1. What is Peptide Exact Mass?

The exact mass of a peptide is the calculated mass of its most abundant isotopic composition. It's the sum of the monoisotopic masses of all atoms in the molecule, accounting for peptide bonds and any modifications.

2. How Does the Calculator Work?

The calculator uses the formula:

Where:

• \( \sum (\text{Amino Acid Masses}) \) — Sum of monoisotopic masses of all amino acids
• \( \text{Modifications} \) — Any additional mass from modifications (in Daltons)
• \( \text{H}_2\text{O} \) — Water loss for each peptide bond (18.01056 Da per bond)

Explanation: The calculator sums the masses of all amino acids in the sequence, adds any modifications, and subtracts water molecules lost during peptide bond formation.

3. Importance of Exact Mass Calculation

Details: Exact mass calculation is crucial for peptide identification in mass spectrometry, peptide synthesis quality control, and experimental design in proteomics research.

4. Using the Calculator

Tips: Enter the peptide sequence in single-letter code (case insensitive) and any additional mass from modifications in Daltons. The sequence should only contain standard amino acid letters.

5. Frequently Asked Questions (FAQ)

Q1: What's the difference between exact mass and average mass?
A: Exact mass uses the most abundant isotope of each element, while average mass considers natural isotopic abundance.

Q2: Are modifications included in the calculation?
A: You need to manually add the mass of any modifications (phosphorylation, acetylation, etc.) in the modifications field.

Q3: How are N-terminal and C-terminal modifications handled?
A: These should be included in the modifications field along with their mass contributions.

Q4: What about non-standard amino acids?
A: This calculator only handles standard amino acids. For non-standard residues, you would need to add their mass in the modifications field.

Q5: Why subtract water for peptide bonds?
A: Each peptide bond forms with the loss of one water molecule (H₂O) during synthesis.