Instantly compute the molecular weight of your amino acid or nucleotide sequence. Understand the science behind it with our detailed guide and examples.
Molecular Weight Calculator
Enter the sequence using standard one-letter codes (e.g., for amino acids: ACDEFGHIKLMNPQRSTVWY; for nucleotides: ACGT).
Average Residue Weights
Monoisotopic Residue Weights
Choose between average atomic weights (common) or monoisotopic masses (precise).
Results:
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Total Residues: —
Average Residue Weight: —
Std. Dev. of Residue Weights: —
Molecular Weight (MW) is calculated by summing the molecular weights of each constituent atom in a molecule. For biological sequences, this is approximated by summing the weighted masses of each amino acid or nucleotide residue, adjusted for peptide bond formation (water loss) or phosphodiester bond formation.
Residue Weight Distribution
Distribution of residue weights in the sequence.
Residue Weight Data (Average)
Residue
Name
Average Mass (Da)
Monoisotopic Mass (Da)
Standard average and monoisotopic masses for common amino acid residues.
What is Molecular Weight from Sequence?
Calculating the molecular weight from a sequence is a fundamental process in biochemistry and molecular biology. It involves determining the total mass of a molecule, typically a protein (peptide sequence) or a nucleic acid (DNA/RNA sequence), based on the specific order of its building blocks, known as residues. This calculation is crucial for various experimental and theoretical applications, from understanding protein function to designing purification strategies and interpreting mass spectrometry data.
Who should use it? Researchers, students, and professionals in fields like molecular biology, genetics, bioinformatics, drug discovery, and biochemistry frequently use this calculation. It's also valuable for anyone needing to estimate the mass of a synthesized peptide or oligonucleotide.
Common misconceptions: A common misunderstanding is that the molecular weight is simply the sum of the atomic weights of all atoms in the sequence. However, when residues link together to form polymers (like proteins or nucleic acids), they do so via condensation reactions, releasing a water molecule (H₂O) or its equivalent. This loss of mass must be accounted for. Another misconception is that using average atomic weights is always sufficient; for high-precision applications, monoisotopic masses are necessary.
Molecular Weight from Sequence Formula and Mathematical Explanation
The molecular weight of a biological sequence is derived by summing the weighted masses of its constituent residues, accounting for the mass lost during polymer formation.
The core principle behind calculating the molecular weight of a polymer sequence is to sum the masses of its individual monomer units and then subtract the mass lost during polymerization. For peptides, this involves the loss of water for each peptide bond formed. For nucleic acids, it involves the loss of water for each phosphodiester bond.
Formula for Peptide Molecular Weight:
MW = (Σ [Mass of amino acid residue] – (n-1) * Mass of H₂O)
Where:
MW is the total molecular weight of the peptide.
Σ [Mass of amino acid residue] is the sum of the molecular weights of each amino acid in the sequence.
(n-1) is the number of peptide bonds formed (where 'n' is the total number of amino acid residues).
Mass of H₂O is the molecular weight of water (approximately 18.015 Da).
Alternatively, and more commonly for direct calculation using residue masses, one sums the *effective* residue masses (which already account for water loss).
MW = Σ [Effective mass of amino acid residue] + Mass of terminal H & OH (for a free N-terminus and C-terminus)
*Simplified Calculation for Calculators:* Many tools sum the individual amino acid masses and then subtract (n-1) * mass of H₂O. Or, they use pre-calculated effective residue masses. For this calculator, we sum the average/monoisotopic mass of each amino acid and subtract the mass of water for each peptide bond formed.
Formula for Nucleotide Molecular Weight (e.g., DNA/RNA):
MW = (Σ [Mass of nucleotide residue] – (n-1) * Mass of H₂O)
Similar to peptides, a water molecule is lost for each phosphodiester bond formed. Nucleotides also have a phosphate group, a sugar (ribose or deoxyribose), and a base. The calculation sums these components' masses for each nucleotide and subtracts water for each bond.
Variables Table:
Variable
Meaning
Unit
Typical Range / Notes
Sequence
The ordered list of amino acids (one-letter code) or nucleotides (ACGT/ACGU).
String
Varies in length; e.g., MKTAYIAK… (protein), AGCTAG… (DNA/RNA).
Residue Mass
The molecular mass of a single amino acid or nucleotide. Can be average or monoisotopic.
Daltons (Da)
Amino Acids: ~71 Da (Glycine) to ~204 Da (Tryptophan). Nucleotides: ~300-330 Da.
N (Number of Residues)
The total count of amino acids or nucleotides in the sequence.
Count
Positive integer (≥ 1).
Number of Bonds
For peptides/nucleic acids, this is N-1 (for linear polymers).
