MS ADDUCT &
EXACT MASS CALCULATOR
Molecule Definition
Awaiting Molecule Data
Precision Mass Analysis
Our Advanced MS Adduct Calculator is built for the rigorous demands of analytical chemistry. Unlike basic mass calculators, we utilize a multi-isotope database (IUPAC standards) to model exact masses and theoretical isotopic envelopes for any molecular formula or peptide sequence.
Exact Mass Database
High-precision monoisotopic and average weights for the 15 elements of organic mass spectrometry, plus the common adduct cations.
Isotope Modeling
Dynamic isotopic profile visualization powered by canvas-based abundance analysis.
Reverse Search
Identify formulas from observed m/z values with configurable PPM error margins.
Adduct Classification
Support for common ESI/APCI adducts including Na+, K+, Cl-, and AcO-.
Peptide Engine
Automated Y-ion and B-ion fragmentation modeling for protein identification.
Computational Speed
High-speed combinatorial search algorithm for real-time formula matching.
MASTERING MASS
SPECTROMETRY ADDUCTS
In Electrospray Ionization (ESI), molecules rarely appear as neutral species. They typically gain or lose protons or associate with charge carriers like Sodium ($[M+Na]^+$) or Potassium. Understanding these adducts is vital for correct formula assignment.
01. Monoisotopic vs Average
Monoisotopic mass (used here) is the mass of the species containing only the most abundant isotope of each element. Average mass is the weighted mean based on natural abundance—useful for low-res MS but unsuitable for formula identification.
02. Understanding PPM Error
High-res MS (Orbitrap, Q-TOF) typically yields errors within 2-5 Parts Per Million (PPM). Our reverse search allows you to filter formulas within this tight window to eliminate false positives.
FREQUENTLY ASKED QUESTIONS
Q. Why do I see [M+Na]+ in my spectrum?
Sodium is a common impurity in glassware and solvents. Oxygen-rich molecules (ethers, alcohols, ketones) have a high affinity for Na+ cations during ionization.
Q. What is the Double Bond Equivalent (DBE)?
DBE (also called unsaturation degree) calculates the total number of rings and double bonds in a formula. A DBE below 0 indicates an impossible chemical structure.
Q. Can this handle multivalent charges?
Yes. By specifying the charge (z) in the settings, the calculator correctly adjusts the m/z ratio ($m/z = [m+H]/1$, $[m+2H]/2$, etc.).
How to calculate an exact mass and its adducts
Five steps from a formula to an m/z you can match against a spectrum.
Enter a formula, or a peptide sequence
The formula parser takes standard notation — C8H10N4O2 for caffeine — and the peptide mode takes a one-letter amino acid sequence and builds the formula from residue masses plus water. Peptide mode also gives you b and y fragment ions, which is what you need when reading a tandem spectrum rather than a precursor.
Read the monoisotopic mass, not the molecular weight
The calculator gives both. Monoisotopic mass uses the lightest stable isotope of every element and is what a high-resolution instrument measures; average molecular weight is the isotope-weighted mean and is what you use for a solution concentration. Comparing an observed m/z against average mass is one of the most common reasons a match fails to come out.
Match the adduct to your ionisation mode and mobile phase
Positive-mode ESI usually gives you [M+H]+, but sodium is unavoidable and ammonium appears whenever ammonium formate or acetate is in the buffer. Negative mode gives [M-H]-, with formate and acetate adducts from the same buffers. The table below lists every adduct the calculator computes with its exact mass shift.
Use isotope spacing to read charge state
Isotope peaks in a singly charged ion are about 1.0 apart; in a doubly charged ion they are 0.5 apart. That spacing is the most reliable way to work out charge from a spectrum, and it is why the calculator offers [M+2H]2+ and [M-2H]2- alongside the singly charged forms.
Work backwards from an observed m/z when you have no candidate
Reverse search takes a measured m/z, an adduct and a tolerance in ppm, and enumerates formulas that fit. Set the tolerance to your instrument's real accuracy — 5 ppm for a well-calibrated Orbitrap or TOF, wider for a quadrupole — because a loose tolerance returns dozens of formulas and tells you nothing.
