Protein Molecular Weight Calculator

Sequence to MW, pI & extinction coefficient (ε280)
Before you start: paste any protein sequence (1-letter or 3-letter, FASTA OK) or pick a preset. Everything below — MW, ε280, A280, pI, charge curve and AA composition — recalculates as you type.
1Amino Acid Sequence ?
Protein Preset
Sequence
Length: 0 aa
2Post-Translational Modifications ?
3Molecular Weight & Properties
0.00
kDa (average)
Molecular Weight
0.00 Da
0.00
Monoisotopic (Da)
0.00
Average (Da)
0
Amino Acids
Spectral & Electrophoretic Properties
0
ε280 (M⁻¹cm⁻¹) cystines
0
ε280 (M⁻¹cm⁻¹) reduced
0.000
A280 (1 mg/mL)
0.00
Isoelectric Point (pI)
0.00
Net Charge (pH 7.0)
-
Molecular Formula
4Charge vs pH & Amino Acid Composition
Net Charge vs pH
Amino Acid Composition
AANameCount%

Frequently Asked Questions

How do you calculate the molecular weight of a protein?

To calculate the molecular weight of a protein, sum the average residue masses of each amino acid in the sequence and subtract (N−1) × 18.015 Da for the water lost at each peptide bond (a protein of N residues has N−1 bonds). For example, BSA (583 residues after signal-peptide cleavage) sums to approximately 66,500 Da, i.e. 66.5 kDa. Standard average residue masses span 57.05 Da (Gly) to 186.21 Da (Trp). ExPASy ProtParam (Gasteiger et al., 2005) applies exactly this residue-sum method, and the calculator here uses the same average residue-mass table documented in Lehninger, Principles of Biochemistry (7th ed.).

What is the average molecular weight per amino acid residue?

The average molecular weight per amino acid residue in a typical protein is approximately 110 Da (weighted for natural amino-acid abundance across the standard 20 amino acids). This lets you estimate MW from sequence length alone: MW (Da) ≈ N × 110, so a 300-residue protein is about 33 kDa. Individual residue averages span 57.05 Da (Gly) to 186.21 Da (Trp), so the 110 Da rule is best for proteins with typical composition and least reliable for very Gly- or Trp-rich sequences. For an exact value, sum the individual residue masses in the calculator above (methodology per ExPASy ProtParam; Lehninger, Principles of Biochemistry, 7th ed.).

How do I calculate protein molecular weight from an amino acid sequence?

To calculate protein molecular weight from an amino acid sequence, sum the average residue mass of each amino acid and subtract 18.02 Da (water) for every peptide bond. A protein of N residues has N−1 peptide bonds, so MW (Da) = Σ(residue masses) − (N−1) × 18.02. The tool applies this automatically using standard residue masses (e.g. Ala 89.09 Da, Gly 75.07 Da, Trp 204.23 Da) and reports the result in Da and kDa.

What is a molecular weight calculator for protein?

A molecular weight calculator for protein takes an amino-acid sequence and returns the protein's mass in Daltons (Da) or kilodaltons (kDa) by summing the average (or monoisotopic) residue masses of each amino acid plus one water for the terminal groups. A complete protein MW calculator also returns the extinction coefficient (ε280), A280 for 1 mg/mL, isoelectric point (pI), amino-acid composition, molecular formula, and net charge vs pH — all from sequence alone, with no ProtParam or ExPASy install required.

How accurate is a sequence-based molecular weight calculator for protein?

For a protein made of standard amino acids and no post-translational modifications (PTMs), a molecular weight calculator for protein is accurate to within 0.01% of the theoretical average mass. Real-world deviations come from PTMs: N-terminal methionine cleavage, signal-peptide processing, glycosylation (∼2.5 kDa per N-linked site), PEGylation, disulfide formation, and phosphorylation can shift observed MW by 5–30% on SDS-PAGE or LC-MS. Toggle the PTMs in Step 2 to bring the predicted MW closer to the measured mass.

How is the extinction coefficient calculated?

The molar extinction coefficient at 280 nm uses the Pace method: ε280 = (nTrp × 5500) + (nTyr × 1490) + (nCystine × 125), where nCystine = floor(nCys / 2). The cystine term assumes pairs of cysteines form disulfide bonds. If all cysteines are reduced, the cystine contribution is omitted.

What is the difference between monoisotopic and average mass?

Monoisotopic mass uses the most abundant isotope of each element (12C, 1H, 14N, 16O, 32S). Average mass uses the weighted average of all natural isotopes. Use monoisotopic for high-resolution MS and average for bench-scale calculations.

How accurate is the pI prediction?

The Bjellqvist method predicts pI within ±0.5 pH units for most proteins. It uses isolated amino acid pKa values and does not account for tertiary structure effects. For precise pI, use isoelectric focusing (IEF).

