Protein analysisFASTA or raw sequenceBrowser-side

Protein Molecular Weight Calculator

Calculate average and monoisotopic protein molecular weight from an amino-acid sequence. Get precise results in Da and kDa, composition details, and explicit chain assumptions.

Calculate molecular weight
Sequence stays in your browser 20 standard amino acids No sign-in required
Protein sequence
Paste one-letter amino-acid sequence or FASTA text.
FASTA headers and whitespace are ignored.0 valid residues

Maximum from 0 Cys: 0

Only valid when the sequence begins with M.

Molecular weight
Results update locally as you edit the sequence.

Paste a sequence to begin

The result will include average and monoisotopic masses, chain length, composition, and every active assumption.

Two mass definitions
Use average mass for routine lab work and monoisotopic mass for defined-isotope comparisons.
Explicit validation
Ambiguous residues and unsupported symbols are identified with their positions, never silently estimated.
Lab-aware options
Account for known disulfide bonds and initiator methionine removal without inferring other processing.
Method

How sequence becomes molecular weight

Residue masses already account for peptide-bond water loss. The calculator sums those masses, adds one terminal water molecule, then subtracts two hydrogen atoms for each specified disulfide bond. Calculations retain full precision until display.

Step 1

Normalize

Remove FASTA headers and whitespace; validate every remaining symbol.

Step 2

Sum residues

Add average and monoisotopic residue masses plus terminal water.

Step 3

Apply options

Adjust only for the Met removal and disulfide bonds you specify.

FAQ

Protein molecular weight questions

How is protein molecular weight calculated from a sequence?+

The calculator adds the residue mass of each amino acid and one water molecule for the complete peptide chain. It reports both average and monoisotopic molecular weight without rounding the underlying result.

Should I use average or monoisotopic molecular weight?+

Average molecular weight is usually the practical choice for routine protein concentration and gel calculations. Monoisotopic mass is most useful when comparing a defined molecule with high-resolution mass spectrometry data.

Can I paste a FASTA sequence?+

Yes. FASTA header lines and whitespace are ignored. Lowercase residues are normalized, while ambiguous residues, gaps, stop symbols, and digits are reported instead of silently removed.

How are disulfide bonds handled?+

Each disulfide bond removes the mass of two hydrogen atoms from the linear chain. Enter only known bonds; the calculator does not infer connectivity and prevents a count greater than half the cysteine count.

Does this include tags or protein modifications?+

Only residues present in the pasted sequence are included. Signal-peptide cleavage, mature-chain processing, tags, multimers, and post-translational modifications are not inferred.