GC-MS: a hyphenated technique

Gas Chromatography Mass Spectrometry                                                               

The tallest peak is arbitrarily assigned an intensity of 100% and is known as the BASE PEAK.

The parent peak (or molecular ion M+.) may or may not be the base peak

GC-MS function:

GC-Separates components 

MS- (which consist of the ion source,mass analyser and detector):

  • Converts molecules into ions – normally positive but negative ions also
  • Separates/distinguishes ions according to their m/z ratios. For most ions m/z = mass
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chemical ionisation (soft ionisation)

                                                  Chemical Ionisation                                                  

There are two types of chemical ionisation reactions : – CI+ and CI-.

  • Positive ion CI (CI+) involves the direct interaction between reagent gas species and the sample molecules.
  • Negative ion (CI-) involves the capture of low energy electrons.

Both chemical ionisation reactions take place simultaneously in the source but the instrument detects only positive ions in CI+ and negative ions in CI- operation.

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Positive Ion Chemical Ionisation

Positive Ion Chemical Ionisation                                                                            

Some important reactions in PICI:

Proton transfer:   CH5+  +  M

                            CH4  +  (MH)+

(Quasimolecular ion (MH)+ has m/z value 1 amu greater than that of the molecular ion)

Electrophilic addition: 

 C2H5+  +  M  

  (M+C2H5)+

(Quasimolecular ion (M+C2H5)+ has m/z value 29 amu greater than that of the molecular ion)

Both reactions can occur in the same sample.

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Modes of ms operation 1. Full Scan Mode

Repeatedly scans a determined mass range e.g. 50-500 

Set scan time e.g. 1 scan/s – limited by instrument.  

 Advantage - Looks for all ions in the range all the time. Full mass spectrum for identification/library searching

Disadvantage – low ion counts for key ions of eluting compounds

To increase time spent on each mass - decrease mass range scan or increase scan time

But if scan time too slow may miss compounds as need 5 scans per peak (each scan is a data point in the chromatogram) or may not count all important

GC-MS chromatogram is 

1. all ions in every mass spectrum added together (total ion count) (TIC)  

2. specific ion(s) extracted (EIC) from the Full Scan data 

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modes of ms operation 2. Selected Ion Monitoring (

detects target compounds of known spectral characteristics with maximum sensitivity.

Typically three ions per compound – one for quantification, further two to calculate ion ratios to confirm identity e.g. methadone 294, 165, 72 – no full mass spectrum

Mass analyser only counts selected ions usually over a set retention time window when known compounds are eluting

Advantage - improves sensitivity and selectivity.

Disadvantage – doesn’t detect unknown compounds

chromatogram is selected ion count as function of time. Can view individual ion chromatograms or combined ion chromatograms.

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