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Lecture 4
Mass Analyzers
Jack Henion, Ph.D. Emeritus Professor, Analytical Toxicology
Cornell University Ithaca, NY 14850
Lecture 4, Page 1
Contents
• Quadrupoles
• Ion traps – 3D ion traps
– Linear ion traps
– ICR FTMS
– Orbitraps
• Time-of-flight (TOF)
• Hybrid mass analyzer systems
• Ion mobility spectrometers
Lecture 4, Page 2
Single Quadrupole MS
Courtesy of Waters.com Lecture 4, Page 3
The Stability Diagram
The quadrupole is scanned with A/Q = constant; the resolution depends on the slope of
the scan line.
If the continuous voltage DC is switched off, the scan line is the Q axis: We have now a
transfer only device like the hexapoles or octopoles used to transfer and focus the ions
into the mass spectrometer optics.
Courtesy of Waters.com
Good
resolution
Poor
resolution
Lecture 4, Page 4
Ion Transmission Through a Quadrupole
Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation. J.T. Watson and O.D.
Sparkman, 4th Ed. John Wiley & Sons, Ltd. P. 61, 2007
To obtain optimal
performance a mass
spectrometer must have
its ion path ‘tuned’ and
mass-axis calibrated
Wide ion beam
Narrow ion beam
Lecture 4, Page 5
Tandem Mass Spectrometry
“Triple Quadrupole” for MS/MS
Collision Cell Partially Removed to Show Detail
Q1 Q2 Q3
CID Gas
m/z 609
MS/MS Vocabulary: MS1 (Q1) Parent ion, precursor ion Collision cell (Q2) Dissociation, fragmentation MS2 (Q3) Product ion, daughter ion SRM (MRM)
MS 1 MS 2
What kind of MS/MS experiment is this?
Lecture 4, Page 6
Tandem MS Scan Functions (Different ways to run the experiments)
• Full-scan of mass range
– Used for qualitative identification of unknowns
• Precursor ion scan
– Used for newborn screening
• Constant neutral loss scan
– Used for detecting common molecular features
• Selected reaction monitoring (SRM)
– Used for quantitative analysis
Lecture 4, Page 7
Ion Trap Mass Analyzers
• 3D ion traps
• Linear ion traps
• Ion cyclotron resonance traps (FTMS)
• Orbitraps
Lecture 4, Page 8
Ion Trapology
• The mass analyzer consists of a ring electrode separating two hemispherical electrodes.
– A mass spectrum is obtained by changing the electrode voltages to eject the ions from the trap.
• Ions are contained by a pseudo-potential.
– A potential-energy distribution which at any instant is
unstable but is oscillating sufficiently quickly that on
average any net force on the ion is restoring.
Lecture 4, Page 9
Spherical (3-D) Ion Traps • Ion species are confined
using dual parabolic
trapping wells before
mass scan.
– 3-dimensional RF trapping
field.
• Ions are focused to a
point.
Lecture 4, Page 10
Example Commercial (3D) Instruments
• Thermo Deca XP, etc.
• Bruker HCT
• Mini 11
• Griffin
• Torrion
Lecture 4, Page 11
Ion Trap Mass Spectrometer Basics
• External Ion Injection:
– 3-Dimensional Ion Traps
• Low trapping efficiency (poor injection efficiency)
• Low capacity
– 2-Dimensional Linear Ion Traps
• Very high trapping efficiency
• Very high capacity
Lecture 4, Page 12
Ion Trap Mass Spectrometers
• Important Figures of Merit
– Trapping efficiency
• What percentage of incoming ions get trapped?
– Trap capacity
• How many ions can the trap hold before spectral artifacts appear?
– Extraction efficiency
• How many ions can you get out of the trap mass selectively?
Lecture 4, Page 13
Excitation & Ejection of Trapped Ions
3-Dimensional Traps:
– Excite along one dimension with auxiliary AC field.
– Ions whose secular frequency comes into
resonance with the applied AC field gain
additional kinetic energy.
– Ions with sufficient KE emerge along the direction
of excitation.
Lecture 4, Page 14
• “Ion bottles” for optical
spectroscopy.
– Frequency standards
• Quantum computers
• Ion accumulation for enhanced
MS sensitivity.
• Mass analyzer:
– RCM, 2002, 16, 512-526.
Linear Ion Traps
Lecture 4, Page 15
Linear Ion Traps
• RF radial containment
and usually DC volts at
the ends.
• Ions are focused to a
line.
• Ions are free to move
the length of the trap.
(speeds of ~102 m/sec)
RF Field
RF Field
DC Field DC Field
Lecture 4, Page 16
Trapping Efficiency: Linear Traps
~ 3 - 20 cm
No RF field along centerline since it is applied radially.
Greater length allows more momentum dissipating collisions.
Results in much higher trapping efficiency.
Lecture 4, Page 17
Linear vs. 3-D Ion Traps: Trapping Efficiency
• Linear Trap
– No quadrupole field on center line.
– Longer flight path
(3-20 cm).
• 3-D Trap
– Quadrupole field
gives amplitude and
phase dependent
trapping efficiencies.
– ~1 cm to lose
injection energy.
Linear trap can be ~10-100X better.
Lecture 4, Page 18
Ion Trap Capacity
3-Dimensional trapping field focuses to a point. Small useful volume.
Ring electrode
~ 1cm ~ 3 - 20 cm
2-Dimensional radial trapping field focuses to a line. Large useful volume.
Lecture 4, Page 19
Excitation & Ejection of Trapped Ions
• Radial Ion Ejection
– Similar concept to 3-D
ion trap.
