intro to mass spec
TRANSCRIPT
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Introduction to Mass Spectrometry
March 2008
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What is a Mass Spectrometer?
A Mass Spectrometer is a machine that weighs molecules !
0 units
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What is a Mass Spectrometer?
A Mass Spectrometer is a machine that weighs molecules !
12 units
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What is a Mass Spectrometer?
A Mass Spectrometer is a machine that weighs molecules !
12 units8 9 10 11 12 13 14 15 16
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What is a Mass Spectrometer?
A Mass Spectrometer is a machine that weighs molecules !
14 units8 9 10 11 12 13 14 15 16
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What is a Mass Spectrometer?
A Mass Spectrometer is a machine that weighs molecules !
12 units8 9 10 11 12 13 14 15 16
mass
Num
ber o
f cou
nts
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Outline
• Basic Chemistry• Analytical Chemistry• Mass Spectrometry
– Types of Ion Sources• EI, CI, ESI, APCI, APPI, MALDI
– Types of MS• Ion Traps, Quads, FT-ICR, TOF, Sector• MS/MS • Performance Comparisons
– Market Segments
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Basic Chemistry
• Everything is made of Atoms– Atoms are made of protons, neutrons, and
electrons– Many atoms together make up molecules
UATOM
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Carbon
Oxygen Hydrogen
Nitrogen
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6 protons (+)
6 neutrons
6 electrons(-)
Carbon Atom
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Carbon
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More Carbon
• 6 protons (1 mass unit each) + 6 neutrons (1 mass unit each) = 12 mass units– Electrons are negligible ( 1/3600 of mass unit)
• Some carbon (about 1%) has 7 neutrons so weigh 13 units
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12.00 x 99%+13.00 x 1% = 12.01 amu
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But how much does an atom weigh ?
• It was found that 12 grams of carbon contains 6.02 x 1023 atoms of carbon.( 1023 seconds have not elapsed since the beginning of time !)
• So one atom of carbon weighs 1.99 x 10-23 grams !
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Caffeine
C8H10N4O2
Total Mass194 Daltons3.22x10-22 grams
N
N
CH3
CH3
N
N
CH3O
O
H
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Caffeine
C8H10N4O2
Total Mass194 Daltons3.22x10-22 grams
N
N
CH3
CH3
N
N
CH3O
O
H
So we must devise a machine which can measure ~ 10-22 grams.
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Analytical Chemistry
Instrumental Methods Chemical Methods
TitrationGravimetric AnalysisSolution Chemistry
Spectroscopy Mass Spectrometry
Optical Absorption
NMRMicrowave
Optical EmissionFT-ICRTOFQuadrupoleIon TrapLinear TrapMagnetic Sector
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Gas Phase/Ionize
Detector
Separate Based on Mass/Charge
Sample
3 Elements to Mass Spectrometry(J.J. Thomson ~ 1910)
Why Ionize ?Difficult to manipulate neutral particles on molecular scale. If they are charged, then we can use electric fields to move them around.
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Gas Phase/Ionize
Detector
Separate Based on Mass/Charge
Sample
3 Elements to Mass Spectrometry(J.J. Thomson ~ 1910)
• Electron Impact (EI)• Chemical Ionization (CI)• Electrospray (ESI)• Atmospheric Pressure Chemical
Ionization (APCI)• Photo-ionization (APPI)• Matrix Assisted Laser Desorption
and Ionization (MALDI)
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Gas Phase/Ionize
Detector
Separate Based on Mass/Charge
Sample
3 Elements to Mass Spectrometry(J.J. Thomson ~ 1910)
• Scanning (Filter)– Linear Quadrupole– Sector
• Pulsed (Batch)– Ion Trap– FT-ICR– Time-of-Flight
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Gas Phase/Ionize
Detector
Separate Based on Mass/Charge
Sample
3 Elements to Mass Spectrometry(J.J. Thomson ~ 1910)
• Faraday Cup• Discrete Dynode• Continuous Dynode• Multi-channel Plate
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Gas Phase/Ionize
Detector
Separate Based on Mass/Charge
Sample
3 Elements to Mass Spectrometry(J.J. Thomson ~ 1856-1940)
So, we could come up with 6x5x4 = 120 Unique Mass Spectrometers.
In reality, not all combinations make sense, but many extra “hybrid” MS systems have value. For example Q-TOF’s and LT-FT-ICR
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6 Types of Ion Sources
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Ion Source Depends on Sample
Solid Sample Liquid Sample Gas Sample
EICIAPCIMALDI ESIAPPI
Make into Solution ?Make into Solid ? Turn into Gas?
Chemical Properties of analyte in gas phase ?
Chemical Properties of analyte in solution phase ?
