The Peptide Mass Calculator is a specialized tool used in biochemistry and molecular biology to calculate the molecular mass of a peptide from its amino acid sequence. This tool is essential for researchers and scientists who work with proteins and peptides, as it helps accurately determine the mass of peptides which is crucial for various experimental protocols and procedures.
Formula of Peptide Mass Calculator
Step-by-Step Calculation:
- List of Amino Acids: Begin by identifying the amino acids present in the peptide sequence.
- Amino Acid Masses: Utilize the standard monoisotopic mass for each amino acid involved in the peptide.
- Sum of Amino Acid Masses: Compute the total mass by adding up the monoisotopic masses of all the amino acids in the sequence.
- Adjust for Water Loss: Account for the mass of water molecules (18.01528 Da per peptide bond) that is lost during the formation of peptide bonds.
Amino Acid Masses:
Here are the monoisotopic masses of the 20 standard amino acids, which are vital for the calculations:
| Amino Acid | Symbol | Monoisotopic Mass (Da) |
|---|---|---|
| Alanine | A | 71.03711 |
| Arginine | R | 156.10111 |
| Asparagine | N | 114.04293 |
| Aspartic acid | D | 115.02694 |
| Cysteine | C | 103.00919 |
| Glutamine | Q | 128.05858 |
| Glutamic acid | E | 129.04259 |
| Glycine | G | 57.02146 |
| Histidine | H | 137.05891 |
| Isoleucine | I | 113.08406 |
| Leucine | L | 113.08406 |
| Lysine | K | 128.09496 |
| Methionine | M | 131.04049 |
| Phenylalanine | F | 147.06841 |
| Proline | P | 97.05276 |
| Serine | S | 87.03203 |
| Threonine | T | 101.04768 |
| Tryptophan | W | 186.07931 |
| Tyrosine | Y | 163.06333 |
| Valine | V | 99.06841 |
Final Calculation:
- Sum of Amino Acid Masses: Σ (Mass of each amino acid)
- Calculate the number of peptide bonds: (n - 1), where n is the number of amino acids in the peptide.
- Peptide Mass (M): Sum of Amino Acid Masses - (Number of Peptide Bonds * 18.01528 Da)
Table for General Terms
| Term | Definition |
|---|---|
| Monoisotopic Mass | The mass of a molecule using the most abundant isotope of each element. |
| Peptide Bond | A covalent chemical bond linking two consecutive amino acid monomers along a peptide or protein chain. |
| Amino Acid | Organic compounds that combine to form proteins, the building blocks of life. |
| Peptide | A short chain of amino acids linked by peptide bonds. |
Example of Peptide Mass Calculator
- Amino Acid Masses:
- Glycine (G): 57.02146 Da
- Alanine (A): 71.03711 Da
- Leucine (L): 113.08406 Da
- Sum of Amino Acid Masses:
- 57.02146 + 71.03711 + 113.08406 = 241.14263 Da
- Number of Peptide Bonds:
- 3 amino acids - 1 = 2 peptide bonds
- Calculate Peptide Mass:
- 241.14263 - (2 * 18.01528) = 205.11207 Da
This calculation demonstrates how to determine the peptide mass for a simple sequence.
Most Common FAQs
The accuracy is highly dependent on the precision of the amino acid mass values provided. It is generally very reliable for theoretical calculations.
No, the standard peptide mass calculator does not account for post-translational modifications. Adjustments or additional tools are needed for such calculations.
For large proteins, the calculator can provide a rough estimate, but more sophisticated methods like mass spectrometry are recommended for higher accuracy.