Using GC-MS to identify sample peaks

  1. Run the sample on EI GC-MS (section 2.2.4.). Examine a peak of interest and make sure that it is a single peak with a symmetrical shape and single apex.
  2. Extract the mass spectrum associated with the peak.
  3. Select a background mass spectrum from a section of baseline (area lacking peaks) near the peak of interest. Subtract the background mass spectrum from the peak spectrum – commands vary between software packages.
  4. Search the mass spectral libraries (NIST, WILEY, and other self-defined libraries) for a match (minimally 80%, 90% for structurally similar compounds such as terpenes) between the peak spectrum and the mass spectra of known library standards.
  5. Closely compare the mass spectrum of the library standard against the mass spectrum of the unknown peak. This peak’s spectrum should have all of the ion fragments present in the library standard plus additional ion fragments from other minor compounds. If the spectrum is missing ions present in the library standard within the m/z sampling range, there is not a match. 
  6. Compare the ion fragment patterns of the compound of interest and the library standard to see if the fragment ratios are similar.
  7. Test the tentative identity of the unknown peak by running a synthetic chemical standard under identical chromatographic conditions as the sample of interest. To be a match, the synthetic standard should have an identical retention time and similar ion patterns as the peak of interest.
  8. Further test the match by running the sample and the synthetic standard separately under different chromatographic conditions (usually a different column type) to determine if the similarities hold.
  9. Confirm the match in retention time by co-injecting the sample with a known amount of the synthetic standard.  The two compound peaks should overlap completely. 
  10. Determine the mass of the molecular ion fragment (M+1, the molecular mass plus one additional mass unit) of the unknown peak and the synthetic standard peak by running the sample and standards on CI GC-MS.