Peptide mass calculator

1. Enter the sequence in one-letter code, N-terminus first. Spaces and line breaks are ignored. Not sure of a letter? See the amino acid codes table.
2. Set the ends. Many synthetic peptides are acetylated at the N-terminus (written Ac-) or amidated at the C-terminus (written -NH₂). Each changes the mass, so match what the certificate says.
3. Add disulfide bridges if the peptide has them. Each bridge removes two hydrogen atoms.
4. Read the result. Use the monoisotopic mass to check a high-resolution mass spectrum of a small peptide, and the average weight for weighing and concentration calculations.

• Monoisotopic mass uses the most abundant isotope of each element (carbon-12, hydrogen-1 and so on). It is the mass of the sharpest peak in a high-resolution mass spectrum of a small peptide, and the one to compare with an [M+H]⁺ value on a certificate.
• Average molecular weight uses natural isotope averages. It is the right number for converting between weight and moles, for example when making up a solution.
• The ions. Mass spectrometers measure mass-to-charge. A peptide that has picked up one proton appears at its monoisotopic mass plus 1.0073 ([M+H]⁺); with two protons, at (mass + 2 × 1.0073) ÷ 2 ([M+2H]²⁺), and so on.

• Counter-ions and water. A freeze-dried peptide is a salt, usually with trifluoroacetate or acetate, and holds some water. The calculator gives the mass of the peptide itself. To work out how much peptide is really in a weighed powder, you also need the net peptide content and purity from the certificate; see peptide purity and net peptide content.
• Unusual modifications beyond the ends and disulfide bridges, such as phosphorylation or lipid tails.
• D amino acids don't change the mass, so enter them as the ordinary letter.

A certificate of analysis should report a measured mass that matches the sequence. Enter the sequence, set the ends to match the certificate, and compare the result with the reported value, taking care to compare the same kind of mass or ion. If they don't match, ask the supplier why. How to read a certificate of analysis covers the other checks.

U-K-M-A-S-T-E-R-P-E-P-T-I-D-E-S starts with selenocysteine (U), the 21st amino acid, which is why the formula above contains one selenium atom. Read the story behind the name, or learn the basics in what is a peptide.