Average Isotopic Mass Calculator for Protein

Protein Mass Equation:

\[ \text{Avg\_mass} = \sum(\text{amino\_acid\_masses}) \]

Average Isotopic Mass:

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1. What is Protein Average Isotopic Mass?

The average isotopic mass of a protein is the sum of the average masses of its constituent amino acids plus the mass of one water molecule (for the protein chain termination). It represents the mass you would measure for the protein in a typical mass spectrometry experiment.

2. How Does the Calculator Work?

The calculator uses the protein mass equation:

\[ \text{Avg\_mass} = \sum(\text{amino\_acid\_masses}) + \text{H}_2\text{O} \]

Where:

\( \text{Avg\_mass} \) — Average isotopic mass of the protein (Da)
\( \text{amino\_acid\_masses} \) — Sum of individual amino acid masses
\( \text{H}_2\text{O} \) — Mass of water molecule (18.01528 Da)

Explanation: The calculator sums the masses of each amino acid in the sequence and adds the mass of one water molecule to account for the protein chain termination.

3. Importance of Protein Mass Calculation

Details: Knowing a protein's mass is essential for mass spectrometry analysis, protein identification, experimental design, and verification of recombinant protein expression.

4. Using the Calculator

Tips: Enter the protein sequence using single-letter amino acid codes (A-Z, case insensitive). The calculator will ignore any non-amino acid characters and provide the total mass including one water molecule.

5. Frequently Asked Questions (FAQ)

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

Q2: Why is water mass added to the calculation?
A: The water molecule accounts for the -H and -OH groups at the N- and C-termini of the protein chain.

Q3: Are modifications like phosphorylation included?
A: No, this calculator only computes the unmodified protein mass. Post-translational modifications require additional mass adjustments.

Q4: What about selenocysteine (U) or pyrrolysine (O)?
A: These rare amino acids are not included in the current version of the calculator.

Q5: How accurate is this calculation?
A: The calculation uses published average isotopic masses and is typically accurate to within 0.1 Da for small proteins.