Polaris Q GC/MSn Ion Trap Technology
Steven T. Fannin
GC & GC/MS
The Column: “heart”
of the Instrument
2
Maintaining GC/MS Ruggedness
“Extra Column” Effects
• Syringes
• Septa
• Liners
• Ferrules
• Gas Filters
3
Chromatography: General Overview
• Resolution
Why Capillary Columns?
• Selectivity
– Spacing between two peaks
– Important role in GC confirmation
analyses
• Capacity Factor (Relative Retention)
The Van Deemter equation: H = A + B/u + C u
A: the multipath term (eddy diffusion)
B: longitudinal diffusion
C: resistance to mass transfer
H = A + B/u + C u
– Retention relative to an unretained
compound
• Column Efficiency:
H = L/N
N.B: Velocity: Pressure regulated vs Flow controlled
H2 vs He vs N2
4
Common Mass Analyzers for GC/MS
• Time of Flight (TOF) - Ionized compounds/fragments from the source are directed
into a flight tube. Ions are separated by virtue of their different flight times over a
known distance.
• Magnetic Sector - Uses a combination of magnetic and electrical fields to sort ions.
The ions are focused and resolved by passing through an electric field then a
magnetic field.
• Quadrupole - consists of two sets on opposing rods. This mass analyzer uses a
combination of RF and DC modulation to sort ions.
• Ion Trap - operates on a principle as the quadrupole; however ions can be stored for
subsequent analysis. The ions are sorted by changing the electric field inside of the
trap by manipulating the RF field and sequentially ejecting the ions from low to high
mass to charge.
5
General Mass Spectrometry Characteristics
What differentiates mass analyzers is how they perform mass analysis
• Mass Analysis - Common to Mass Analyzers
– All determine the m/z ratio
– All measure gas-phase ions
– All operate at low pressure (<10-4 Torr) to allow appropriate mean
free path of gas phase ions
• General Mass Spectrometry Instrument Characteristics
– Sensitivity
– Tandem Mass Spectrometry
–
–
–
–
6
Mass Range
Resolution
Mass Accuracy
Scan Speed
GC/MS Ionization Methods
Electron Ionization: EI (“Hard Ionization”)
• Transfer of energy to a neutral molecule (in the gaseous state) to
eject one of its own electrons and produce an ion (charged
molecule), with a mass of m and a charge of z.
8
Example of PFTBA EI+
9
Chemical Ionization
Soft Ionization Techniques
Filament
EI Ion Volume
e-
To Mass
Analyzer
CH4
Removable
Ionization
Volume
10
Lenses
CI Ion Volume
Positive Ion Chemical Ionization
 Reagent gas reactions (methane)
m/z 16, 15, 14
m/z 17
m/z 29
m/z 28
m/z 27
m/z 41
11
Positive Ion Chemical Ionization
 Proton transfer
M  CH  M  H   CH 4


5
M  C 2 H 5  M  H   C 2 H 4


[M+1]+
 Hydride abstraction
M  C 2 H  M  H   C 2 H 6

5

[M-1]+
 Adduct formation
M  C 2 H 5  M  C 2 H 5 
[M+29]+
M  C 3 H 5  M  C 3 H 5 
[M+41]+


12


Common PICI Reagent Gases
Reagent Gas
•
Methane [CH5+ & C2H5+]
–
–
•
•
Low purity (ion source gets dirty quickly)
Anhydrous ammonia [H+(NH3)n=1-3]
–
–
–
–
Very selective protonation (nitrogen compounds)
Forms [M+NH4]+ adduct with many compounds
Keeps ion source clean
Highly corrosive (short mech. pump lifetime)
reaction must be exothermic, i.e., PA (analyte) > PA (reagent gas)
* kJ/mol
13
•
549 &
687
Protonates most organic molecules
C2H5+ reacts with alkanes primarily by hydride abstraction
Isobutane [C4H9+]
–
Proton
Affinity*
Hydride Ion
Affinity*
•
1126 &
1135
•
821
•
976
•
858
•
825
Less
fragmentation
with
higher PA
Less
[M-H]+
with
lower HIA
EI vs.PICI for Pesticides
EI Spectrum of Heptachlor
Intensity is low for any
single m/z ion.
14
PICI Spectrum of Heptachlor
Intensity is concentrated in
[M+H]+ ion.
Spectrum is simpler.
Adduct Formation in PICI
15
Negative Ion Chemical Ionization (EC-NICI)
•
Reagent gas reactions (methane)


