Quick Answer: A protein’s molecular weight is the sum of its amino acid residue weights plus one water molecule (18.015 Da). Paste any one-letter amino acid sequence into the free calculator below and you’ll instantly get the molecular weight in Daltons (Da), kilodaltons (kDa), the sequence length, and a full amino acid composition breakdown.
Protein Molecular Weight Calculator
Enter Amino Acid Sequence (One-Letter Code)
Paste any protein sequence. Spaces, numbers, line breaks, and non-standard letters are automatically ignored.
What Is Protein Molecular Weight?
Protein molecular weight (MW) is the total mass of all atoms in a protein molecule, expressed in Daltons (Da) or kilodaltons (kDa). One Dalton equals one atomic mass unit (1 g/mol). A typical protein ranges from 10 kDa (small peptide hormones) to over 500 kDa (large enzymes and structural proteins). Knowing the MW is essential for SDS-PAGE band identification, mass spectrometry, recombinant protein expression, and buffer molarity calculations.
How to Calculate Protein Molecular Weight (Formula)
The protein molecular weight is calculated by summing the residue weights of every amino acid in the sequence and adding the mass of one water molecule (18.015 Da):
MW = Σ (residue weights of each amino acid) + 18.015
Residue weight = amino acid molecular weight − 18.015 Da (water lost when each peptide bond forms). The final +18.015 accounts for the two extra hydrogens and one oxygen at the chain’s N- and C-termini.
Amino Acid Residue Weight Table
| 1-Letter | 3-Letter | Amino Acid | Residue Weight (Da) | Free Amino Acid MW (Da) |
|---|---|---|---|---|
| A | Ala | Alanine | 71.0788 | 89.0935 |
| R | Arg | Arginine | 156.1875 | 174.2022 |
| N | Asn | Asparagine | 114.1038 | 132.1184 |
| D | Asp | Aspartic acid | 115.0886 | 133.1032 |
| C | Cys | Cysteine | 103.1388 | 121.1590 |
| E | Glu | Glutamic acid | 129.1155 | 147.1293 |
| Q | Gln | Glutamine | 128.1307 | 146.1451 |
| G | Gly | Glycine | 57.0519 | 75.0669 |
| H | His | Histidine | 137.1411 | 155.1552 |
| I | Ile | Isoleucine | 113.1594 | 131.1736 |
| L | Leu | Leucine | 113.1594 | 131.1736 |
| K | Lys | Lysine | 128.1741 | 146.1882 |
| M | Met | Methionine | 131.1926 | 149.2124 |
| F | Phe | Phenylalanine | 147.1766 | 165.1900 |
| P | Pro | Proline | 97.1167 | 115.1310 |
| S | Ser | Serine | 87.0782 | 105.0930 |
| T | Thr | Threonine | 101.1051 | 119.1197 |
| W | Trp | Tryptophan | 186.2132 | 204.2262 |
| Y | Tyr | Tyrosine | 163.1760 | 181.1894 |
| V | Val | Valine | 99.1326 | 117.1469 |
Worked Example — Calculating MW of a Pentapeptide
Let’s calculate the molecular weight of the sequence Met-Ala-Gly-Leu-Lys (MAGLK):
- M (Met): 131.1926
- A (Ala): 71.0788
- G (Gly): 57.0519
- L (Leu): 113.1594
- K (Lys): 128.1741
- Sum of residues: 500.6568 Da
- Add water (18.015): 518.67 Da
So MAGLK has a molecular weight of 518.67 Da (or 0.519 kDa).
Why Protein Molecular Weight Matters
- SDS-PAGE: Bands migrate by MW — knowing the expected weight tells you which band is your protein of interest.
- Western Blot: Confirms protein identity at the expected MW. Off-target bands indicate degradation or post-translational modifications.
- Mass Spectrometry: MS measures the exact MW — comparing it to the predicted value verifies sequence integrity.
- Recombinant Expression: Calculating expected MW lets you predict band patterns from new constructs.
- Buffer & Stock Preparation: Converting between mg/mL and molar concentration requires MW (mol = mass ÷ MW).
- Size-Exclusion Chromatography: Elution volume correlates with MW for globular proteins.
Average vs. Monoisotopic Molecular Weight
This calculator returns the average molecular weight, which uses the natural isotopic abundance of each element. It is the standard value reported in literature and used for SDS-PAGE.
