Peptide Molecular Weight Calculator – Exact Mass, m/z and Extinction Coefficient
Paste a sequence and this peptide molecular weight calculator returns the molecular formula, the monoisotopic, average and most-abundant mass, the [M+zH]ᶻ⁺ ladder with the isotope envelope of every charge state, the amino-acid composition and the absorbance at 280 nm. It reads one-letter, three-letter and FASTA input, and it accounts for termini, disulfide bonds and post-translational modifications (PTMs).
Residues, not amino acids, and one water
A peptide is built from residues: each free amino acid minus H₂O, because a water leaves at every peptide bond. The molecule then carries one free amine and one free acid at its ends, which together add a single water back:
M = Σ residues + H₂O
That is why Leu-enkephalin, YGGFL, is C₂₈H₃₇N₅O₇ (555.2693 u) and not the sum of five free amino acids. A head-to-tail cyclic peptide has no free ends, so no water is added.
Monoisotopic, average and most-abundant mass
The monoisotopic mass uses the exact mass of the lightest, most abundant isotope of each element and is the first peak of a small peptide. The average mass weights all isotopes by abundance and is the molecular weight you use when weighing powder. As a molecule grows, the chance that it contains no ¹³C at all shrinks: for ubiquitin (8.5 kDa) the monoisotopic peak is under 5 % of the tallest one. High-resolution work on proteins therefore uses the most-abundant mass, and low-resolution work the average.
Disulfides and common modifications
Each disulfide bond removes two hydrogens, −2.01565 u. Modifications are entered in square brackets, such as S[Phospho], and add a fixed composition change:
- Oxidation +15.9949, phospho +79.9663, acetyl +42.0106, carbamidomethyl +57.0215 and deamidation +0.9840.
- Amidation of the C-terminus −0.9840 and pyroglutamate formation −17.0265 (from Gln) or −18.0106 (from Glu).
- Acetylation (+42.0106) and trimethylation (+42.0470) differ by only 36 mDa, a gap a high-resolution instrument must resolve.
Reading a charge-state ladder
Electrospray gives multiply protonated ions, m/z = (M + z·1.007276) / z. A rough guide to how many charges to expect is the number of basic sites: lysine, arginine, histidine and the free N-terminus. The ladder marks charge states beyond that count with hollow sticks and shades your scan window. Neighbouring isotope peaks are 1.00336 / z apart, so the spacing tells you the charge.
Extinction coefficient at 280 nm
The Pace formula estimates absorbance from the chromophores: ε₂₈₀ = 5500·nTrp + 1490·nTyr + 125·nSS (M⁻¹ cm⁻¹). Dividing by the molecular weight gives the absorbance of a 1 mg/mL solution. A peptide without Trp, Tyr or Cys is practically invisible at 280 nm, so measure it at 205 or 214 nm instead.
Net peptide content and TFA salts
Synthetic peptides are usually delivered as trifluoroacetate salts that also hold water, so the powder is often only 70 to 90 % peptide. Enter the net peptide content and the stock-solution box corrects the mass before working out the volume for your target concentration.