– Excite ion motion
between a pair of
opposing rods.
– Resonant ions emerge
through the rods.
Lecture 4, Page 20
Excitation & Ejection of Trapped Ions
• Axial Ion Ejection
– Excite ion motion
radially between a pair
of opposing rods.
– Fringing fields couple
the radial & axial ion
motion
– Resonant ions emerge
axially.
Lecture 4, Page 21
Hybrid Triple Quad/Linear Ion Trap MS
• Axial ejection linear ion trap is a good match for the triple quadrupole mass spectrometer detection system.
• Allows for use as a triple quad and a hybrid linear ion trap instrument.
Lecture 4, Page 22
Why Hybridize? • Optimize each component independently
• Provide additional functionality – Mass accuracy
– Resolving power
– Dynamic Range
– Selectivity
– Enhanced duty cycle
– Reactions (ion-molecule, ion-ion)
– Charge state separation
• Samples are becoming more and more complicated – Specificity
• e.g.: Bio-transformations: PTM’s and metabolites
• Reduce multiple MS purchases
Lecture 4, Page 23
Hybridization Approaches:
Ion Trap Mass Analyzer
Quad. IT
LIT
LTQ
ToF
FT-ICR
Orbitrap
Lecture 4, Page 24
Hybridization Approaches:
Ion Trap Mass Analyzer
QTRAP®
Ion Trap Mass Analyzer
Previous Approach
Lecture 4, Page 25
Hybrid Triple Quad/Linear Ion Trap MS
Q0 Q1 Q2 Q3
LIT MS and Quadrupole Mass Filter
Lecture 4, Page 26
NO ions due to lower mass cut-off (1/3 of precursor)
Few fragment ion due to low energy fragmentation processes.
(A)
(B)
3D Trap VS Hybrid Linear Trap
3D Ion Trap
Linear Ion Trap
Lecture 4, Page 27
1. Precursor ion selection in Q1.
2. Fragmentation in Q2.
3. Trap products in LIT.
4. RF/DC isolation in LIT.
5. Single frequency excitation in LIT.
6. Mass scan.
7. Concurrent trapping in Q0.
Isolation widths of ~1-5amu.
Excitation selectivity <1 amu.
Fragmentation efficiency of ~70-90%.
Q0 Q1 Q2 Q3
LIT LINAC
Trap
Isolate
Excite
Scan
Select
precursor ion Fragment
N2 CAD Gas
Hybrid MS3 Scan
Lecture 4, Page 28
FTMS (ICR Mass Spectrometry)
Lecture 4, Page 29
Ions are trapped at their cyclotron Frequency
Lecture 4, Page 30
Fourier Transformation of the ICR Signal produces a Mass Spectrum
Lecture 4, Page 31
FTMS Features • Very High Resolving PowerBroadband: >500,000
• Isotopic Resolution for proteins
• Isotopic fine structure for peptides and small molecules
• High mass measurement accuracyAccurate monoisotopicmass
• Protein database searching
• Elemental composition
• Fast and sensitive –all ions are detected simultaneously
• •Ion storage for many minutes
• •Ion isolation and dissociation using Collisionallyinduced dissociation (CID)
Lecture 4, Page 32
Benefits of low error mass measurement
Lecture 4, Page 33
Lecture 4, Page 34
(generate molecular formula)
Lecture 4, Page 35
Lecture 4, Page 36
The Orbitrap
Lecture 4, Page 37
Principle of Trapping in the Orbitrap
Orbital traps Kingdon (1923)
• The Orbitrap is an ion trap – but there are no RF or magnet fields!
• Moving ions are trapped around an electrode
- Electrostatic attraction is compensated by centrifugal force arising from the initial tangential velocity
• Potential barriers created by end-electrodes confine the ions axially
• One can control the frequencies of oscillations (especially the axial ones) by shaping the electrodes appropriately
• Thus we arrive at …
Lecture 4, Page 38
Performance Specifications
• Resolution (at m/z 200)
100,000 at 1 scan per second
10,000 at 10 scans per second
• Mass accuracy
< 2 ppm (internal)
< 5 ppm (external)
• Dynamic Range
> 4000 within a spectrum
• Sensitivity
Sub pg range for small molecules
• Scan speed
Up to 10 scans per second
• Mass Range
m/z 50-4000
• Polarity switching
Yes, 1 full cycle < 1 sec
Lecture 4, Page 39
zm
k
/
Retaining the Ions in the Orbitrap
•Many ions in the Orbitrap generate a complex signal whose
frequencies are determined using a Fourier Transformation
•Lighter ions enter Orbitrap earlier, therefore they are squeezed
closer to the central electrode than heavier ions
Lecture 4, Page 40
The Basic Components of the Exactive Orbitrap
Ionisation Source
Ion Optics
Lecture 4, Page 41
Exactive C-Trap and HV Lens Stack
Lecture 4, Page 42
Orbitrap
The Basic Components of the Exactive
Orbitrap
Ion Optics
Ionisation Source
Lecture 4, Page 43
The LTQ Orbitrap- What is it?
• The LTQ Orbitrap is a hybrid MS and MSn System based on a fundamentally new analyzer principle: An electrostatic ion trap
• It inherits all the features of the Finnigan LTQ – All ionization and inlet methods, outstanding sensitivity,
ruggedness, ease of use and, of course, MSn operation
• It adds capabilities for the most demanding analyses – High mass resolution
– Accurate mass determination with external mass calibration
• It is fast - even with high resolution accurate mass detection
Lecture 4, Page 44