade names observe no such discipline. The heptapeptide widely sold under one shows several failures stacked together: the material is acetylated, it is a fragment rather than the parent protein, and the name communicates neither fact. Thymosin beta-4 and the fragment takes that case apart, while peptide nomenclature deals with the conventions in general.
Two caps and what each costs in mass
A chain has two ends and both get modified routinely. Each change is tiny on the scale of the molecule and substantial in what it does.
| C-terminal amidation | The terminal carboxyl is exchanged for an amide. One negative charge is lost. Mass lands roughly one dalton below the free acid. |
| N-terminal acetylation | An acetyl group caps the terminal amine. One positive charge is lost. Mass climbs by 42 daltons. |
Neither is exotic. Both arise naturally as post-translational modifications, and both are reproduced deliberately during synthesis whenever the target sequence carries them.
Take away a charged terminus and several things move
Net charge shifts first, which drags the isoelectric point along with it, and with that the pH at which the peptide is least soluble — a relationship set out in isoelectric point and pH-dependent solubility.
A recognition point disappears as well. Aminopeptidases and carboxypeptidases work on free termini, and a capped terminus is simply not a substrate for them. That structural fact explains why terminal modification appears so frequently in analog design, next to the other alterations discussed in peptide half-life and analog modifications.
The practical upshot is that an amidated peptide and its free-acid counterpart, for all that they share a residue sequence and sit about one dalton apart, are not the same compound. Charge differs. Chromatographic behavior differs. Registry numbers differ. Sermorelin is the familiar case in this catalog: GHRH(1-29) carries a C-terminal amide, and the free-acid version is a separate compound, with the sequence given in sermorelin as the reference GHRH analog.
Seeing one dalton requires looking properly
A gap that narrow puts real demands on the measurement. Resolution has to be sufficient, and the two figures being compared have to be the same species of number — monoisotopic set against monoisotopic, average against average, never one against the other. Monoisotopic and average mass explains why that distinction bites hardest at precisely this scale.
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