4
CH4  (70eV )e  CH  e
*
Thermal electron
•
Kinetic energy of electrons reduced by collisions with reagent gas
•
Resonance electron capture mechanism of ionization
AB  e
*

 AB  Heat
[M]-
• Reagent gas reacts with electrons to form “plasma” of thermal electrons
• Ionization is favored by molecules which have a high electron affinity – electron capture
• Useful for selective analysis in heavy matrices, e.g., pesticides in food or waste matrix.
16
Common NICI Reagent Gases
e- Thermalization
Rate*
Reagent Gas
• Methane
• 8.6x10-10
• Isobutane
• ~2.1x10-9
– Low purity (ion source get dirty quickly)
• Carbon dioxide
– Can produce less fragmentation than methane or
isobutane
• Anhydrous ammonia
• 5.8x10-9
• 5.9x10-9
– Keeps ions source clean
– Highly corrosive (short mech. pump lifetime)
* cm3/s
17
Better
sensitivity
with higher
rate
NICI of Carboxy THC - PFPA
Negative Ion spectrum of the PFPA/PFPOH derivative of 11-nor-9-Carboxy-D9-THC
18
Analysis of Catecholamines using NICI-MS
753
Pentafluoropropionyl (PFP) Derivatives of
Norepinephrine, Epinephrine and Dopamine
19
Ion Trap vs Quadrupole
Basic Principles
Voltage Relationship During a Mass Scan (Quadrupole)
+1500
+Vdc
VRF
0
VRF
+180°
-Vdc
RF Potential
DC Potential
+250
• Ions scanned by varying
the DC/Rf voltage across
the quadrupoles
-1500
-250
+/-(U+Vocoswt)
Complete Mass Scan
77001-1380
970608
m/z
Ion beam
21
-/+(U+Vocoswt)
What is a Quadrupole Ion Trap?
Entrance
Endcap
Ring
Electrode
ro
zo
V  cost 
22
Exit
Endcap
Potential Energy Surfaces (Ion Traps)
R ing V oltage (V )
150
100
50
0
-50
-100
-150
0
V
90
180
270
360
RF Phase (deg)
V
V
r
z
r
23
z
r
z
General Principles of Stability Diagrams
•
Operating line for
mass selective instability
–
0.4
z stability
0.2
bZ
aZ
0.2
0.3
0.4
0.5
0.6
1.0
0.8
0.7
0.1
0.2
0.3
0
Basic Ion Trap Principles
q cut-off~.91
0.4
qz
0.5
Mathieu stability diagram and stability/reduced
parameters
•
Ion trap function : “Mass Selective Instability”
•
Quadrupole: Mass Selective Stability mode of
scanning
•
The (a,q) coordinates are simply related to m/z
and the operating voltage - whereas b values
are related to ion motion
bX Y
,
-0.2
0.6
r stability
U  V  cost 
0.7
-0.4
0.8
Operating line for
Mass selective stability
U0
0.9
1.0
-0.6
qz =
az =
8eV
m(r O2+ 2 Z O2 )  2
16eU
2
0.5
24
2
m(r O+ 2z O)  2
q
Z
1.0
1.5
ro
zo
 az  0
Stability Line and Mass Selective Ejection
az
Mass-selective
Instability Scan
with Resonant
Ejection
476 kHz
0.908
0.0
*
qz 
V
m/z
az  0
25
qz
1.0
Mass-selective Instability Scanning
Ramp RF voltage (V) to sequentially
eject ions from low m/z to high m/z.
Trapping Injected Ions
V  cost 
+
Dz 
eV
2
2
4mz o 
2
ro
zo
+ + +
+ ++
• Correct RF voltage
• Helium buffer gas
26
Full Scan MS Scan Function
Mass Analysis
Mass Analysis
Ion Injection
Ion Injection
V
Gate Lens
Eject (V’)
Multiplier
AGC Prescan*
One complete scan constitutes a “microscan”
27
Mass Analysis Scan
Fixed Ion Injection Time
Number of Ions Trapped (arbitrary units)
100000
Space
Charge
Effects
10000
1000
100
10
1
1
10
100
1000
10000
100000
Amount of Sample (arbitrary units)
28
DYNAMIC RANGE: ~103
1000000
10000000
Ion Injection Time Optimized with AGC
Number of Ions Trapped (arbitrary units)
100000
Space
Charge
Effects
10000
1000
* User
Selectable
100
** 5 µs PolarisQ,
10 µs LCQ,
30 µs GCQ
10
1
1
10
100
1000
10000
100000
Amount of Sample (arbitrary units)
DYNAMIC RANGE: >106
29
1000000
10000000
Polaris Q Tune Parameters (AGC and Injection
RF)
30
Quadrupole vs. Ion Trap
Quadrupole
quadrupoles
use SIM to enhance
sensitivity
Transmits one m/z ion at a time
Mass-Selective Stability scanning
Ion Trap
In full scan
ion traps are
more sensitive
than quadrupoles.
Trap all m/z ions simultaneously
Mass-Selective Instability scanning
31
Quadupoles and Sensitivity
Quadrupole
• Duty cycle is important for
determining mass analyzer
