Installation manual

Operating in Chemical Ionization (CI) Mode 4
5975 Series MSD Operation Manual 113
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 From the Tune and Vacuum Control view, perform a standard Positive CI
autotune with methane and PFDTD.
2 Under the Setup menu, click CI 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 Select Gas B. Follow the instructions and 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
don’t want to overwrite the existing values. Accept the default temperature
and other settings.
4 Click Isobutane (or Ammonia) Flow Adjust on the Setup 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).