Precisely calculate the molecular weight of your peptides. Enter the amino acid sequence and get instant results, including intermediate values and a detailed explanation.
Enter the sequence using standard 3-letter or 1-letter codes, separated by hyphens or no separator.
No (Linear)
Yes (Cyclic)
Yes (N-terminus amine, C-terminus carboxyl)
No (Unmodified ends)
Typically, linear peptides have a free amine (-NH2) at the N-terminus and a free carboxyl (-COOH) at the C-terminus. Cyclic peptides do not have these free termini in the same way.
Peptide molecular weight refers to the total mass of a peptide molecule, typically expressed in Daltons (Da) or grams per mole (g/mol). A peptide is a short chain of amino acids linked together by peptide bonds. Understanding the precise molecular weight is crucial in various scientific disciplines, including biochemistry, molecular biology, pharmacology, and synthetic chemistry. It's a fundamental property used for identification, quantification, and predicting behavior in biological systems.
Who should use it: Researchers in proteomics, drug discovery, peptide synthesis, and analytical chemistry will find this metric indispensable. Anyone working with synthesized peptides, analyzing protein fragments, or performing mass spectrometry needs an accurate peptide molecular weight. It is also valuable for students learning about protein chemistry and biochemistry.
Common misconceptions: A frequent misconception is that molecular weight calculation is a simple sum of individual amino acid weights. However, the formation of a peptide bond involves the release of a water molecule (H2O), which must be accounted for. Another misunderstanding is the difference between average molecular weight and monoisotopic molecular weight, with the latter being more precise for mass spectrometry applications. Also, users may forget to account for terminal modifications or cyclic structures, leading to inaccurate calculations.
Peptide Molecular Weight Formula and Mathematical Explanation
The calculation of peptide molecular weight involves summing the weights of the constituent amino acid residues and then adjusting for the peptide bond formation and terminal groups. For precise calculations, especially for mass spectrometry, the monoisotopic mass of each atom is used.
The general formula for a linear peptide with standard N- and C-termini is:
Molecular Weight = Σ(Monoisotopic Weight of each Amino Acid Residue) + (Monoisotopic Weight of H2O)
However, this simplifies based on how residues are defined. When considering residues, the water molecule is effectively lost during peptide bond formation. A more practical approach accounts for the mass added by each amino acid monomer and then the structure of the termini.
A commonly used approach considers the full amino acid monomer weight minus the mass of a water molecule for each peptide bond formed, plus the mass of the terminal groups. A more direct and often preferred method, especially when using residue weights that already account for water loss, is:
Molecular Weight = Σ(Monoisotopic Weight of Amino Acid Residue) + Mass of N-terminus + Mass of C-terminus
Where:
Σ(Monoisotopic Weight of Amino Acid Residue): This is the sum of the monoisotopic molecular weights of each amino acid in the sequence, *after* the loss of water during peptide bond formation. Standard residue weights already reflect this loss.
Mass of N-terminus: For a standard linear peptide, this is the mass of a hydrogen atom (-H).
Mass of C-terminus: For a standard linear peptide, this is the mass of a hydroxyl group (-OH). The combined addition for standard termini is -H + -OH = +17.0073 Da (for H2O). If N-terminal modification or C-terminal amidation occurs, these values change.
For a cyclic peptide: The water molecule is lost at both ends, so there are no free N- or C-terminal groups to add. The weight is simply the sum of the residue weights.
Molecular Weight (Cyclic) = Σ(Monoisotopic Weight of each Amino Acid Residue)
Variable Explanations:
Let's break down the components:
Variable Definitions
Variable
Meaning
Unit
Typical Range
Sequence Length (N)
The number of amino acid residues in the peptide chain.
Count
1 to >100
Amino Acid Residue Weight (MWAA)
The mass of an individual amino acid after the loss of a water molecule during peptide bond formation.
Daltons (Da)
~57 (Glycine) to ~204 (Tryptophan)
Total Residue Weight (ΣMWAA)
The sum of the molecular weights of all amino acid residues in the peptide sequence.
Daltons (Da)
Varies greatly with sequence length and composition.
N-terminus Mass
The mass added at the N-terminus. Typically, -H for a free amine. Can vary with modifications.
Daltons (Da)
~1.0078 (H) for standard N-terminus; 14.01565 (CH2) for amidation; 15.0238 (CH3) for N-methylation etc.
