About This Calculator
Peptide fragment ions help explain tandem mass spectra. A peptide breaks at each backbone bond. The calculator lists common product ions for every valid split. It supports a, b, c, x, y, and z series. It also supports several charge states and neutral loss rows. This makes early spectrum checks easier.
Why Fragment Ions Matter
Proteomics software uses theoretical fragments to match measured peaks. A strong match can confirm peptide identity. It can also reveal missed cleavages, residue changes, or unexpected shifts. Manual review still matters. A clear ion table helps you inspect key peaks without opening a large search suite.
Advanced Inputs
Enter a clean amino acid sequence first. Remove spaces, numbers, and labels. Select monoisotopic masses for high resolution data. Use average masses for low resolution work. Add fixed carbamidomethyl cysteine when the sample was alkylated. Custom residue shifts can model oxidation, phosphorylation, or labeling. Terminal shifts let you test tagged peptides.
Reading The Results
Each row shows an ion label, charge, fragment sequence, neutral mass, and mass to charge value. The cleavage column shows where the peptide bond was cut. Loss rows show water or ammonia loss from the same base ion. Use the minimum and maximum mass filters to focus on the active scan range.
Good Practice
The output is theoretical. It does not predict intensity. Instrument type, collision energy, charge mobility, and residue chemistry all affect real spectra. Proline rich peptides often fragment in special ways. Acidic and basic residues can change peak balance. Use this table as a fast guide, then compare it with actual peak lists.
Export And Review
The CSV export is useful for spreadsheets and search notes. The PDF export is useful for lab records. Keep the entered options with each report. That makes later checks easier. When several settings are tested, save each table separately. Clear records reduce mistakes during annotation and reporting.
Limits To Remember
Some fragments may be unlikely. The tool still reports them for comparison. This is helpful during broad annotation. Use sensible charge settings for your instrument. Very high fragment charges may clutter the table. For routine work, start with one and two charges, then expand only when spectra show higher charged peaks.