Neutral losses and fragment groups

Accepts C6H12O6, Ca(OH)2, CuSO4·5H2O, [13C]6H12O6, SO42-; ion notation [M+H]+, [M+2H]2+, [2M+H]+, M-e.

Give an accurate mass (or m/z plus ionization) with a tolerance, and every formula inside the element limits is enumerated, ranked by nitrogen rule, RDBeq and isotope-pattern similarity.

Per-element binomial/multinomial expansion convolved across elements, binned by neutron number (M, M+1, M+2 …) with peak positions from exact masses; Gaussian broadening mimics the instrument response. The input can be a molecular formula or an amino acid composition (A3R2K1, termini included); pick a charge z and the peak table is reported on the m/z scale, with monoisotopic and average m/z on the cards.

Enter the precursor formula to list feasible neutral losses (are there enough atoms, what formula is left, how much mass), plus searchable fragment-group and adduct tables.

Sequences accept one-letter (PEPTIDE), three-letter (ALA-GLY-…) and modification syntax (P(Phos), [Cit+71.984]) plus termini (-NH2). The fragment table follows the a/b/c and x/y/z series with self-consistent complements and lists monoisotopic and average m/z on every row. Switching the input mode to amino acid composition (A3R2K1) gives the intact formula, masses and adduct average m/z when only the counts are known; a composition has no order, so no fragment or digest table is drawn.

Monomers are nucleoside monophosphates (dA 331.068 / dC 307.057 / dG 347.063 / dT 322.057 / dU 308.031), condensed into the strand; 5′/3′ ends can be hydroxyl or phosphate. Fragments are defined on the four cleavable phosphodiester-backbone bonds, so both sides of one bond add up to the parent strand.

End groups + Σ(repeat unit × count) + ionization: enumerate formula, monoisotopic/average mass and m/z for every n; the spacing between neighbouring n equals the repeat-unit mass.

Data comes from a NIST Atomic Weights and Isotopic Compositions snapshot, abundances normalised per element; bracketed standard atomic weights are IUPAC interval values.

Search by name, formula or tag; press Load to send a formula to the Formula tab and inspect its adducts and isotope envelope.