Protein Molecular Weight Calculator

The molecular weight is calculated by summing the residue masses of all amino acids in the sequence and adding the mass of one water molecule (18.02 Da) to account for the free N- and C-termini. Each amino acid has a known residue mass (the monomer minus water lost during peptide bond formation). The formula is: MW = Σ(residue masses) + 18.02.

Average mass uses the natural weighted average of all stable isotopes for each element (e.g., carbon at 12.011 Da), reflecting the distribution seen in a standard mass spectrum. Monoisotopic mass uses only the lightest (most abundant) isotope of each element (e.g., carbon-12 exactly). Monoisotopic mass is preferred for small peptides in high-resolution mass spectrometry; average mass is more appropriate for larger proteins and gel electrophoresis.

Use the standard IUPAC single-letter codes: A (Alanine), C (Cysteine), D (Aspartic acid), E (Glutamic acid), F (Phenylalanine), G (Glycine), H (Histidine), I (Isoleucine), K (Lysine), L (Leucine), M (Methionine), N (Asparagine), P (Proline), Q (Glutamine), R (Arginine), S (Serine), T (Threonine), V (Valine), W (Tryptophan), and Y (Tyrosine). Ambiguous characters like X, B, Z, and U are ignored in this calculator.

Yes. The calculator automatically strips FASTA header lines (any line beginning with '>') and whitespace, then processes only the amino acid characters. You can paste sequences directly from databases like UniProt or NCBI without any manual editing.

The molar extinction coefficient (ε) at 280 nm reflects how strongly your protein absorbs UV light, based on its content of Tryptophan (W), Tyrosine (Y), and Cysteine (C, when forming disulfide bonds). It is calculated using the Pace formula: ε = (nW × 5500) + (nY × 1490) + (nC_disulfide × 125). You can use it with Beer-Lambert law (A = εcl) to determine the concentration of a purified protein solution by measuring absorbance at 280 nm.

Epitope tags like His6, FLAG, or c-myc are short peptide sequences commonly fused to recombinant proteins for purification or detection. Appending the tag sequence before calculating MW gives you the theoretical mass of the final fusion protein, which is useful for confirming protein identity on a western blot or predicting migration on an SDS-PAGE gel.

The calculated MW is the theoretical mass based solely on the primary sequence and does not account for post-translational modifications (PTMs) such as glycosylation, phosphorylation, acetylation, or signal peptide cleavage. Actual observed mass by mass spectrometry or apparent mass on SDS-PAGE may differ. For unmodified, fully denatured proteins it is highly accurate to within ~0.01%.

The Abs(0.1%) value, also called A(1 mg/mL), is the theoretical absorbance of a 1 mg/mL protein solution in a 1 cm path-length cuvette at 280 nm. It is calculated as ε × 0.001 / MW(Da). This is a convenient normalization that lets you estimate protein concentration directly from a UV absorbance reading without knowing the molar concentration.