C-terminus Mass
The mass added at the C-terminus. Typically, -OH for a free carboxyl. Can vary with modifications like amidation.
Daltons (Da)
~17.0027 (OH) for standard C-terminus; often 0 for C-terminal amides.
Water Mass (MWH2O)
The mass of a water molecule (18.01528 Da). Used conceptually in bond formation, but often implicitly handled by residue weights and terminal additions.
Daltons (Da)
~18.01528
The calculator uses the following standard monoisotopic masses for amino acid residues:
Practical Examples
Let's illustrate with common peptide sequences:
Example 1: Linear Peptide – Gly-Ala-Ser
Inputs:
Sequence: GLY-ALA-SER
Is Cyclic: No
Add Terminal Groups: Yes
Calculation Breakdown:
Glycine (G) Residue Weight: 57.0519 Da
Alanine (A) Residue Weight: 71.0793 Da
Serine (S) Residue Weight: 87.0782 Da
Total Residue Weight = 57.0519 + 71.0793 + 87.0782 = 215.2094 Da
N-terminus Addition (H): 1.0078 Da
C-terminus Addition (OH): 17.0027 Da
Total Molecular Weight = 215.2094 + 1.0078 + 17.0027 = 233.2299 Da
Result Interpretation: A linear peptide sequence GLY-ALA-SER with standard N- and C-termini has a molecular weight of approximately 233.23 Da. This value is essential for verifying synthesis and for quantitative analysis.
Example 2: Cyclic Peptide – Cyc(10)Lys-Gly-Val
Inputs:
Sequence: Lys-Gly-Val (assume the cyclic bond is between Lys side chain and C-terminus Val)
Is Cyclic: Yes
Add Terminal Groups: No (as it's cyclic, standard termini are not present)
Calculation Breakdown:
Lysine (K) Residue Weight: 128.0940 Da
Glycine (G) Residue Weight: 57.0519 Da
Valine (V) Residue Weight: 99.1326 Da
Total Residue Weight = 128.0940 + 57.0519 + 99.1326 = 284.2785 Da
Since it's cyclic, no terminal groups are added.
Total Molecular Weight = 284.2785 Da
Result Interpretation: A cyclic peptide formed from Lys-Gly-Val has a molecular weight of approximately 284.28 Da. The cyclic nature eliminates the addition of terminal H and OH groups that would be present in a linear version.
How to Use This Peptide Molecular Weight Calculator
Using our peptide molecular weight calculator is straightforward. Follow these simple steps:
Enter Amino Acid Sequence: In the "Amino Acid Sequence" field, type your peptide sequence. You can use either the standard 3-letter codes (e.g., ALA, GLY) or the 1-letter codes (e.g., A, G). Separate them with hyphens for clarity, or enter them without separators (e.g., AGV or A-G-V).
Specify Cyclic Nature: Select "Yes (Cyclic)" from the "Is the peptide cyclic?" dropdown if your peptide forms a ring structure. Choose "No (Linear)" for standard open-chain peptides.
Select Terminal Groups: For linear peptides, choose "Yes (N-terminus amine, C-terminus carboxyl)" if you want to include the standard terminal functional groups. If your peptide has modified termini (e.g., N-terminal acetylation, C-terminal amidation) or you are calculating the weight of just the residues, select "No (Unmodified ends)". Cyclic peptides typically do not have standard terminal groups, so "No" is usually appropriate.
Calculate: Click the "Calculate Molecular Weight" button.
How to Read Results:
Primary Highlighted Result: This displays the final calculated molecular weight in Daltons (Da).
Intermediate Values: These show the breakdown:
Total Residue Weight: The sum of the weights of all amino acid residues in the sequence.
Terminal Group Adjustment: The mass added or subtracted due to the N- and C-termini (if applicable).
Final Molecular Weight: This reiterates the primary result.
Formula Used: A clear explanation of the calculation logic applied.
Amino Acid Table: A reference table showing the molecular weights of common amino acid residues.
Chart: A visual representation comparing the contribution of each residue and terminal groups to the total weight.
Decision-Making Guidance: The calculated molecular weight is critical for validating peptide synthesis success (e.g., via mass spectrometry). Deviations can indicate synthesis errors, incomplete reactions, or unexpected modifications. For applications like drug delivery or formulation, precise molecular weight influences stoichiometry and concentration calculations. Accurate peptide mass is a cornerstone of reliable biochemical experimentation.
