Peptide Molarity Calculator

Convert between the mass of peptide on the balance and the molar concentration an assay is designed around. In Mass → molarity mode, enter the molecular weight, the peptide mass in mg and the solution volume in mL to get mM, µM, µmol, nmol and mg/mL. In Molarity → mass mode, enter a target in µM and a volume to get the mass to weigh. The compound menu fills in molecular weights from our compound monographs; for any other sequence, take the average MW from the peptide molecular weight calculator.

Receptor binding, enzyme kinetics and concentration–response curves count molecules, not milligrams, so a peptide weighed in mg has to be converted through its molecular weight before it means anything in an assay. The calculator does that conversion in both directions.

The formulas

A useful check: keep the prefix and multiply by 1,000 ÷ MW. A concentration in mg/mL becomes mM, µg/mL becomes µM and ng/mL becomes nM. For a 1,000 g/mol peptide, 1 mg/mL is exactly 1 mM.

Worked example: Epithalon in both modes

Epithalon (Ala-Glu-Asp-Gly) has an average MW of 390.35 g/mol.

Same mass, different molarity

Molar concentration scales inversely with molecular weight, so equal mass concentrations of different peptides are not equal in molecules:

At 1 mg/mL, GHK supplies more than four times as many molecules as BPC-157. Comparing two peptides at the same µg/mL therefore compares different molar concentrations, so design comparisons in molar units. The copper complex sold as GHK-Cu has a higher MW than the free tripeptide, and the GHK-Cu guide explains which figure to use.

Net peptide content and salt form

The calculator assumes the mass entered is all peptide. A lyophilised powder also contains counter-ions and water, so apply net peptide content (NPC):

• Mass → molarity: enter gross mass × NPC.
• Molarity → mass: divide the result by NPC (0.488 mg ÷ 0.80 = 0.610 mg above).

Counter-ion mass can be worked out from the sequence. Each protonated basic group pairs with one counter-ion: trifluoroacetic acid adds 114.02 g/mol and acetic acid 60.05 g/mol. A 1,000 g/mol peptide carrying two trifluoroacetates weighs 1,228.05 g/mol as the salt, so only 81.4% of the dry mass is peptide before any water is counted; as the diacetate it would be 89.3%. The TFA versus acetate guide covers how salt forms arise.

Counter-ions also travel at molar ratios. A 1 µM working solution of a peptide with three trifluoroacetates contains 3 µM trifluoroacetate. In fetal rat osteoblast cultures, trifluoroacetate at 10–100 nM reduced cell numbers and thymidine incorporation after 24 h, and TFA salts of amylin and calcitonin showed less proliferation than the hydrochlorides ^[1]. Where exact quantities matter, NPC is measured rather than assumed; a consensus group led by the US National Cancer Institute's proteomics consortium recommended well-characterised peptide reference standards so that amino acid analysis methods agree ^[2]. For APL vials, ask for the batch documentation.

Unit pitfalls

• Mass is in mg. Enter 250 µg as 0.25.
• Volume is in mL. Enter 500 µL as 0.5.
• Targets are in µM. Enter 10 nM as 0.01 and 2 mM as 2,000.
• Use the right variant's MW. A C-terminal amide, an N-terminal acetyl group or a disulfide changes the formula; the molecular weight calculator handles these options.
• Complete dissolution is assumed. A cloudy solution has a lower concentration than calculated; see peptide solubility.

The molarity calculations guide works through the full chain from vial to assay well.