How do I account for post-translational modifications?

Use the Modifications panel in Step 2 to toggle common PTMs such as Met removal, His/FLAG tags, PEGylation, and N-glycosylation. Each modification updates all calculated values in real-time.

What if my protein has no Trp or Tyr residues?

Without Trp or Tyr, ε280 will be near zero (only Cys contributes). A280 measurements cannot reliably measure concentration. Use alternative methods like BCA assay, Bradford assay, or absorbance at 205 nm.

How does disulfide bonding affect the extinction coefficient?

Each cystine (disulfide bond) adds ~125 M−1cm−1 at 280 nm. The calculator shows both cystine-assumed and fully-reduced values. Under denaturing/reducing conditions (DTT, TCEP), use the reduced value.

About the Molecular Weight Calculator for Protein

This free molecular weight calculator for protein turns any amino-acid sequence into the seven numbers you need most: average and monoisotopic mass (Da / kDa), extinction coefficient (ε280) in oxidised and reduced forms, A280 for 1 mg/mL, isoelectric point (pI), net charge at pH 7.0, and the protein's molecular formula (CxHyNzOwSn). Paste a sequence in 1-letter or 3-letter code, with or without FASTA headers, spaces, or numbering — the parser strips junk and validates against the 20 standard amino acids.

Behind the scenes, a sequence-based protein molecular weight calculator sums the residue masses of each amino acid (averaged or monoisotopic, depending on whether you need bench-scale or high-resolution MS values) and adds one water for the terminal groups. The extinction coefficient is computed by the Pace / Edelhoch method — ε280 = (nTrp × 5500) + (nTyr × 1490) + (ncystine × 125) — with cystine count taken as floor(nCys / 2). Both the oxidised (cystine-assumed) and fully reduced values are reported, so you know which to use for protein quantification under denaturing/reducing conditions (DTT, TCEP, urea) versus native ones. The pI is solved with a binary search on the Bjellqvist titration curve, accurate to ±0.5 pH unit for most proteins.

Real-world proteins are rarely just plain sequence. Use the modifications panel in Step 2 to model the common shifts: N-terminal methionine cleavage (−131 Da), signal-peptide processing, C-terminal His6 or FLAG tag addition, PEGylation (specify kDa added), and N-glycosylation (~2.5 kDa per complex N-glycan). The hero MW, ε280, A280, pI, charge curve and AA composition all update in real time as you toggle them, so you can match the predicted mass to what you actually see on SDS-PAGE or LC-MS.

This molecular weight calculator for protein pairs cleanly with the protein concentration calculator (use your ε280 to turn an A280 reading into mg/mL, or run BCA / Bradford with a standard curve), the BCA assay calculation guide for proteins with no Trp/Tyr, the inclusion bodies refolding guide when you need a buffer pH well away from the pI, and the refolding generator to plan redox/buffer screens informed by the disulfide count from this tool.

From extinction coefficient to protein concentration (A280 to mg/mL)

Once you have the extinction coefficient (ε280) and molecular weight from this molecular weight calculator for protein, you can turn a single A280 reading into concentration. The molar concentration is c (M) = A280 / (ε × pathlength), and the mass concentration follows directly from the MW: c (mg/mL) = c(M) × MW = A280 × MW / (ε × pathlength). At a 1 cm pathlength this simplifies to mg/mL = A280 / A280, 1 mg/mL, where A280, 1 mg/mL = ε / MW is the absorbance of a 1 mg/mL solution (the “A280 (1 mg/mL)” value reported in Step 3). The related specific absorbance E1%280 (absorbance of a 10 mg/mL, i.e. 1 % w/v, solution) is simply ten times larger: E1%280 = 10 × ε / MW.

The ε280 comes from the protein's Trp, Tyr, and cystine content (the Pace / Edelhoch method above). Use the cystine (oxidised) ε when disulfide bonds are intact, and the reduced ε under reducing conditions (DTT, TCEP), because breaking disulfides removes the small cystine contribution at 280 nm. Both values are reported side by side in Step 3, so pick the one that matches your buffer.

Worked example. Mature BSA has an average MW of about 66,430 Da and an oxidised ε280 of about 43,824 M−1cm−1. With a 1 cm pathlength, the absorbance of a 1 mg/mL solution is A280, 1 mg/mL = ε / MW = 43,824 / 66,430 ≈ 0.66 (so E1%280 ≈ 6.6). An A280 reading of 0.66 therefore corresponds to roughly 1 mg/mL, and a reading of 0.33 to about 0.5 mg/mL. To run this conversion (and cross-check against BCA or Bradford), take your ε280 here and continue in the protein concentration calculator.

Resources & further reading

Related Tools & Articles

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A280, BCA, Bradford — mg/mL from absorbance
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4-parameter standard curve, common pitfalls
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Buffer + redox + chaotrope matrix planner