Advanced Peptide Mass Calculator

Calculator Inputs

Use the responsive input grid below. It shows three columns on large screens, two on smaller screens, and one on mobile.

Peptide Sequence

Supported one-letter codes: A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V, and U.

Mass Basis

Ion Mode

Reported Charge State

Max Charge for Plot

Oxidized Methionines

Phosphorylation Count

Custom Modification Label

Custom Modification Count

Custom Delta Each

Add N-terminal acetylation

Add C-terminal amidation

Carbamidomethylate all cysteines

Example Data Table

Example	Sequence	Mass Basis	Applied Modifications	Neutral Mass	Reported Ion	m/z
Simple tetrapeptide	ACDE	Monoisotopic	None	436.1264	[M+1H]1+	437.1337
Phosphorylated peptide	PEPTIDE	Average	N-terminal acetylation × 1; Phosphorylation × 1	921.8397	[M+2H]2+	461.9273
Modified sulfur-rich peptide	MCRSYK	Monoisotopic	C-terminal amidation × 1; Carbamidomethylation of cysteine × 1; Methionine oxidation × 1; Phosphorylation × 1	938.3503	[M+3H]3+	313.7907

Formula Used

Neutral peptide mass
Neutral Mass = Σ(residue masses) + H2O + terminal deltas + modification deltas

Positive-ion m/z
m/z = (Neutral Mass + z × proton mass) / z

Negative-ion m/z
m/z = |(Neutral Mass - z × proton mass) / z|

Average residue mass
Average Residue Mass = Σ(residue masses) / residue count

The calculator starts with residue masses for the sequence, adds one water molecule for the peptide termini, then applies selected terminal and chemical modification deltas. It finally converts the neutral mass to charge-state m/z using the selected ion mode.

How to Use This Calculator

Enter the peptide sequence using one-letter amino acid codes.
Select monoisotopic or average mass mode.
Choose positive or negative ion mode and enter the reported charge state.
Add optional terminal changes or common modifications.
Use custom delta fields for extra chemistry not covered by the built-in options.
Submit the form to display the result section above the calculator.
Review the summary, modification table, residue composition, and Plotly charge-state graph.
Download the result as CSV or PDF for reporting or lab records.

FAQs

1. What is the difference between monoisotopic and average mass?

Monoisotopic mass uses the lightest stable isotope for each atom. Average mass uses isotope-weighted averages. Monoisotopic values are common in high-resolution mass spectrometry, while average values are often used for lower-resolution or broader reporting.

2. Why does the calculator add water to the sequence total?

Residue tables usually list amino acid residues after peptide bond formation. A complete neutral peptide also includes terminal hydrogen and hydroxyl groups, which together equal one water molecule.

3. How is the reported m/z value calculated?

The calculator first determines the neutral peptide mass. It then adds or removes proton mass according to ion mode and divides by the chosen charge state. The result is the displayed mass-to-charge ratio.

4. Can I model common peptide modifications?

Yes. The page includes N-terminal acetylation, C-terminal amidation, carbamidomethylated cysteine, methionine oxidation, and phosphorylation counts. You can also supply a custom delta and count for other chemistries.

5. Why does oxidation count fail for some sequences?

Oxidation count is limited by the number of methionine residues present. If you enter a larger value than available methionines, the calculator stops and asks you to correct the input.

6. Why does phosphorylation count have a site limit?

This calculator checks phosphorylation against serine, threonine, and tyrosine counts. Entering more phosphorylation events than available S, T, and Y residues would create an unrealistic peptide model.

7. Which residue symbols are accepted?

The calculator accepts standard one-letter peptide codes and optional U for selenocysteine. Ambiguous or unsupported letters such as B, Z, X, and O are rejected to keep the mass model explicit.

8. What do the CSV and PDF files contain?

Both exports contain the calculation summary and residue composition data. They help with experiment notes, reports, and data transfer when you want to keep a portable record of the current peptide model.