Protein Molecular Weight Calculator
Calculate a protein's molecular weight in Daltons from its amino acid sequence, using standard average residue masses.
🧬 What is the Protein Molecular Weight Calculator?
The protein molecular weight calculator computes a protein or peptide's molecular weight in Daltons directly from its amino acid sequence, entered as standard single-letter codes (like MKV) or three-letter codes (like Met-Lys-Val). It sums the average residue mass of every amino acid present, then adds the mass of one water molecule to account for the free N-terminal and C-terminal groups of the finished chain.
Biochemistry students use it to check hand calculations, molecular biologists use it to quickly estimate the expected size of a translated protein or a synthesized peptide before running gel electrophoresis or mass spectrometry, and lab technicians use it when ordering custom peptides that are priced or specified by molecular weight.
An important distinction is that this calculator reports the theoretical unmodified polypeptide weight from sequence alone, it does not account for post-translational modifications like glycosylation or phosphorylation, disulfide bond formation, or bound cofactors and metal ions, all of which can shift a real purified protein's measured weight away from this sequence-based value.
This calculator is useful for biochemistry and molecular biology students, researchers designing peptides, and lab staff who need a fast, correct molecular weight without manually looking up and summing 20 different residue masses.
📐 Formula
📖 How to Use This Calculator
Steps
💡 Example Calculations
Example 1 - Short tripeptide (1-letter codes)
Example 2 - All 20 standard amino acids (1-letter codes)
Example 3 - Short tripeptide (3-letter codes)
❓ Frequently Asked Questions
🔗 Related Calculators
How do you calculate a protein's molecular weight from its sequence?
Sum the average residue mass of every amino acid in the sequence, then add 18.02 Da for one water molecule, which accounts for the free N-terminal hydrogen and C-terminal hydroxyl group. Residue masses already exclude the water lost at each peptide bond.
Why do you add 18.02 Da at the end?
Each peptide bond formed between two amino acids releases one water molecule (18.02 Da), so a chain of n residues loses n-1 waters relative to n free amino acids. Using residue masses (already minus one water each) and adding back exactly one water accounts for the two free terminal groups of the finished chain.
What is the difference between average and monoisotopic mass?
Average mass uses each element's natural isotopic abundance-weighted atomic weight, monoisotopic mass uses only the most abundant isotope of each element. This calculator uses average mass, the standard convention for reporting bulk protein molecular weight in Daltons.
Can I enter three-letter amino acid codes instead of single letters?
Yes, switch to 3-Letter Code mode and enter codes like Ala, Gly, or Met separated by spaces, hyphens, or commas, the calculator converts them to the equivalent single-letter sequence internally before computing molecular weight.
What amino acid codes does this calculator accept?
The 20 standard proteinogenic amino acids: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y in 1-letter mode, or their standard three-letter equivalents (Ala, Cys, Asp, and so on) in 3-letter mode.
Why does my calculated molecular weight differ from a published value?
Published protein molecular weights often include post-translational modifications (like glycosylation or phosphorylation), disulfide bonds, or bound cofactors and metals, none of which this sequence-only calculator accounts for. It gives the theoretical unmodified polypeptide weight.
What is a Dalton?
A Dalton (Da), also called an atomic mass unit, is the standard unit for molecular weight at the scale of individual molecules like proteins and peptides, roughly the mass of one hydrogen atom. Protein molecular weights are commonly reported in Daltons or kilodaltons (kDa, thousands of Daltons).
Does amino acid order affect the molecular weight?
No, molecular weight from this formula depends only on which amino acids are present and how many of each, not their order in the chain. Two peptides with the same amino acid composition but different sequences have identical molecular weights.
How accurate is this calculator for very large proteins?
The summation method is exact for the theoretical unmodified polypeptide at any length, accuracy relative to a real purified protein decreases mainly due to post-translational modifications, which become more likely as sequence length increases, not due to any limitation in the arithmetic itself.
What happens if I enter an invalid amino acid code?
The calculator checks every character (1-letter mode) or token (3-letter mode) against the list of 20 standard amino acids and shows an inline error naming exactly which character or code was not recognized, instead of silently ignoring it.