Protein Molecular Weight Calculator
Solve a protein's molecular weight by summing the average residue mass of every amino acid in its sequence, then adding back one water molecule for the chain's two free ends. Two 3D diagrams compare a short peptide chain to a long one, and charts show how molecular weight builds up as a chain grows and how residue mass varies across amino acids.
Reviewed by the ToolNestr Editorial Team — July 2026
Short vs. long peptide chain
1. Short peptide
Few residues linked together — a low total molecular weight.
2. Long polypeptide
Many residues linked together — a much higher total molecular weight.
Molecular weight charts
How it works
The core idea in one line: a protein's total weight is simply the sum of its building blocks' weights, with one small correction for the water molecule chemistry removes every time two amino acids link together — and adds back only once, at the very ends of the finished chain.
MW = Σ(residue masses) + 18.02
18.02 Da (one water molecule) restores the mass of the chain's two free ends
Every time two amino acids join to form a peptide bond, the cell removes one water molecule as a byproduct — so a chain's individual amino acid residues each weigh slightly less than their free, unlinked form. Standard residue mass tables already account for this loss, which means summing residue masses across an entire sequence, then adding exactly one water molecule back (18.02 Da, for the chain's two untouched terminal ends), gives the finished protein's true molecular weight directly from its sequence alone.
Worked example 1 — a short tripeptide
Given: The tripeptide Ala-Gly-Ser (A-G-S).
Even a tiny 3-residue peptide already shows the pattern — every additional amino acid adds its own residue mass directly to the running total.
Worked example 2 — a four-residue peptide with larger side chains
Given: The tetrapeptide Met-Lys-Val-Leu (M-K-V-L).
Despite having only one more residue than the first example, this peptide is noticeably heavier — its amino acids simply have larger side chains, illustrating that molecular weight depends on composition, not just chain length.
Residue mass range across amino acids
Residue mass depends entirely on side chain size.
| Amino acid | Residue mass (Da) | Side chain size |
|---|---|---|
| Glycine (G) ★ | 57.05 | Smallest (just an H) |
| Alanine (A) | 71.08 | Small (methyl group) |
| Leucine (L) | 113.16 | Medium (branched) |
| Tryptophan (W) | 186.21 | Largest (bicyclic ring) |
★ Reference row. Glycine's minimal side chain (a single hydrogen atom) makes it both the smallest and most structurally flexible amino acid.
Where protein molecular weight actually matters
🧬 Mass spectrometry protein identification
Comparing a measured protein's molecular weight against sequence-predicted values is a standard first check in proteomics for confirming protein identity and detecting modifications.
💊 Therapeutic protein and antibody development
Molecular weight is a fundamental quality-control specification for biologic drugs (like antibody therapeutics), verified at every manufacturing stage against the sequence-predicted value.
🔬 Gel electrophoresis (SDS-PAGE) interpretation
Predicted molecular weight from a protein's sequence lets researchers identify which band on an SDS-PAGE gel corresponds to their protein of interest.
🧪 Recombinant protein expression
Researchers cloning and expressing a new recombinant protein calculate its expected molecular weight in advance to confirm successful expression and correct size on later analysis.
Common misconceptions
"Protein molecular weight is just the sum of the free amino acid weights."
Simply adding up free amino acid weights overcounts the mass — each peptide bond formed during protein synthesis releases one water molecule, so residue masses (which already account for this) must be used instead, with only one water added back at the very end.
"Two proteins with the same number of amino acids always have similar molecular weights."
Molecular weight depends heavily on amino acid composition, not just chain length — a chain rich in large amino acids (like tryptophan) will be substantially heavier than an equally long chain rich in small ones (like glycine).
"Sequence-based molecular weight calculations always match experimentally measured values exactly."
Real, mature proteins often carry post-translational modifications (phosphate groups, sugar chains, cleaved signal sequences) that change their actual mass from the simple sequence-based prediction — the calculated value is a starting-point estimate, not always the final word.
"Molecular weight tells you everything about a protein's size and shape."
Molecular weight only measures total mass — it says nothing about a protein's 3D shape, whether it exists as multiple subunits bound together, or how compactly it folds, all of which matter for a protein's actual physical size and function.
Formula sources & further reading
The formulas here are standard, traceable to:
- • OpenStax, Biology 2e — Chapter 3, "Biological Macromolecules" (free, peer-reviewed). openstax.org
- • ExPASy (Swiss Institute of Bioinformatics) — standard reference amino acid residue masses.
- • Alberts et al., Molecular Biology of the Cell — Protein structure fundamentals chapter.
MW = Σ(residue masses) + 18.02 Da. Uses standard average (not monoisotopic) residue masses. Does not account for post-translational modifications. Results are rounded for display.
How to use this calculator
Enter a protein sequence
Type the sequence using standard one-letter amino acid codes (A, R, N, D, C, etc.).
Read molecular weight
Total mass in Daltons calculates instantly from the sequence.
Check composition
The amino acid breakdown chart shows which residues contribute most to the total mass.
Related tools
Frequently asked questions
How is protein molecular weight calculated from a sequence?
Sum the average residue mass of every amino acid in the sequence, then add 18.02 Da (one water molecule) to account for the free amino and carboxyl groups at the two ends of the finished chain.
Why is water added back at the end?
Standard residue mass tables already subtract one water molecule per amino acid to account for the water lost when each peptide bond forms during protein synthesis — adding one water back at the end restores the mass of the two terminal groups that never lost their water in the first place.
Why do different amino acids have different residue masses?
Residue mass depends entirely on the size and composition of each amino acid's side chain (R group) — small amino acids like glycine have a residue mass around 57 Da, while large ones like tryptophan reach about 186 Da.
Is this the exact same molecular weight reported by mass spectrometry?
This calculation gives the average (not monoisotopic) molecular weight, and doesn't account for post-translational modifications like phosphorylation or glycosylation — real proteins measured by mass spectrometry can differ from this sequence-only estimate for exactly those reasons.
Does protein molecular weight relate to gene/DNA length?
Yes — since each amino acid is encoded by a 3-base codon, a protein's amino acid count (and therefore roughly its molecular weight) scales directly with the length of its coding DNA sequence, though untranslated regions and introns don't contribute to protein length.