Monoisotopic versus average mass

Carbon is 98.93 % ¹²C and 1.07 % ¹³C. A molecule with 187 carbons therefore exists as a distribution of isotopologues, and there are two different sensible ways to report its mass.

• Monoisotopic mass: the mass of the isotopologue in which every atom is its most abundant isotope. All ¹²C, all ¹H, all ¹⁴N, all ¹⁶O. This is the mass a high-resolution instrument measures when it resolves the isotope pattern and reports the first peak.
• Average (molecular) mass: the abundance-weighted mean over the whole isotope distribution. This is the mass a low-resolution instrument reports, because it cannot resolve the individual isotopologues and returns the centroid of the unresolved cluster. It is also the mass you get from a periodic table.

The size of the difference

The difference is approximately 600 ppm across the whole mass range, because it scales with the number of carbon atoms and so does the mass. That is forty times the index's tightest class limit. Comparing an observed monoisotopic mass against a theoretical average mass produces a mass error that looks like a serious identity problem and is entirely an arithmetic one.

Which to use

1. Below about 3 kDa on a high-resolution instrument, use monoisotopic. The isotope pattern is resolved and the monoisotopic peak is clearly visible.
2. Above about 10 kDa, the monoisotopic peak becomes vanishingly small relative to the rest of the distribution and average mass is the practical choice, reported from the centroid.
3. Between 3 and 10 kDa — where most of this index lives — it depends on the instrument's resolving power. State which was used. The index computes theoretical monoisotopic masses and requires observed monoisotopic values; where a report supplies an average mass, the index converts and records the conversion.