1. GCMS Ionization Modes
for the QP2010 Plus:
EI, CI and NCI
Bill Dougherty – September 30, 2008

2. © 2007 SHIMADZU2
GCMS Ionization Modes
EI: Electron Ionization
CI (or PCI): Positive ion Chemical Ionization
NCI: Negative ion Chemical Ionization
All 3 ionization mode use the same filaments.
No additional (secondary) rotary pump is
required to perform CI or NCI.

3. © 2007 SHIMADZU3
QP2010 Plus Models
EI: + Ion Detection
Just uses filament for ionization
Positive ion detection
EI and PCI: + Ion Detection
Needs extra reagent gas plumbing,
electronics, ion box and reagent gas
EI, CI and NCI: + and – Ion Detection
Needs third ion box and extra power supplies
and boards to change polarity of lens,
quadrupole and conversion dynode voltages.

4. © 2007 SHIMADZU4
Modifications to FilamentModifications to Filament
The filament wire is heavier
gauge. Possible warping of
filaments is reduced.
Aperture is enlarged to allow
transmission of more
electrons.
Improved filaments now being
used on GCMS-QP2010 and
GCMS-QP2010s
Result: Filaments can be
operated at higher emission
current (150µA) to produce
more ions.
More ions =
increased
sensitivity
225-10340-91

5. © 2007 SHIMADZU5
New Filament vs. Old Filament
New Filament: 225-10340-91
Changed coil windings, support distance and size of shield
window to make less susceptible to bending.
Average lifetime of 1000 hours at 150 microamps.
Old Filament: 225-10197-91
Average lifetime of 1500 hours at 60 microamps.

6. © 2007 SHIMADZU6
EI – Electron Ionization
The electron source filament has
high current that puts electrons on
its surface.
Electrons on the filament surface
are accelerated into the ion
chamber because it is 70 Volts
more positive than the filament.
The “Ionization Voltage” is 70 Volts.
The average “Electron Energy” is
70eV (Electron Volts).
Determines how much the molecule
is fragmented, the appearance of
the mass spectrum.
70eV is the standard set for all
GCMS.
All GCMS library spectra are
acquired at this energy.

7. © 2007 SHIMADZU7
EI – Creation of + Ions
High energy filament electron
(70eV) passes by and transfers
energy to Benzophenone.
Benzophenone internalizes this
energy then dissociates electrons
within bonds of its atoms.
Bonds come apart
Fragments are created
Fragments are missing electrons
therefore they are + charge
The more energy that is transferred
from the filament electron to the
molecule; the more fragmentation
of molecule.

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EI – Ion Box open to vacuum
For the molecules to dissociate electrons and
form ions they must stay isolated from other
species or they will give away energy to other
species and not form ions.
The space in the ion chamber must be at low
pressure to keep the molecules isolated.
The EI on box and repeller plate have large openings
so that the ion chamber is at low pressure

9. © 2007 SHIMADZU9
EI Mass Spectrum of Benzophenone
The EI mass spectrum for Benzophenone below shows the
distribution of ions created by dissociation of electrons.
Benzophenone molecules that absorb more energy from the filament
electrons fragment more, like m/z 51 and 77.
Benzophenone molecules that fragment less produce the base peak
ion at m/z 105
The benzophenone molecular ion is m/z 182, it dissociated only one
electron and did not fragment.

10. © 2007 SHIMADZU10
Positive ions are attracted to -70 Volt Filament without
shielding and increased distance. Positive ion transmission to
the lenses, quadrupoles and detector is increased.
GCMS-QP2010 GCMS-QP2010 Plus
:Filament
: Electrical
field : Flow of ions
: Ion source (set temperature)
: Ion source (Above set temperature)
: Heat rays
shield plate
Ion Source

11. © 2007 SHIMADZU11
QP2010 PlusQP2010
The ions are extracted by the electric potential formed by the second lens
(Lens 2).
The filament electric potential (-70V,10V)does not penetrate the ion box.