The 10 adducts this calculator computes
Exact mass shift for each, and the reason it turns up — several come from your mobile phase rather than your sample.
| Adduct | Mode | z | Mass shift | When you see it |
|---|---|---|---|---|
| [M+H]+ | Positive | 1 | +1.007276 | The default in positive-mode ESI. One proton added, so m/z is the neutral monoisotopic mass plus 1.00728. |
| [M+NH4]+ | Positive | 1 | +18.033823 | Common when ammonium formate or acetate is in the mobile phase. Frequently mistaken for an unexplained +18 until you check the buffer. |
| [M+Na]+ | Positive | 1 | +22.989221 | Sodium is everywhere — glassware, solvents, skin — so this appears whether you want it or not. A peak 21.98 above your [M+H]+ is almost always this. |
| [M+K]+ | Positive | 1 | +38.963158 | Less common than sodium but the same story. Sits 37.96 above [M+H]+. |
| [M+2H]2+ | Positive | 2 | +2.014552 | Doubly charged, so the spacing between isotope peaks halves to 0.5 rather than 1.0. That spacing is how you read charge state off a spectrum. |
| [M-H]- | Negative | 1 | -1.007276 | The default in negative mode, for acids and anything that deprotonates readily. |
| [M+Cl]- | Negative | 1 | +34.968853 | Chloride attachment. Carries the chlorine isotope signature, so look for the M+2 partner at about a third the height. |
| [M+HCOO]- | Negative | 1 | +44.998201 | Formate adduct, from formic acid or ammonium formate in the mobile phase. |
| [M+CH3COO]- | Negative | 1 | +59.013851 | Acetate adduct, from acetic acid or ammonium acetate. |
| [M-2H]2- | Negative | 2 | -2.014552 | Doubly deprotonated, the negative-mode counterpart to [M+2H]2+. |
Mass shifts are applied to the neutral monoisotopic mass and divided by charge. Isotope envelopes are modelled for C, S, Cl, Br, N, O.
What the numbers mean at the instrument
Five things worth knowing before you trust a match, including exactly which 15 elements are covered.
- Monoisotopic mass versus average molecular weight
- Monoisotopic mass sums the lightest stable isotope of each element: carbon as exactly 12.000000, hydrogen as 1.007825. Average molecular weight sums each element weighted by natural isotope abundance: carbon as 12.011 because 1.07% of it is carbon-13. For caffeine the two differ by roughly 0.1 — trivial on a quadrupole, enormous at 5 ppm. High-resolution instruments measure the monoisotopic peak, so that is the number to compare against.
- Chlorine and bromine announce themselvesCl 3:1 · Br 1:1
- Chlorine is about 76% ³⁵Cl and 24% ³⁷Cl, so one chlorine gives an M+2 peak roughly a third the height of the monoisotopic peak. Bromine is almost half and half, so one bromine gives an M+2 peak of nearly equal height — a pair of twin peaks two mass units apart is a bromine until proven otherwise. Two chlorines give a 9:6:1 triplet. Reading the M+2 ratio tells you the halogen count before you calculate anything.
- Sodium is not a contaminant you can avoid
- Sodium leaches from glass, sits in solvents and comes off skin, so [M+Na]+ turns up in almost every positive-mode spectrum whether or not you added any. The practical consequence: a peak exactly 21.98 above your protonated ion is the sodium adduct of the same compound, not a different species. Recognising that spacing saves a lot of wasted formula searching.
- What the reverse search actually searches
- It enumerates carbon up to 60, nitrogen up to 10 and oxygen up to 20, with sulfur, phosphorus, chlorine and bromine enabled individually. That covers most small-molecule and metabolite work and deliberately does not cover everything: an unbounded search over fifteen elements returns so many formulas at any realistic tolerance that the result is meaningless. Narrow the tolerance and enable only the heteroatoms your chemistry could plausibly contain.
