Calculator Inputs
Example Data Table
| Compound | Parent Formula | Fragment Formula | Neutral Loss | Adduct | Charge | Calculated m/z |
|---|---|---|---|---|---|---|
| Glucose fragment | C6H12O6 | C5H10O5 | CH2O | [M+H]+ | 1 | 151.060100 |
| Benzoate ion | C7H6O2 | C7H6O2 | None | [M-H]- | 1 | 121.029503 |
| Acetophenone fragment | C8H8O | C7H7O | CH | [M+H]+ | 1 | 108.056966 |
Formula Used
1. Neutral exact mass: Sum every element count multiplied by its monoisotopic atomic mass.
2. Fragment neutral mass: Parent neutral mass minus neutral loss mass, or the exact mass of the fragment formula when supplied.
3. Ion mass: Fragment neutral mass plus adduct mass plus isotope index multiplied by 1.00335483507 Da.
4. Mass-to-charge ratio: m/z = ion mass / charge state.
5. Mass defect: Exact fragment mass minus its integer floor.
6. DBE estimate: DBE = (2C + 2 + N - H - X) / 2, where X includes F, Cl, Br, and I.
7. PPM error: ((observed m/z - calculated m/z) / calculated m/z) × 1,000,000.
How to Use This Calculator
- Enter the parent molecular formula exactly as elemental symbols and counts.
- Add a fragment formula if you already know the proposed fragment composition.
- Otherwise, enter a neutral loss formula or an additional loss mass.
- Select positive or negative mode, then choose the matching adduct.
- Set the charge state and the isotope peak you want to inspect.
- Optionally enter an observed m/z to calculate the ppm error.
- Submit the form and review the result block above the form.
- Download the summary as CSV or PDF after calculation.
What This Page Helps You Check
This calculator supports exact-mass fragment checking for common small-molecule workflows. It is useful when you want a fast estimate of whether a candidate fragment formula, neutral loss pattern, or adduct assignment matches an expected mass spectrum peak.
You can work from a known fragment formula, or start only with a parent formula and a loss hypothesis. That makes the page practical for quick screening during interpretation of LC-MS, GC-MS, or direct infusion fragment evidence.
The isotope table gives a simple carbon-based abundance estimate for nearby peaks. It is not a full elemental fine-structure simulator, but it helps with quick pattern checks and with basic peak spacing validation across different charge states.
The DBE estimate helps you check whether a proposed fragment remains chemically plausible. The ppm field is useful when you already have an observed instrument value and want a fast comparison against the calculated m/z from the fragment assignment.
Because this tool uses direct formula parsing, keep entries clean. Avoid parentheses, hydrate dots, charges inside the formula string, or vendor-specific annotation styles. Enter the neutral molecule formula first, then set ion mode and adduct separately.
FAQs
1. What does the fragment formula field do?
If you know the proposed fragment composition, enter it there. The calculator then uses that exact fragment mass directly instead of deriving the fragment only from parent mass and losses.
2. Can I calculate a fragment using only a neutral loss?
Yes. Leave the fragment formula blank and enter a neutral loss formula, extra loss mass, or both. The page subtracts that total loss from the parent neutral mass.
3. Why is the isotope pattern only an estimate?
The quick pattern uses a simple carbon-based abundance model. It is useful for screening nearby peaks, but it does not replace full isotopic fine-structure or instrument-response modeling.
4. What is the difference between exact mass and m/z?
Exact mass refers to the neutral or ion mass from monoisotopic atomic masses. m/z is the ion mass divided by the selected charge state seen by the instrument.
5. How should I enter adducts?
Enter the neutral molecular formula in the formula fields. Then choose ion mode and adduct separately from the controls. That keeps the formula parsing clean and consistent.
6. What does the DBE value help with?
DBE gives a fast unsaturation estimate. It helps you judge whether a proposed fragment composition is chemically reasonable before spending more time on deeper structural interpretation.
7. Why can fragment and loss calculations disagree?
If you enter both a fragment formula and a neutral loss, the page compares them. A nonzero delta means those two assumptions do not describe the same fragment mass.
8. Can I use formulas with parentheses or embedded charges?
No. This version accepts plain molecular formulas made from element symbols and counts. Enter charges with the ion mode and charge fields instead of the formula text.