12. © 2007 SHIMADZU12
Huge Improvement in ion extraction efficiency
QP2010 PlusQP2010
The ions are extracted only in the direction of the mass analyzer.
Ion transmission is greatly improved.
Mass analyzer

13. © 2007 SHIMADZU13
Chemical Ionization – CI & NCI
Ion Box must be pressurized with reagent
gas with high vacuum on its outside.
CI (PCI) box needs higher pressure;
holes in it are smaller than NCI box.
Filament holes are very small
PCI has 2 holes; NCI has 4 holes
Ion exit hole is small
Repeller electrode “spacer” seals ion box.
Spacer has no hole for DI probe if not used.

14. © 2007 SHIMADZU14
Ion Box and Spacer – EI, CI & NCI

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Chemical Ionization Reagent Gases
3 possible types of reagent gas
Methane (CH4)
cheapest, most common, cleanest
Isobutane (C4H10)
softer ionization for more fragile molecules
expensive, “hard to come by,” purity not so good
Ammonia (NH3)
negative ion for alcohols, destructive to rotary pump oil and
rotary pump
2 Reagent Gas Ports on back of MS
Can select from 2 types of reagent gas when perform
autotune.

16. © 2007 SHIMADZU16
Chemical Ionization – CI & NCI
Definition of Chemical Ionization:
Some part of the reagent gas molecule must end up
as part of the ion that is detected.
Positive Ion Chemical Ionization
Called CI (or PCI)
Addition of proton or + ion from reagent gas
Negative Chemical Ionization
Called NCI
Addition of electron from filament
Jokingly referred to as “Not Chemical Ionization.”

17. © 2007 SHIMADZU17
CI – Positive Ion Chemical Ionization
CI adds positively charged ions of the reagent
gas to the sample molecules with much less or no
fragmentation, compared to EI.
The ion chamber must be pressurized with the reagent
gas. (To reduce fragmentation and create abundant
reagent gas ions.)
Filament electrons ionize the reagent gas producing +
charged reagent gas ions.
Sample molecules to be ionized must be able to
capture a proton or + charged reagent gas ion.
A “molecular adduct ion” is created when the + ion is
created with no fragmentation. This identifies the
molecular ion; the main reason for chemical ionization.

18. © 2007 SHIMADZU18
CI with Methane Reagent Gas
Methane, CH4, produces these ions:
CH5+ (17 amu)
Adds a proton (+1 amu) to the sample molecule
C2H5+ (29 amu)
Combines with sample molecule
C3H5+ (41 amu)
Combines with sample molecule

19. © 2007 SHIMADZU19
Benzophenone – EI vs. CI Spectra
EI
M = 182
CI
M+1=183
M+29=211
M+41+223

20. © 2007 SHIMADZU20
NCI – Negative Chemical Ionization
NCI adds negatively charged electrons from the
filament to the sample molecules with less
fragmentation than EI.
The ion chamber must be pressurized with the reagent
gas to reduce fragmentation.
Reagent gas pressure does not need to be as high as for CI.
Filament electrons lose energy to the buffer gas.
Sample molecules form negative ions by capturing low
energy filament electrons.
Sample molecules to be ionized must be able to
capture an electron. The same types of molecules that
are detected by an ECD are also detected by NCI.
NCI is “ECD with Quadrupoles.”

21. © 2007 SHIMADZU21
Hexachlorobenzene – EI vs. NCI
The mass of
an electron is
negligible
compared to 1
amu.
The ion is
the same
mass whether
it loses (EI) or
captures (NCI)
an electron.

22. © 2007 SHIMADZU22
NCI Ion Box “Sub” modes
You need to break vacuum to change
between the EI, CI or NCI ion box.
Without changing the ion box you can use
the NCI ion box to run:
SEI, SCI and NCI (all 3 ionization modes)
SCI is CI using the NCI ion box
SEI is EI using the NCI ion box
The software will run autotune for each or all
of the 3 modes NCI, SCI and SEI.
The ionization mode is changed in the
method file. Reagent gas in the tune file.

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Sensitivities of Ionization Modes
Most sensitive to least sensitive:
NCI (- ion, capture electron)
Extremely sensitive; like ECD
EI (+ ion, lose electron)
SEI (+ ion, lose electron)
CI (+ ion, add reagent gas ion)
SCI (+ ion, add reagent gas ion)

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A Final Question
What is
another name
for a positively charged ion?

25. © 2007 SHIMADZU25
Thank You for Coming
A “Cat” ion (Lion King+1
)