efficiency
• Efficiency of the mass analyzer:
Transmits one m/z ion at a time
Mass-Selective Stability scanning
Duty Cycle for a Quadrupole
Width of transmitted ion
total width of m/z range
32
= Duty Cycle
EMassAnalyzer  ETransmission  DutyCycle
• Ionization and mass analysis
occur simultaneously: Mass
resolution and scan range are
important when determining duty
cycle
SIM, MIM and SRM,MRM
(Target Compound Techniques)
• Single Quadrupole Technology (single-stage MS techniques)
– SIM (Selected or Single Ion Monitoring)
• Set quadrupole to pass a single characteristic ion during a retention time window in the
chromatogram
• Increases sensitivity 10-100X
• Lose spectral specificity
– MIM (Multiple Ion Monitoring)
• Monitor 2 to 5 characteristic ions in addition to SIM quanitiation ion
• Set acceptable qualifier ion “ratios” to confirm detection
• More qualifier ions boost confidence but reduce sensitivity gains
• Triple Quadrupole Technology
(MS/MS Techniques)
– SRM (Single Reaction Monitoring)
• Single product ion monitored
– MRM (Multiple Reaction Monitoring)
• Multiple product ions monitored
33
Ion Traps and Sensitivity
External Source Ion Trap
• Efficiency of the mass analyzer:
EMassAnalyzer  ETransmission  DutyCycle
Trap all m/z ions simultaneously
Mass-Selective Instability scanning
Duty Cycle for an Ion Trap
Ion Accumulation Time (ion gate time)
Total scan time
34
= Duty Cycle
• Ionization and mass analysis
occur consecutively: Scan time (or
rate) relative to ion accumulation
is important for determining duty
cycle
Tandem MS Principles
Tandem Mass Spectrometry
Why use MS/MS?
• Enhanced Selectivity (Qualitative and Quantitative)
– TRACE Analyses Criteria for Target Compounds
• Sensitivity and Selectivity are important
– MS/MS Improves Trace Level Analyses in complex matrices and enhances
confirmatory analyses (Enhanced confirmation of identification)
• Combined with Soft Ionization techniques
– Most signal in [M+H]+ ions; Added selectivity and s/n
– Confirmatory assays (MW ions plus 2-3 unique ions)
– Qualitative and quantitative with digital reagent gas flow
• Structural Characterization Applications
– MS/MS provides unique evidence to an unknowns identity providing further
information about fragments in the MS spectrum
S/N
TRACE DSQ uses SIM to increase S
Polaris Q uses MS/MS to reduce N
36
MS/MS “Tandem-In-Time”Ion Trap Technology
MS/MS and MSn Capability
MS/MS “Tandem-In-Space”
Triple Stage Quadrupole Technology
37
77001-1383
970602
MS/MS “Tandem-In-Time”
Ion Trap Technology
MS/MS in an Ion Trap
1. Inject
2. Isolate
38
3. Fragment
4. Detect
How Do We Isolate Ions for MS/MS?
az
Ion we wish to isolate
Mass-selective
Instability Scan
with Resonant
Ejection
476 kHz
0.908
0.0
*
qz 
1.0
V
How MS/MS works
m/z
qz Mp = VRF
77001-1383
970602
az  0
39
qz
υ(ion) = (n + β) Ω/2
Isolation Waveforms
m/z 1000
Fast Fourier
m/z 300
Transform
m/z 100
Time Domain
40
Frequency Domain
CID using Resonant Excitation
qz
0.0
0.908
How MS/MS works
t=15 ms
qz Mp = VRF
υ(ion) = (n + β) Ω/2
Product ions
qz
0.0
41
0.908
Polaris Q Excitation Event Characteristics
Stability Diagram: Where parent ions reside
on the q axis during the excitation event
Excitation “q”
0.225
qz
0.300
0.450
P = precursor mass
qz 
V
m/z
MS/MS
qz Mp = VRF
42
The choice of ‘q’ is also a function of the MS/MS lower
limit of the product ion m/z range. A ‘q’ of 0.225 is 1/4Mp
(where Mp is the m/z of the parent ion), and a ‘q’ of 0.3 is
1/3Mp, and a ‘q’ of 0.45 is 1/2Mp. For example, if a ‘q’ of
0.45 is used, and Mp is m/z 400, then the daughter ion
lower limit that can be observed in the spectrum will be
m/z 200. If the same ‘q’ is used for an Mp at m/z 800,
then the daughter ion lower limit that can be observed
will be m/z 400, and so on
Higher qz Means Higher Energy
D 
z
eV
4mz 
2
o
Dz
qz = 0.225
43
2
mq  z
2
2