For high-resolution mass spectrometry (Orbitrap, FT-ICR, MALDI-TOF), the monoisotopic mass is needed — calculated using only the most abundant isotope of each element (¹H, ¹²C, ¹⁴N, ¹⁶O, ³²S). The monoisotopic mass is typically 0.05–0.07% lower than the average mass. For small peptides (under 10 kDa), the difference is critical; for larger proteins, average mass is used.
Factors That Change a Protein’s Actual Molecular Weight
Post-Translational Modifications (PTMs)
- Phosphorylation: +79.97 Da per site
- Glycosylation (N-linked): +1,000 to +10,000+ Da depending on glycan
- Methylation: +14.02 Da per methyl group
- Acetylation: +42.01 Da per acetyl group
- Ubiquitination: +8,564 Da per ubiquitin (76 aa, 8.5 kDa)
- Disulfide bonds: −2.02 Da per S–S bond (loss of 2H)
Signal Peptide Cleavage
Many secreted proteins are translated with an N-terminal signal peptide (~20 aa) that is cleaved during maturation. The mature protein weighs roughly 2 kDa less than the predicted sequence.
Affinity Tags
Recombinant proteins often carry tags that add to the MW. Common tags:
- His-tag (6xHis): +0.84 kDa
- FLAG tag: +1.0 kDa
- HA tag: +1.1 kDa
- Myc tag: +1.2 kDa
- GST tag: +26 kDa
- MBP tag: +42 kDa
- SUMO tag: +12 kDa
How to Find a Protein’s Sequence
- Go to UniProt (uniprot.org) and search the protein name or gene symbol.
- Open the entry and find the Sequence section.
- Copy the one-letter amino acid sequence (ignore the FASTA header line starting with “>”).
- Paste it into the calculator above.
UniProt also lists the canonical molecular weight — use it to verify the calculator’s output.
Frequently Asked Questions
What is a Dalton (Da)?
A Dalton is the standard unit of molecular mass equal to 1/12 of the mass of a ¹²C atom — approximately 1.66 × 10⁻²⁴ g. 1 kDa = 1,000 Da.
Why do I need to add 18.015 Da?
Because the residue weights already have water subtracted (water is lost when each peptide bond forms). The full protein has one water molecule’s worth of atoms remaining at the N- and C-termini, so you add it back once.
Is the calculator accurate for proteins with modifications?
The calculator returns the MW of the unmodified polypeptide chain. For modified proteins, manually add the modification mass (e.g., +80 Da per phosphorylation).
What if my sequence contains unusual amino acids like selenocysteine (U)?
Selenocysteine (U, 150.04 Da residue) and pyrrolysine (O, 237.30 Da residue) are not included in this calculator. Add them manually if present.
How accurate is the calculated MW compared to mass spectrometry?
The calculator uses average isotope weights, which match SDS-PAGE estimates very closely. Mass spec measures monoisotopic mass, which differs by 0.05–0.07%. For proteins under 10 kDa, the difference can affect identification.
What is the difference between protein MW and protein size?
MW is mass in Daltons; size usually refers to the number of amino acids (residues). They correlate roughly at 110 Da per residue, but proline-rich or glycine-rich proteins deviate from this average.
Why does my protein run at a different MW on SDS-PAGE?
Highly acidic proteins, glycosylated proteins, or membrane proteins often migrate anomalously on SDS-PAGE. Hydrophobic proteins frequently appear smaller than predicted; heavily glycosylated proteins appear larger.
How do I calculate molar concentration from mg/mL using MW?
Molar concentration (M) = concentration in g/L ÷ MW in g/mol. Example: 1 mg/mL of a 50 kDa protein = 1 g/L ÷ 50,000 g/mol = 2 × 10⁻⁵ M = 20 µM.
Conclusion
Calculating protein molecular weight is one of the most frequently performed tasks in molecular biology, biochemistry, and structural biology — and the math is just addition. Sum the residue weights from the amino acid sequence, add 18.015 for the terminal water, and you have the MW in Daltons. Use the calculator above to get instant results plus a full amino acid composition table, then adjust for tags, signal peptides, or post-translational modifications as needed. Bookmark this page for buffer math, gel interpretation, and stock solution preparation in your next experiment.
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