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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.
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.
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.
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.
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).
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.
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.
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.