Operating in Chemical Ionization (CI) Mode 4
5975 Series MSD Operation Manual for MassHunter 119
Ammonia CI
Ammonia (NH
3
) is commonly used for chemical ionization when less
fragmentation is desired in the chemical ionization spectrum. This is because
the proton affinity of ammonia is higher than that of methane; hence less
energy is transferred in the ionization reaction.
Because many compounds of interest have insufficient proton affinities,
ammonia chemical-ionization spectra often result from the addition of NH
4
+
and then, in some cases, from the subsequent loss of water. Ammonia reagent
ion spectra have principal ions at m/z 18, 35, and 52, corresponding to NH
4
+
,
NH
4
(NH
3
)
+
, and NH
4
(NH
3
)
2
+
.
To adjust your MSD for isobutane or ammonia chemical ionization, use the
following procedure:
Procedure
1 Perform a standard Positive CI autotune with methane and PFDTD. See
“To Perform a PCI Autotune (Methane Only)” on page 124.
2 In the Tune and Vacuum Control view from the Tune menu, click Tune Wizard
and when prompted select Isobutane or Ammonia. This will change the
menus to use the selected gas and select appropriate default tune
parameters.
3 When prompted, select Gas B. (the port where Isobutane or Ammonia is
plumbed). Continue to the prompts from the Tune Wizard and set the gas
flow to 20%.
If you use an existing tune file, be sure to save it with a new name if you do
not want to overwrite the existing values. Accept the default temperature
and other settings.
4 Click Isobutane (or Ammonia) Flow Adjust on the Execute menu.
There is no CI autotune for isobutane or ammonia in PCI.
If you wish to run NCI with isobutane or ammonia, load NCICH4.U or an
existing NCI tune file for the specific gas.
NOTE
Be sure to read the following application note: Implementation of Ammonia Reagent
Gas for Chemical Ionization on the Agilent 5975 Series MSDs (5989-5170EN).
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