QiLing Tools

🧫Peptide Calculator - Molecular Weight, pI, Extinction Coefficient & m/z

The mass of a peptide is the sum of its amino acid residue masses plus one water (the N-terminal H and C-terminal OH). Angiotensin II (DRVYIHPF), for example, is C₅₀H₇₁N₁₃O₁₂ with a monoisotopic mass of 1045.5345 Da, so its [M+H]⁺ ion appears at m/z 1046.542; the dipeptide Gly-Ala is C₅H₁₀N₂O₃, 146.0691 Da. This calculator accepts one-letter or three-letter sequences (auto-detected, FASTA headers, spaces and numbers are stripped) and computes the molecular formula, monoisotopic mass and average mass from elemental composition using the same atomic weights as ExPASy ProtParam, with N-terminal acetylation or formylation, C-terminal amidation and disulfide bonds. The isoelectric point is found by summing Henderson–Hasselbalch charges of all ionisable groups and bisecting for zero net charge, with a choice of Bjellqvist (ExPASy), EMBOSS or Lehninger pKa values and a net charge vs pH curve; ubiquitin gives an average mass of 8564.84 Da and a Bjellqvist pI of 6.56, matching ExPASy. You also get the 280 nm extinction coefficient by the Pace method (5500·W + 1490·Y + 125·cystine) and the A₂₈₀ of a 1 mg/mL solution, the Kyte–Doolittle GRAVY score with a sliding-window hydropathy plot, the aliphatic index, an ESI m/z table for charge states 1+ to 10+ and an amino acid composition table. A DNA/mRNA tab translates three (or six) reading frames with the standard genetic code and finds the longest ORF, and a reference table lists the 20 amino acids with names, codes, side-chain class, side-chain pKa and residue masses.

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How to use Peptide & Protein Calculator

  1. 1Type or paste a sequence (one-letter, three-letter or FASTA), or pick an example peptide
  2. 2Set N- and C-terminal modifications, the number of disulfide bonds and the pKa set
  3. 3Read the formula, masses, pI, charge curve, extinction coefficient, m/z table and composition — or translate a DNA sequence in the DNA tab and send it to the calculator

FAQ

How is peptide molecular weight calculated?
Add the masses of all residues (each amino acid minus one water) and then add one water: 18.0106 Da monoisotopic or 18.015 Da average. Each disulfide bond removes two hydrogens (about 2.016 Da), C-terminal amidation lowers the mass by about 0.984 Da and N-terminal acetylation adds 42.011 Da. Use the monoisotopic mass for high-resolution mass spectrometry and the average mass for weighing out solutions.
How is the isoelectric point (pI) of a peptide calculated, and why do tools disagree?
For each ionisable group — the free N-terminus and C-terminus and the side chains of Lys, Arg, His, Asp, Glu, Cys and Tyr — the Henderson–Hasselbalch equation gives its fractional charge at a given pH; the pI is the pH where the sum is zero, found here by bisection. Programs use different pKa tables, so results can differ by 0.1–1 pH unit. The default Bjellqvist set reproduces ExPASy Compute pI/Mw (ubiquitin: 6.56).
How do I estimate a protein’s extinction coefficient at 280 nm?
Absorbance at 280 nm comes mainly from tryptophan, tyrosine and cystine. The Pace et al. (1995) formula is ε₂₈₀ = 5500 × nTrp + 1490 × nTyr + 125 × nCystine in M⁻¹cm⁻¹. Dividing by the molecular weight gives the A₂₈₀ of a 1 mg/mL solution in a 1 cm cell, which converts a UV reading into concentration. Peptides without Trp or Tyr barely absorb at 280 nm and are better measured at 205 or 214 nm.
How do I calculate the m/z of multiply charged peptide ions?
In electrospray ionisation a peptide picks up z protons, so m/z = (M + z × 1.007276) / z, where M is the neutral monoisotopic mass and 1.007276 Da is the proton mass. For angiotensin II, M = 1045.5345, so [M+H]⁺ = 1046.542 and [M+2H]²⁺ = 523.775. The calculator lists monoisotopic and average m/z values for charge states 1+ through 10+.