ExactMass

ExactMass[molecule]⟹mass

computes the most probable exact mass of molecule.

ExactMass[oligomer]⟹mass

computes the most probable exact mass of a sequence, strand, or structure.

Details

ExactMass computes the most probable exact molecular mass arising from isotopic variation.
The exact mass of a molecule is a distribution of possible quantities because each atom can exist as one of multiple isotopes (with varying probability). Set OutputFormat to List or Distribution to view the full distribution of masses.
The MolecularWeight of a molecule is the mean of its exact mass distribution.
MonoisotopicMass represents the exact mass of a molecule in which each atom exists as its most frequently occurring isotope.

Input

Output

General Options

Examples

Basic Examples (4)

Compute the most probable exact mass of caffeine:

List the probabilities and exact masses for caffeine:

Compute the most probable exact mass of a Model[Molecule]:

ExactMass is listable:

Additional Examples (9)

Input Types (7)

Exact mass of a DNA sequence:

Exact mass of a peptide sequence:

Exact mass of a strand:

Exact mass of a strand with a modification:

Exact mass of a structure:

Exact mass of a Model[Molecule,Oligomer]:

Exact mass is listable across all valid input types:

Large Molecules: (2)

The monoisotopic mass of large molecules is often distinct from the most probable mass:

Options (9)

ExactMassProbabilityThreshold (2)

Exclude exact masses which occur with probability less than 10^-3:

Set the probability threshold and mass resolution to zero to do an exact calculation. Note that this can be computationally expensive, as even for small molecules there are a large number of possible exact masses:

ExactMassResolution (2)

Combine the probability of exact masses which differ by less than ExactMassResolution, replacing these masses with their probability-weighted center of mass:

Set the ExactMassResolution to 0.0 Dalton to disable averaging of similar masses. Note that this may generate a very large number of possible masses:

IsotopeDistribution (2)

Override the default isotope distribution of Carbon to be 100% Carbon-14:

Compute the ExactMass distribution of chloroform if the hydrogens are 99% deuterated:

OutputFormat (3)

By default, only the most probable mass is returned:

Set OutputFormat to List to return a list of {{probability,exact mass}..} pairs representing the distribution of exact masses:

Set OutputFormat to Distribution to return a Mathematica distribution object representing the discrete distribution of exact masses:

Messages (7)

DegenerateMassUncertain (1)

The exact mass of a degenerate monomer is not defined, and the average molecular weight of possible degenerate substitutions will be used instead:

InvalidExtinctionCoefficientsModel (1)

Show a warning if the Molecule field of input SLL object is not a valid Molecule[]:

missMatchPolymer (1)

Return $Failed if the input Strand could not be resolved to a valid type:

MoleculeInfoNotFound (1)

Show a warning if the Molecule field of input SLL object is not a valid Molecule[]:

nintrp (1)

Return $Failed if an invalid Molecule[] is provided:

UndefinedMass (1)

Show a warning if the Molecule field of input SLL object is not a valid Molecule[]:

UnknownComposition (1)

If the molecular composition of a Modification or Monomer is undefined, its averaged molecular weight will be used as an approximation when calculating exact mass: