MassCalc Molecular Formula & Mass Spectrometry Calculator - exact mass, isotope distribution, MF finder

Molecular formula calculation

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

What this tool is

MassCalc is a molecular formula and mass-spectrometry toolkit: give it a formula and it returns monoisotopic, average and nominal mass, element composition, RDBeq and adduct m/z values, and computes the isotope distribution from NIST abundances. Give it an accurate mass or m/z and it enumerates every candidate formula within your element limits and tolerance, ranking them with the nitrogen rule, RDBeq and your measured isotope peaks. It also covers peptide and oligonucleotide fragment tables, enzyme digests, polymer oligomer distributions, neutral losses and an exact-mass compound library. Peptides accept a full sequence or just an amino acid composition such as A3R2K1, and report monoisotopic and average m/z side by side.

Everything runs inside your browser: the algorithms and the data (a NIST snapshot of 94 elements and 298 isotopes, plus residue / modification / adduct / loss / compound dictionaries) ship with the page. There is no backend and nothing is uploaded.

Features

Formula parsingNested brackets Ca(OH)2, K4(Fe(CN)6); hydrates CuSO4·5H2O / MgSO4*7H2O; isotope labels 13C2, [13C]6; trailing charges SO42-, Fe3+; ion notation [M+H]+, [M+2H]2+, [M+Na+K-2H]2+, [2M+H]+, M-e.

Three mass basesMonoisotopic mass (lightest stable isotope combination), average mass (standard atomic weights) and nominal mass (integer mass numbers) for the same formula, with an element table and RDBeq.

Isotope distributionExact per-element expansion convolved across elements, binned by neutron number (M, M+1, M+2 …) and positioned by exact mass; stick plot or Gaussian profile makes the Br/Cl/S/Fe signatures obvious. Accepts a molecular formula or an amino acid composition (termini included), and with a charge selected the table is on the m/z scale with monoisotopic and average m/z reported.

MF finderEnumerate all formulas inside your element ranges and ppm tolerance, with mass error, RDBeq and nitrogen-rule flags; paste measured isotope peaks to rank candidates by cosine similarity.

Peptides and oligonucleotidesResidue tables with modifications (phospho, acetyl, methyl…) and termini give formula and mass; enter a full sequence or just an amino acid composition such as A3R2K1, and every intact mass and fragment comes out as monoisotopic and average m/z side by side; fragment tables cover the a/b/c and x/y/z series, secondary ions and multiple charges, plus enzyme digest product lists (trypsin, Lys-C, Glu-C, Asp-N …).

Polymer distributionsPresets for PEG, mPEG, PLA, polystyrene, PMMA, nylon 6 and PDMS, or your own end groups and repeat units, enumerated per n with formula and m/z to match MALDI/ESI adduct series.

Reference librariesNeutral-loss table (atom feasibility and the remaining formula), fragment-group library, 173 common compounds with exact masses and the 94-element isotope table.

Local and shareableNo network calls during calculation; inputs are encoded into the URL hash so a copied link reproduces exactly what you see. Dark/light theme and Simplified / Traditional Chinese / English.

How to use it

Type a formula in the Formula tab, pick one or more ionizations and read off the masses, composition table, adduct m/z list and isotope stick plot.

When you only have an accurate mass or a peak, go to MF finder: enter m/z, ionization, ppm tolerance and allowed elements, then compare the candidates by error and RDBeq.

For sequence work, fill in the Peptides or Oligonucleotides tab with a sequence (peptides also accept a plain amino acid composition), pick termini, modifications, series and charges, then copy the whole table out.

Press Copy link to share the current result; reloading the page keeps your inputs.

Frequently asked questions

Monoisotopic or average mass?

Use the monoisotopic mass (the lightest stable isotope combination) for high-resolution formula assignment and theoretical exact masses; use the average mass (standard atomic weights) for weighing out material, assay content and average molecular weights. Molecules with several Br or Cl atoms differ by whole daltons, so the tool always shows both.

How is the [M+H]+ m/z computed?

Atomic masses in the table are neutral-atom masses (electrons included), and a net charge z means z fewer electrons, so ion mass = Σ atomic masses − z·m(e) and m/z divides that by |z|. That makes [M+H]+ exactly «neutral + one proton mass (1.00728)» and [M-H]- exactly «neutral − one proton mass», with no double-counted electrons.

How accurate is the isotope pattern?

It uses a NIST natural-abundance snapshot (94 elements, 298 isotopes) and exact binomial/multinomial expansion, matching the major simulators (chemcalc.org, IsoPro) to the last decimal places shown. It models natural abundance only - no rearrangement chemistry, no instrument mass bias.

Can I enter a structure (SMILES / InChI)?

No, this page takes molecular formulas. Converting SMILES needs a chemistry structure parser, a separate concern: convert the structure to a formula with any public converter and paste it here. The compound library already carries formulas for 173 common substances.

Is anything uploaded?

No. Every calculation happens in the browser and the page has no backend; your input only enters the URL when you deliberately press Copy link.

MassCalc Molecular Formula & MS Toolkit

Molecular formula calculation

Find the formula from m/z

Isotope distribution calculator

Neutral losses and fragment groups

Peptide mass, amino acid composition, digest and fragments

Oligonucleotide mass and fragments

Polymer oligomer distribution

Element and isotope data

Exact masses of common compounds

What this tool is

Features

How to use it

Frequently asked questions

Each section has its own page

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