Reading Mass Spectrometry Data
How to interpret mass spectrometry reports and understand what the data tells you about peptide identity.
Last updated: 16 April 2026
What mass spectrometry does
Mass spectrometry ionizes molecules and measures their mass-to-charge ratios. For peptides, it determines the molecular weight with high precision. This confirms the peptide has the correct sequence and mass.
A peptide's theoretical molecular weight is calculated from its amino acid composition. The measured mass should match this within the instrument's tolerance (typically ±0.05%).
Reading a mass spec report
Look for: the measured mass, the theoretical mass, the deviation (usually expressed in ppm — parts per million), and the method used (MALDI, ESI, etc.). A small deviation confirms identity.
The spectrum itself should show a clear peak at the expected mass. Multiple peaks or noise suggest either impurity or poor data quality.
Interpretation limits
Mass spec confirms molecular weight and identity. It does not measure purity — a 50% pure peptide will show the same mass peak as a 99% pure one. Use HPLC to assess purity.
For complex peptides or those with post-translational modifications, interpreting mass spec requires expertise.
Mass spec red flags
No spectrum shown, only a summary number. Measured mass far from theoretical mass. No mention of method or tolerance. Multiple unexplained peaks.