Calculator inputs
Use the form below to compute peptide precursor mass and backbone fragment ladders.
Examples: M[+15.9949], C[+57.0215], S[+79.9663]
Example data table
This example uses the peptide PEPTIDE with no terminal shifts and a 2+ precursor.
| Example Item | Value | Why It Matters |
|---|---|---|
| Neutral peptide mass | 799.360005 Da | Defines the uncharged molecular mass before protonation. |
| [M+2H]2+ precursor | 400.687279 m/z | Shows the expected doubly charged precursor signal. |
| b3+ | 324.155416 m/z | Tracks the N-terminal ladder after the third residue. |
| y4+ | 477.219141 m/z | Tracks the C-terminal ladder for the final four residues. |
Formula used
For an unmodified peptide, the neutral peptide mass equals the sum of residue masses plus the terminal group masses. This becomes residue sum plus H and OH, which is equivalent to adding water.
Core equations
- Peptide neutral mass = residue sum + N-term + C-term
- an neutral = N-term + prefix sum − CO − H
- bn neutral = N-term + prefix sum − H
- cn neutral = N-term + prefix sum + NH2
- xn neutral = C-term + suffix sum + CO − H
- yn neutral = C-term + suffix sum + H
- zn neutral = C-term + suffix sum − NH
- m/z = (neutral mass + z × proton mass) ÷ z
Neutral loss handling
Optional satellite ions are reported for a, b, and y series.
- −H2O losses are enabled when the fragment contains S, T, E, or D.
- −NH3 losses are enabled when the fragment contains R, K, N, or Q.
- Inline mass shifts and terminal shifts are added before charge conversion.
- Common presets cover carbamidomethylated cysteine and oxidized methionine.
How to use this calculator
- Enter a peptide sequence. You may also add inline shifts such as M[+15.9949].
- Choose the precursor charge and the highest fragment charge to report.
- Select the ion series you want to inspect, such as b and y or the full a/b/c/x/y/z set.
- Add terminal shifts when your peptide carries custom N- or C-terminal chemistry.
- Enable common fixed changes if every cysteine is carbamidomethylated or every methionine is oxidized.
- Turn on optional neutral losses when you want a, b, and y satellite ions.
- Press the calculate button. The result section appears above the form, directly below the header.
- Review the plot, scan the fragment table, and export the report as CSV or PDF.
Frequently asked questions
1) What does this calculator return?
It returns theoretical precursor mass, precursor m/z, and fragment-ion m/z values across selected cleavage sites. It also lists charge states, optional neutral losses, and a plot for rapid visual inspection.
2) Can I enter modified residues?
Yes. Add numeric inline shifts in brackets after a residue, such as M[+15.9949]. The calculator adds that shift to the residue before computing precursor and fragment masses.
3) Which ion series are supported?
The calculator reports a, b, c, x, y, and z series. You can enable only the ladders you need or inspect all six families at once.
4) Why do some neutral-loss ions appear?
When enabled, the calculator adds water-loss and ammonia-loss satellite ions for eligible a, b, and y fragments. This helps mirror common interpretation workflows for peptide tandem spectra.
5) Does the tool handle terminal chemistry?
Yes. You can add custom N- and C-terminal mass shifts. Those changes affect the precursor mass and every fragment that contains the modified terminus.
6) Is the output measured or theoretical?
The output is theoretical. It does not read raw spectra or score experimental peaks. Use it to predict ions before or during manual spectrum interpretation.
7) What export options are included?
You can download the fragment table as CSV for spreadsheet work or create a PDF report for sharing, printing, or method documentation.
8) Why are monoisotopic masses useful here?
Monoisotopic values are commonly used for accurate peptide and fragment matching in tandem mass spectrometry. They provide sharper theoretical targets than average masses during sequence interpretation.