2
z
2
o
16e
0.30
0.45
Resonant Excitation qz Value
Fragment ions
not trapped
qz
0.0
1/4
x
1/3
2x
1/2
4x
0.908
0.225
qz
0.0
Product Ion Fragmentation
m/z Range
Energy
0.30
0.908
qz
0.0
44
0.45
0.908
Tandem MS:
Polaris Q MS/MS Scan Function
Mass Analysis
Ion Isolation
Ion Injection
Ion Injection
Mass Analysis
Ion Isolation
Resonant
Excitation
V
Gate Lens
Isolate
Excite
Eject (V’)
How MS/MS works for all
RF-Traps
qz Mp = VRF
υ(ion) = (n + β) Ω/2
45
Multiplier
AGC Prescan
Mass Analysis Scan
MS/MS Example - Chlordane
GC/MS Spectrum
Isolation of
Precursor Ion
46
GC/MS/MS Product Ion Spectrum
Fragment
Precursor Ion
Polaris Q MS/MS Parameters
MS/MS Parameters
Choice of
Excitation q’s
47
MS/MS: Optimizing Conditions
‘q’ is a function of the RF
voltage applied to the ring
electrode during excitation
Dexamethasone
Product ion intensity vs Collision Voltage
7.E+05
Excitation Event – higher
excitation ‘q’s may provide
improved conversion
efficiencies (ECID =  Fi / P0)
Product Ion Intensity
6.E+05
5.E+05
4.E+05
3.E+05
2.E+05
1.E+05
0.E+00
0
0.2
0.4
0.6
0.8
1
1.2
Collision Voltage (p-p)
48
1.4
1.6
1.8
2