- Fifteen elements, chosen for organic mass spectrometry
- The mass table covers H, C, N, O, F, P, S, Cl, Br, I, Na, K, Li, B and Si — the elements that appear in organic and pharmaceutical work plus the cations that form adducts. It is not a full periodic table, and for organometallic or inorganic work with transition metals you will need a tool that models those isotope envelopes properly.
Frequently asked questions
What is an adduct in mass spectrometry?
An ion formed when your neutral molecule picks up or loses a small charged species during ionisation, rather than being ionised directly. In positive-mode electrospray that is usually a proton, but sodium, potassium and ammonium are all common; in negative mode it is loss of a proton, or attachment of chloride, formate or acetate. Each shifts the observed m/z by a known amount, so identifying the adduct is what lets you work back to the neutral mass.
What are the most common adducts, and what mass do they add?
In positive mode: [M+H]+, [M+NH4]+, [M+Na]+, [M+K]+ and the doubly charged [M+2H]2+. In negative mode: [M-H]-, [M+Cl]-, [M+HCOO]-, [M+CH3COO]- and [M-2H]2-. The table on this page lists the exact mass shift for each, along with when you should expect to see it — several of them come from your mobile phase rather than your sample.
What is the mass of a sodium adduct?
A sodium adduct adds 22.98922 to the neutral monoisotopic mass, against 1.00728 for a proton. The useful number in practice is the difference: [M+Na]+ sits 21.98 above [M+H]+ for the same compound. If you see two peaks with that spacing, they are the same molecule with different cations, and you should not be searching formulas for the second one.
What is the difference between monoisotopic mass and molecular weight?
Monoisotopic mass uses the lightest stable isotope of each element — carbon exactly 12.000000. Average molecular weight weights each element by natural isotope abundance — carbon 12.011, because about 1% is carbon-13. High-resolution instruments measure the monoisotopic peak, so that is the value to compare an observed m/z against; average weight is for weighing out material. The gap widens with molecule size, which is why it matters more for peptides than for small molecules.
How do I tell the charge state of an ion?
From the spacing between isotope peaks. Singly charged ions have isotope peaks about 1.0 apart, doubly charged about 0.5, triply charged about 0.33 — because the mass difference of one neutron is divided by the charge. If a cluster of peaks is 0.5 apart, you are looking at a 2+ ion and the neutral mass is roughly twice the m/z.
How do I know if my compound contains chlorine or bromine?
Look at the M+2 peak. One chlorine gives an M+2 about a third the height of the main peak, because ³⁵Cl and ³⁷Cl are roughly 76:24. One bromine gives an M+2 of almost equal height, because ⁷⁹Br and ⁸¹Br are close to 50:50. Two chlorines give a 9:6:1 pattern across M, M+2 and M+4. That ratio identifies the halogen count directly from the spectrum.
What ppm tolerance should I use for a formula search?
Match it to your instrument. A well-calibrated Orbitrap or TOF is good to about 5 ppm, so 5 is a sensible default; a quadrupole needs much wider and correspondingly returns far more candidates. Widening tolerance to force a match defeats the point — at 50 ppm on a mass of 300 you are searching a window of 0.015, which admits many formulas, and the search will happily give you all of them.
Does it handle peptides?
Yes. Enter a one-letter amino acid sequence and it builds the formula from residue compositions plus water, then reports the monoisotopic mass and the b and y fragment ions. Fixed and variable modifications are not modelled, so for a search involving phosphorylation or other PTMs you want dedicated proteomics software.
Which elements are supported?
Fifteen: H, C, N, O, F, P, S, Cl, Br, I, Na, K, Li, B and Si — the elements that appear in organic and pharmaceutical mass spectrometry plus the common adduct cations. Isotope patterns are modelled for carbon, nitrogen, oxygen, sulfur, chlorine and bromine. Transition metals and the rest of the periodic table are not covered.
Is my data sent anywhere?
No. Formula parsing, exact mass, isotope modelling and the reverse search all run in your browser. There is no account and nothing is uploaded, which also means the reverse search is limited by your own device rather than by a server quota.