Key Factors That Affect Peptide Molecular Weight Results
Several factors influence the calculated molecular weight of a peptide. Understanding these is key to accurate interpretation:
Amino Acid Sequence Composition: The types and number of amino acids directly determine the base molecular weight. Heavier amino acids like Tryptophan (W) or Tyrosine (Y) increase the weight more than lighter ones like Glycine (G) or Alanine (A).
Peptide Length: Longer peptides naturally have higher molecular weights due to the accumulation of residue masses.
Post-Translational Modifications (PTMs): Modifications like phosphorylation, glycosylation, acetylation, or methylation add significant mass to specific amino acid residues, deviating from standard weights. This calculator assumes standard unmodified residues unless specific terminal groups are chosen.
Cyclic vs. Linear Structure: Cyclic peptides lack the free -H (N-terminus) and -OH (C-terminus) groups, resulting in a lower molecular weight compared to their linear counterparts by the mass of a water molecule (approx. 18 Da).
Terminal Group Modifications: Standard linear peptides have a free amine (-NH2) at the N-terminus and a free carboxyl (-COOH) at the C-terminus. If these are modified (e.g., N-terminal acetylation, C-terminal amidation), the added or removed mass changes the total molecular weight. C-terminal amidation, for instance, replaces -OH with -NH2, significantly altering the mass.
Isotopic Composition: While this calculator uses monoisotopic masses (the mass of the most abundant isotope for each element), natural peptides contain isotopes. Mass spectrometry often detects a distribution of masses reflecting this natural isotopic abundance. Using monoisotopic mass is standard for precise identification.
Counter-ions and Salts: In practical sample preparation, peptides are often associated with counter-ions (like trifluoroacetate, TFA, from synthesis) or exist as salts. These are not part of the peptide's intrinsic molecular weight but affect the measured mass in analytical techniques.
Frequently Asked Questions (FAQ)
Q1: What is the difference between monoisotopic and average molecular weight?
A: Monoisotopic molecular weight uses the mass of the most abundant isotope for each atom (e.g., 1H, 12C, 16O). Average molecular weight uses the weighted average of all naturally occurring isotopes. For mass spectrometry, monoisotopic mass is crucial for accurate identification.
Q2: Does the calculator account for disulfide bonds?
A: This calculator does not directly account for disulfide bonds. A disulfide bond forms between two cysteine residues, resulting in the loss of two hydrogen atoms (2 * 1.0078 Da = 2.0156 Da). To account for it, you would subtract this value from the total calculated weight after entering the sequence with two cysteines.
Q3: Can I use this calculator for proteins?
A: While the principle is the same, this calculator is designed for shorter peptide sequences. For very large proteins, the computational load and potential for accumulated errors increase. Specialized protein calculators or software are recommended for large biomolecules.
Q4: What does 'Residue Weight' mean in the context of peptides?
A: Residue weight refers to the mass of an amino acid *after* it has been incorporated into a peptide chain. During peptide bond formation, a molecule of water (H2O) is removed. So, the residue weight is the monomeric amino acid weight minus the weight of water.
Q5: What if my peptide has non-standard amino acids?
A: This calculator uses standard amino acid weights. For peptides containing non-standard or modified amino acids (e.g., hydroxyproline, citrulline), you would need to manually find the monoisotopic mass of that specific modified residue and substitute it into the calculation logic or sum.
Q6: How do I handle N-terminal acetylation?
A: N-terminal acetylation adds an acetyl group (CH3CO-) to the N-terminal amino group. This adds a mass of approximately 42.0106 Da (C2H2O). If using the calculator for a linear peptide with acetylation, you would select 'No' for 'Add Standard Terminal Groups' and then manually add 42.0106 Da to the final result.
Q7: What are typical units for peptide molecular weight?
A: The most common units are Daltons (Da) for molecular mass and sometimes grams per mole (g/mol). For peptides, Daltons is standard, particularly when referring to monoisotopic mass.
Q8: Can this calculator predict peptide stability?
A: No, this calculator only determines the molecular weight. Peptide stability is influenced by factors like amino acid sequence, secondary structure, environmental conditions (pH, temperature), and the presence of degrading enzymes, not just its mass.