Count
N-1. For cyclic structures, it's N.
Mass of H₂O
The molecular weight of a water molecule.
Da
Approx. 18.015 Da (average).
MW
The calculated total molecular weight of the sequence.
Da
Depends on sequence length and residue composition.
Practical Examples (Real-World Use Cases)
Example 1: Calculating the Molecular Weight of a Small Peptide
Sum these masses: 131.19 + 128.17 + 101.11 = 360.47 Da.
Determine the number of residues (N): 3.
Determine the number of peptide bonds: N – 1 = 3 – 1 = 2.
Subtract the mass of water for each bond: 360.47 Da – (2 * 18.015 Da) = 360.47 Da – 36.03 Da = 324.44 Da.
Calculator Output (Average):
Total Residues: 3
Average Residue Weight: ~120.16 Da (360.47 / 3)
Std. Dev. of Residue Weights: ~17.01 Da
Molecular Weight: 324.44 Da
Interpretation: This value of 324.44 Da represents the estimated molecular weight of the free peptide MKT, assuming average atomic weights. This is useful for preliminary estimations in cloning or peptide synthesis.
Example 2: Calculating Monoisotopic Mass of a Short DNA Oligonucleotide
Look up their monoisotopic residue masses (for DNA, this includes base, sugar, and phosphate):
A (deoxyadenosine monophosphate): ~313.03 Da
T (deoxythymidine monophosphate): ~304.05 Da
G (deoxyguanosine monophosphate): ~329.05 Da
C (deoxycytidine monophosphate): ~289.03 Da
Sum these masses: 313.03 + 304.05 + 329.05 + 289.03 = 1235.16 Da.
Determine the number of residues (N): 4.
Determine the number of phosphodiester bonds: N – 1 = 4 – 1 = 3.
Subtract the mass of water for each bond: 1235.16 Da – (3 * 18.015 Da) = 1235.16 Da – 54.045 Da = 1181.115 Da.
Add the mass of a terminal H atom (for 5′ end): 1181.115 Da + 1.008 Da ≈ 1182.12 Da.
Calculator Output (Monoisotopic):
Total Residues: 4
Average Residue Weight: ~308.79 Da (1235.16 / 4)
Std. Dev. of Residue Weights: ~19.19 Da
Molecular Weight: ~1182.12 Da
Interpretation: The monoisotopic mass of 1182.12 Da is critical for accurate interpretation of mass spectrometry data, which measures the precise mass of molecules. This value allows for unambiguous identification of the oligonucleotide. For precise experimental validation, monoisotopic mass is preferred.
How to Use This Molecular Weight from Sequence Calculator
Follow these simple steps to calculate the molecular weight of your biological sequence accurately.
Input Your Sequence: In the "Amino Acid or Nucleotide Sequence" field, carefully enter your sequence using the standard one-letter codes. For proteins, use codes like ACDEFGHIKLMNPQRSTVWY. For nucleic acids (DNA/RNA), use ACGT (for DNA) or ACGU (for RNA). Ensure there are no spaces or special characters unless they are part of a defined code (which is rare for standard calculations).
Select Calculation Type: Choose between "Average Residue Weights" (commonly used for general estimations) and "Monoisotopic Residue Weights" (required for high-precision applications like mass spectrometry). The average type uses the weighted average of isotopic abundances for each element in the atom's mass, while monoisotopic uses the mass of the most abundant isotope only.
Click Calculate: Press the "Calculate" button. The calculator will process your sequence based on the selected type.
Review Results: The results section will display:
Main Result (Molecular Weight): The primary calculated molecular weight in Daltons (Da).
Total Residues: The number of amino acids or nucleotides in your sequence.
Average Residue Weight: The average mass of a single residue in your sequence.
Std. Dev. of Residue Weights: The standard deviation, indicating the variability in residue masses within your sequence.
Understand the Formula: A brief explanation of the calculation is provided below the results. It highlights the summation of residue masses and the subtraction of water molecules lost during bond formation.
Examine the Table: The table provides the standard average and monoisotopic masses for common amino acid residues, serving as a reference for the calculation.
Interpret the Chart: The dynamic chart visualizes the distribution of residue weights within your sequence, offering a quick overview of its compositional characteristics.
Copy Results: Use the "Copy Results" button to easily transfer the main result, intermediate values, and key assumptions to your notes or reports.
Reset: If you need to start over or clear the fields, click the "Reset" button.
Decision-Making Guidance: The calculated molecular weight is fundamental for planning experiments. For instance, knowing the precise molecular weight helps in preparing solutions of specific molar concentrations. It is also essential for interpreting data from techniques like SDS-PAGE (where migration often correlates with size) or mass spectrometry. Choose the monoisotopic calculation when exact mass determination is critical.
