106 5977 Series MSD Operation Manual
4 Operating in Chemical Ionization (CI) Mode
To Use Other Reagent Gases
This section describes the use of isobutane or ammonia as the reagent gas. You
should be familiar with operating the CI-equipped 5977 Series MSD with
methane reagent gas before attempting to use other reagent gases.
Changing the reagent gas from methane to either isobutane or ammonia
changes the chemistry of the ionization process and yields different ions. The
principal chemical ionization reactions encountered are described in general
in the 5977 Series Concepts Guide. If you are not experienced with chemical
ionization, we suggest reviewing that material before you proceed.
CAUTION
Do not use nitrous oxide as a reagent gas. It radically shortens the life span of the
filament.
CAUTION
Not all setup operations can be performed in all modes with all reagent gases. See
Table 19 for details.
Table 19 Reagent gases
Reagent gas/mode
Reagent ion masses
PFDTD
Calibrant ions
Flow adj ions: Ratio
EI/PCI/NCI MSD Performance turbo pump
Recommended flow: 20% PCI 40% NCI
Methane/PCI 17, 29, 41
*
41, 267, 599 28/27: 1.5 – 5.0
Methane/NCI 17, 35, 235
†
185, 351, 449 N/A
Isobutane/PCI 39, 43, 57 N/A 57/43: 5.0 – 30.0
Isobutane/NCI 17, 35, 235 185, 351, 449 N/A
Ammonia/PCI 18, 35, 52 N/A 35/18: 0.1 – 1.0
Ammonia/NCI 17, 35, 235 185, 351, 517 N/A
* There are no PFDTD ions formed with any reagent gas but methane. Tune with methane and use the same parameters
for the other gas.
† There are no negative reagent gas ions formed. To pretune in negative mode, use background ions: 17 (OH-), 35 (Cl-),
and 235 (ReO3-). These ions cannot be used for reagent gas flow adjustment. Set the flow to 40% for NCI and adjust as
necessary to get acceptable results for your application.
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