Mass accuracy and calibration

Mass accuracy is the difference between the measured and the theoretical mass, expressed in parts per million of the theoretical value. It is a relative measure, which means the same ppm figure corresponds to very different absolute errors at different masses — and that is why the index sets its limits by compound class.

ppm  =  (m_observed − m_theoretical) / m_theoretical × 10⁶

At 342.23 Da (KPV):
  20 ppm = 0.0068 Da   —  well below one dalton; cannot distinguish a +1 Da species

At 1 024.52 Da (bremelanotide):
  20 ppm = 0.0205 Da   —  the 0.98 Da difference to melanotan II is 956 ppm
                          → distinguishable in principle at 20 ppm accuracy

At 4 810.41 Da (tirzepatide):
  20 ppm = 0.0962 Da   —  a deamidation (+0.98 Da) is 204 ppm
                          → distinguishable; a diastereomer (0 Da) is not, ever

Where drift comes from

• Temperature. A time-of-flight flight tube expands with temperature; a 1 °C change shifts calibration by several ppm. This is why laboratory temperature control appears on instrument specifications.
• Detector ageing. Gain changes shift the centroid of a peak subtly over months.
• Space charge. At high ion density the measured m/z shifts; the effect is concentration-dependent, so an overloaded injection reads differently from an on-scale one.
• Lock-mass absence. A continuously infused reference compound corrects drift in real time. Without it, calibration is only as good as the last external calibration.

Diagnostic sequence when a large error appears

1. Confirm the theoretical mass is monoisotopic, not average. This is the most common cause of a spurious flag on a large peptide.
2. Confirm the charge state assignment. An error of one in z produces a mass error of hundreds of daltons.
3. Check whether the observed mass matches a known adduct — sodium at +21.982, potassium at +37.956, or the same species at a different charge.
4. Check whether the observed mass matches a near-neighbour compound. Survodutide against tirzepatide, hexarelin against GHRP-6, bremelanotide against melanotan II.
5. Re-measure with a lock mass or after external recalibration. In the index's experience, 31 of 40 flagged records that were re-measured came back within tolerance.