Laboratory glossary
Molecular mass, molar mass and vial content
A mass-related value for a defined chemical entity; interpretation requires the stated form and convention.
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The distinction that matters
A free base, salt and complex should not be interchanged in a calculation without checking composition.
What the value expresses
Molecular mass is the sum of the constituent atomic masses for the declared molecular formula. For a peptide, that formula depends on sequence and terminal chemistry. The expected value is calculated from the structure and then compared with the measured mass, rather than allowing a measured value to define an unspecified structure.
The dalton, Da, also called the unified atomic mass unit, u, is one twelfth of the mass of a carbon-12 atom. Molar mass refers to one mole and is expressed in g/mol; its numerical value corresponds to the molecular mass in Da at ordinary laboratory precision. Relative molecular mass, Mr, is dimensionless. Consult the compound data sheet for its stated convention.
Average and monoisotopic mass
Average mass weights elemental isotope masses by their natural abundances. Monoisotopic mass uses one isotope per element, conventionally the most abundant isotope: for common peptide elements these include carbon-12, hydrogen-1, nitrogen-14, oxygen-16 and sulfur-32. The distinction generally becomes larger as molecular size increases.
Spectral resolution and data processing determine which mass can be reported. Where an isotopic pattern is resolved and assigned, a monoisotopic mass may be available; other results may use an average-mass convention. Comparing unlike conventions can create a discrepancy unrelated to sample identity. The certificate should state the convention used.
Calculations that depend on molecular mass
Converting a mass quantity into a molar concentration, such as µM or mM, requires division by the applicable molar mass. This connects a documented material quantity with an amount-of-substance calculation.
- For a compound with molar mass 1000 g/mol, 1 mg corresponds to 1 µmol. At a fixed mass, increasing molar mass decreases the number of moles.
- Using the wrong molecular form or mass biases a stock prepared to a target molar concentration, and every derived dilution inherits that error.
- Mass differences can reflect recognizable chemical changes: water contributes about 18 Da, while C-terminal acid and amide forms differ by about 1 Da.
Molecular mass is not powder composition
A lyophilized solid can include counterions from purification, such as acetate or trifluoroacetate, and residual water. A published molecular mass may refer to the free peptide, while weighed vial material includes those additional components. Verify the declared basis.
- Treating all gross milligrams as free peptide can overestimate the actual molar concentration. Batch-specific net peptide content, when available, helps close that calculation.
- Mass agreement supports identity but does not establish purity. Batches with the same target mass can contain different amounts or patterns of impurities.
Common confusion
Molecular mass is not the amount supplied in a vial. Different vial sizes of the same molecular form have the same molecular mass but different total quantities. Converting mass to moles requires both. A separate pitfall is comparing average mass with monoisotopic mass, producing an apparent identity discrepancy simply because the conventions differ.
How to record it
Entity, unit, chemical form and mass convention used.