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