Peptide molecular weight and molar calculations
Average versus monoisotopic mass, free peptide versus salt, theoretical versus observed, and worked molar calculations for the catalogue.
The molecular weight on a peptide specification looks like a single unambiguous number, but there are several closely related figures in play (average versus monoisotopic mass, free peptide versus salt, theoretical versus observed) and using the wrong one in a molar calculation or a mass-spec comparison produces errors that are small enough to miss and large enough to matter. This note sorts them out with the Alphex catalogue as worked examples. All Alphex products are for laboratory and in-vitro research only.
Average versus monoisotopic mass
Elements occur as mixtures of isotopes. The average molecular weight uses the natural-abundance-weighted atomic masses (C = 12.011, and so on) and is the number used for weighing and molar calculations. The monoisotopic mass uses the mass of the most abundant isotope of each element (C = 12.000 exactly) and is the number a high-resolution mass spectrometer reports for the lightest peak in an isotope cluster. For a peptide of 1,400 Da they differ by under 1 Da; for GLP-3 (RT) at 4,731 Da they differ by about 3 Da. When comparing an observed mass to a theoretical one, compare like with like: the COA states which it is using.
Free peptide versus salt
The specification-table molecular weight (BPC-157 1419.5, TB-500 889.0, Ipamorelin 711.9, GLP-3 (RT) 4731.3 g/mol) is the free peptide: the sequence itself, no counter-ions. The material in the vial is a salt (acetate for Alphex peptides), and its formula weight is higher by one counter-ion mass per basic site. For molar calculations, use the free-peptide mass together with a net peptide content correction, not the salt mass; the counter-ion contribution is already accounted for in net content. See net peptide content and acetate versus TFA.
GHK-Cu is the special case: the specification gives both the copper complex (403.9 g/mol) and the free tripeptide (340.4 g/mol). Molar calculations should use the complex, since that is the species supplied and the one with the relevant chemistry.
Theoretical versus observed
The theoretical mass is calculated from the sequence and modifications. The observed mass is what the mass spectrometer measured for the batch. A genuine COA that reports mass shows both and states the difference, and a 1 Da tolerance is the usual acceptance criterion. An observed mass off by +16 suggests oxidation, +1 deamidation, +42 an unexpected acetylation, +22 a sodium adduct rather than a chemical change; large negatives indicate truncation. See what a 1 Da mass tolerance means.
Reading a mass spectrum for a larger peptide
Electrospray gives multiply charged ions. A 4,731 Da peptide appears not at m/z 4731 but as a series of peaks at (M + nH)/n: about 1578 for the 3+ ion, 1184 for the 4+, 947 for the 5+, and so on. Software deconvolutes these to a single neutral mass, which is what the COA reports. If a supplier's COA for a large peptide shows a single peak at the full molecular weight with no charge-state envelope, ask how it was obtained.
Worked molar calculations
- BPC-157, 5 mg nominal, assume 80% net content: 4.0 mg / 1419.5 g/mol = 2.82 µmol; in 1 mL, 2.82 mM.
- TB-500, 10 mg nominal, 75% net content: 7.5 mg / 889.0 = 8.44 µmol; in 2 mL, 4.22 mM.
- GHK-Cu, 50 mg nominal, 90% net content: 45 mg / 403.9 = 111 µmol; in 5 mL, 22.3 mM.
- GLP-3 (RT), 5 mg nominal, 85% net content: 4.25 mg / 4731.3 = 0.90 µmol; in 1 mL, 0.90 mM.
The net content figures are illustrative assumptions, not batch data; measure or state your own. The dilution arithmetic is in how to calculate peptide concentration.
Frequently asked questions
Why do different sources give slightly different molecular weights for the same peptide?
Average versus monoisotopic, free versus salt, and rounding. Differences of a few tenths are usually that; differences of tens of daltons mean a different modification or a different compound.
Which value should I quote in a methods section?
The free-peptide average molecular weight, with the salt form and any net-content correction stated separately.
Alphex research peptides are supplied for laboratory and in-vitro research by qualified researchers only. They are not authorised for human or veterinary use.
Research use only. Alphex products are supplied exclusively for laboratory and in-vitro research by qualified researchers. They are not authorised for human or veterinary use, and nothing in this note is advice on any such use.
Published 6 July 2026. Alphex reviews research notes when the testing method, the catalogue or UK guidance changes.