Peptide calculator

The method. The calculator adds the residue mass of every amino acid in the chain, adds one molecule of water for the two free ends, then applies the modifications you tick. An acetyl group on the N-terminus adds 42.011 Da; an amide in place of the C-terminal acid takes off 0.984 Da; each disulfide bridge takes off two hydrogen atoms. The residue masses are in our table of amino acid codes.

Checking a certificate. The mass found by mass spectrometry on a batch certificate should match the mass the sequence predicts. If the certificate reports the protonated ion, [M+H]⁺, add 1.007 to the monoisotopic mass before you compare. How to read a certificate of analysis

The method.

• 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.

Why the third line matters. A freeze-dried peptide powder is never all peptide. It carries water and counter-ions, and the HPLC purity tells you how much of the peptide is the intended sequence. Take 5 mg of powder with 85.0% net peptide content and 98.7% purity: it holds 4.195 mg of the target peptide, about 16% less than the balance showed. Leave that out and every concentration you report overstates the true figure by nearly a fifth. Peptide purity explained

Dissolving a weighed powder to a known volume, which some calculators call reconstitution, is exactly the sum the second calculator does, for laboratory stock solutions.