Key Factors That Affect Molecular Weight Results
Several factors influence the calculated molecular weight of a biological sequence, impacting its accuracy and interpretation.
Choice of Residue Masses (Average vs. Monoisotopic): This is the most significant factor. Average masses provide a good estimate but are less precise than monoisotopic masses, which are essential for high-resolution mass spectrometry. The difference can be noticeable, especially for larger molecules.
Sequence Length: Longer sequences naturally have higher molecular weights. The cumulative effect of residue masses and bond formations becomes more pronounced with increasing length. A sequence of 100 amino acids will have a significantly larger molecular weight than one with 10.
Amino Acid/Nucleotide Composition: Different residues have vastly different molecular weights. Sequences rich in heavier amino acids like Tryptophan (W) or Tyrosine (Y), or longer nucleic acids, will weigh more than sequences composed primarily of lighter residues like Glycine (G) or Alanine (A), or shorter nucleic acids.
Post-Translational Modifications (for Proteins): Proteins often undergo modifications after synthesis (e.g., phosphorylation, glycosylation, acetylation, methylation). These modifications add or sometimes remove mass from the protein, significantly altering its final molecular weight. Standard calculations usually don't account for these unless specified.
Presence of Non-Standard Residues: While the calculator uses standard residue masses, biological molecules can sometimes incorporate non-standard amino acids or modified bases. These would require specific mass data not included in basic tables.
Cyclic vs. Linear Structure: The calculator assumes linear sequences. If a peptide or nucleic acid forms a cyclic structure, the number of bonds (and thus the amount of water lost) changes. For a cyclic peptide of N residues, there are N peptide bonds, not N-1. This increases the calculated molecular weight.
Calculation Basis (Effective Mass vs. Summation): Some databases provide "effective" residue masses that already account for water loss. If such values are used incorrectly with the water subtraction formula, the result will be inaccurate. Our calculator sums individual masses and subtracts water, a common and reliable method.
Terminal Groups: For very precise calculations, especially with synthesized peptides or oligonucleotides, the exact chemical nature of the N-terminus and C-terminus (or 5′ and 3′ ends) matters. For example, a peptide might have a free amine (-NH₂) at the N-terminus and a free carboxyl (-COOH) at the C-terminus. For nucleic acids, a 5′-phosphate and 3′-hydroxyl are typical. The specific addition/subtraction of these terminal atoms contributes slightly to the overall mass.
Frequently Asked Questions (FAQ)
Q1: What is the difference between average molecular weight and monoisotopic molecular weight?
Average molecular weight uses the natural abundance-weighted average mass of isotopes for each element in the molecule. Monoisotopic molecular weight uses the mass of only the most abundant isotope for each element. Monoisotopic mass is more precise and essential for techniques like high-resolution mass spectrometry.
Q2: Does the calculator account for post-translational modifications (PTMs)?
No, this standard calculator does not automatically account for PTMs like phosphorylation, glycosylation, etc. These modifications add specific masses that would need to be manually added to the calculated base molecular weight.
Q3: Can this calculator be used for DNA and RNA sequences?
Yes, the calculator can be used for both amino acid sequences (proteins) and nucleotide sequences (DNA/RNA). Ensure you use the correct one-letter codes for each. The underlying principle of summing residue masses and accounting for bond formation is similar.
Q4: What does "Da" stand for in molecular weight calculations?
"Da" stands for Dalton, the standard unit of molecular mass. One Dalton is defined as 1/12th the mass of an unbound neutral atom of carbon-12 in its ground state. It is approximately equal to the mass of a single proton or neutron.
Q5: How accurate is the molecular weight calculation for long proteins?
The accuracy depends on using the correct residue masses (monoisotopic preferred for precision) and accounting for any post-translational modifications. For very long proteins, slight variations in residue mass tables or the inclusion of PTMs can lead to noticeable differences.
Q6: What if my sequence contains non-standard amino acids?
This calculator uses standard amino acid residue masses. If your sequence includes non-standard or modified amino acids, you would need to find their specific molecular weights and manually adjust the calculation or use a more specialized bioinformatics tool.
Q7: Why do I subtract water (H₂O)?
When amino acids link to form a peptide bond (or nucleotides form phosphodiester bonds), they do so through a dehydration or condensation reaction. This reaction releases a molecule of water (H₂O), effectively removing its mass (~18.015 Da) from the total sum of individual amino acid/nucleotide masses.
Q8: Can this tool predict protein folding or function?
No, this tool is strictly for calculating molecular weight based on sequence. Protein folding and function are complex properties determined by factors like amino acid sequence, 3D structure, environmental conditions, and interactions with other molecules, which are beyond the scope of a simple molecular weight calculation.