Peptide calculator

How it is worked out. The calculator adds up the residue mass of each amino acid in the chain, then adds one molecule of water for the free amino and carboxyl ends. The modifications you tick come last. An acetyl group on the N-terminus adds 42.011 Da. An amide in place of the C-terminal acid removes 0.984 Da. Each disulfide bridge removes two hydrogen atoms, 2.016 Da. The residue masses are listed in our table of amino acid codes.

Checking a certificate. The mass a laboratory finds by mass spectrometry should agree with the mass the sequence predicts. Certificates often report the protonated ion, written [M+H]⁺: add 1.007 to the monoisotopic mass before you compare the two. How to read a certificate of analysis

How it is worked out.

• Concentration (mg/mL) = mass weighed (mg) ÷ volume (mL).
• Molar concentration (mmol/L) = concentration (mg/mL) ÷ molecular weight (g/mol) × 1,000.
• Mass of target peptide = mass weighed × net peptide content × HPLC purity.

A worked example. Weigh 2 mg of a peptide with a molecular weight of 1,000 g/mol and make it up to 2 mL. The solution is 1 mg/mL, which is 1 mmol/L: 1 mM, or 1,000 µM.

Why the correction matters. A freeze-dried peptide is never pure peptide by weight. It holds water and counter-ions, and its HPLC purity says how much of the peptide present is the intended sequence. Bachem's worked example uses a net peptide content of 85.0% and an HPLC purity of 98.7%. On those figures, 10 mg on the balance holds 8.39 mg of target peptide, 16% less than the weighed mass. Leave the correction out and every concentration in your records is about 19% too high. Peptide purity explained

Some sites call this sum a peptide reconstitution calculator: a weighed powder dissolved to a known volume. The second calculator does exactly that, for laboratory stock solutions and nothing else.