Extinction coefficient calculator
Work out how strongly a peptide absorbs ultraviolet light, so you can measure its concentration with a spectrophotometer.
ε280 = 5,500 × Trp + 1,490 × Tyr + 125 × cystine (Pace et al., 1995)
What the extinction coefficient is
The molar extinction coefficient, ε, is how strongly a substance absorbs light at one wavelength, in M⁻¹ cm⁻¹. It links an absorbance reading to a concentration through the Beer–Lambert law, A = εlc. For a peptide it can be estimated from the sequence, because only some residues absorb.
Extinction coefficient at 280 nm (A280)
At 280 nm only tryptophan, tyrosine and cystine (two cysteines joined by a disulfide bridge) absorb meaningfully. The calculator uses the values from Pace et al. (1995): ε280 = 5,500 × Trp + 1,490 × Tyr + 125 × cystine, in water. A peptide with none of these has no usable absorbance at 280 nm, so use 205 nm instead.
Extinction coefficient at 205 nm
Every peptide bond absorbs in the far ultraviolet, so 205 nm works for any sequence. Anthis and Clore (2013) give 2,780 M⁻¹ cm⁻¹ per peptide bond plus terms for the side chains that absorb there: Trp 20,400, Phe 8,600, Tyr 6,080, His 5,200, Met 1,830, Arg 1,350, Cys 690, Asn and Gln 400 each, and 2,200 per cystine. Far-UV readings need a solvent that doesn't absorb at 205 nm, which rules out many common buffers and additives.
Absorbance of a 1 mg/mL solution
Dividing ε by the molar mass gives the absorbance of a 1 mg/mL solution in a 1 cm path, sometimes written A0.1%. It lets you read a concentration in mg/mL straight from a measured absorbance: a reading of 0.5 for a peptide whose 1 mg/mL absorbance is 2.0 means 0.25 mg/mL.
These are estimates from the sequence alone, and a measured coefficient is more accurate. The guide to measuring peptide concentration compares the methods.