Protein Molecular Weight Calculator

Enter your protein sequence and choose a mass type (average or monoisotopic), and the Protein Molecular Weight Calculator will compute your protein's molecular weight in Da and kDa, along with sequence length, total atomic composition, and extinction coefficient at 280nm — with an option to remove the initiator methionine for processed proteins.

Enter amino acid sequence using standard single-letter codes

Average mass is more common for lab applications

Remove the first methionine if present (common in expression systems)

Results

Molecular Weight

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Molecular Weight (kDa)

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Sequence Length

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Total Atoms

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Extinction Coefficient (280nm)

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Amino Acid Composition

Results Table

Frequently Asked Questions

What is the difference between average and monoisotopic mass?

Average mass accounts for the natural isotope distribution of elements, while monoisotopic mass uses only the most abundant isotope of each element. Average mass is more commonly used in laboratory applications.

Should I remove the initiator methionine from my sequence?

This depends on your protein expression system and processing. Many proteins have their initiator methionine removed during translation or processing. Check your specific protein's known sequence or expression conditions.

What sequence formats are accepted by this calculator?

The calculator accepts both FASTA format (with headers) and plain amino acid sequences using standard single-letter codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y).

How accurate is the molecular weight calculation?

The calculation is based on standard amino acid residue masses and includes the mass of one water molecule for the terminal amino and carboxyl groups. Post-translational modifications are not included in the calculation.

Why is water mass added to the molecular weight?

Water mass is added because protein synthesis involves the removal of water molecules during peptide bond formation. The final protein retains one water molecule equivalent representing the N- and C-termini.

What is the extinction coefficient used for?

The extinction coefficient at 280nm helps estimate protein concentration using UV absorbance. It's calculated based on the content of tryptophan, tyrosine, and cysteine residues in your sequence.

Can this calculator handle modified amino acids?

This calculator only handles the 20 standard amino acids. Modified amino acids, post-translational modifications, or non-standard amino acids are not included in the molecular weight calculation.

How do I convert between mass and moles for my protein?

Use the formula: moles = mass (g) / molecular weight (g/mol). Since 1 Da is equivalent to 1 g/mol, you can use the calculated MW directly for conversions between micrograms and nanomoles.

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