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Polarity, MW and Volatility
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Polarity, MW and Volatility
Caffeine
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Gas Phase Ionization•EI and CI are gas phase ionization techniques•Sample is heated to cause volatilization•The molecule must have a low enough MW and polarity so that:
TBoil< TDecomposition
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Electron Impact
M
e- e- e-
M(g) + e- M+(g) + 2e-
This reaction creates the molecular ion so is very useful. However, the excess energy from the electron can cause the molecular ion to fall apart:
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s0
s1
IP
s0
s1
IP2NeutralMolecule
Ionized Molecule
Excess Energy get redistributed throughout ion to cause fragmentation.
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Electron Impact
A+M
e- e- e-
M(g) + e- M+(g) + 2e-
M+(g) A+
Fragment 1 (g) + BFragment 2 (g)•Electron energy is chosen by compromise. •Fragment Information is useful. It can help structural determination. However, many ions produce only fragments with no molecular ion remaining. Molecular ion often very unstable.•70 eV “Classical Spectra” to be used for comparisons
BB
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N
N
CH3
CH3
N
N
CH3O
O
H
MW 194
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N
N
CH3
CH3
N
N
CH3O
O
H 109 m/z
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N
N
CH3
CH3
N
N
CH3O
O
H
55 m/z
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Chemical Ionization
• EI is not appropriate for some molecules (it causes too much fragmentation)
• Instead, ionize a reagent gas (by EI) then react it with a analyte molecules
• Typically use methane or ammonia for reagent gas
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CI: Form Reagent Ions First
• For Example - Methane CI1. electron ionization of CH4:
• CH4 + e- CH4+ + 2e-
– Fragmentation forms CH3+, CH2
+, CH+
2. ion-molecule reactions create stable reagent ions:• CH4
+ + CH4 CH3 + CH5+
• CH3+ + CH4 H2 + C2H5
+ – CH5
+ and C2H5+ are the dominant methane CI reagent
ions
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Methane CI Reagent Ions
– Ions at m/z 17, 29, and 41 are from methane; • H3O+ is also formed from water vapor in the
vacuum system
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Reagent Ions React with Analytes• Several Types of Reactions May Occur
– Form Pseudomolecular Ions (M+1)– CH5
+ + M CH4 + MH+
– M+1 Ions Can Fragment Further to Produce a Complex CI Mass Spectrum
– Form Adduct Ions– C2H5
+ + M [M + C2H5]+ M+29 Adduct– C3H5
+ + M [M + C3H5]+ M+41 Adduct
– Molecular Ion by Charge Transfer– CH4
+ + M M+ + CH4
– Hydride Abstraction (M-1)– C3H5
+ + M C3H6 + [M-H]+
» Common for saturated hydrocarbons
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EI Spectrum of Cocaine
• Extensive Fragmentation• Molecular Ion is Weak at m/z 303
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Methane CI of CocainePseudo molecular Ion and Fragment Ions
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Isobutane CI of Cocaine
• Soft Reagent - Less Fragmentation
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Polarity, MW and Volatility
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Liquid Techniques
• Depending on solvent composition and molecular properties either– APPI– ESI– APPI
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APPI
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• Lamp Wavelength chosen to only excite analytes not solvent/background– Low amount of
photo dissociation results
• New technique with few novel applications
• Less universal than electrospray
APPI
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APCI Principles• Rapidly vaporize entire liquid flow• Ionize solvent molecules in corona
discharge• CI process ionizes sample molecules• Positive mode: proton transfer or charge
exchange• Negative mode: proton abstraction or
electron capture
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APCI – Cut Away View
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What applications need APCI?
• APCI works well for small molecules that are moderately polar to non-polar
• APCI works well for samples that contain heteroatoms
• Avoid samples that typically are charged in solution
• Avoid samples that are very thermally unstable or photosensitive
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Why Electrospray ?
• Most Samples are delivered as liquids.– GC analysis requires heating sample to cause
evaporation– Ionization occurs through electron impact or
chemical reaction– Not all analytes are thermally stable
• Electrospray was designed to provide a gentle method of creating gas phase ions
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Three Step Process1)Droplet formation 2)Droplet Shrinkage3)Gaseous Ion Formation
Electrospray process does not ionize samples !
Taylor Cone
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•Solutions delivered to the tip of the electrospray capillary experience the electric field associated with the maintenance of a high potential. •Assuming a potential gradient, positive ions will accumulate at the surface. •Positively Charged Ions will “bud” off the surface when the applied electrostatic force is bigger than the surface tension.
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Assisted Electrospray
NebulizingGas
LC Column Flow
High Voltage (5 kv)Low Voltage (0.5 kv)
MS
DryingGas
Low Voltage (0.1 kv)
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MALDI
• Matrix Assisted Laser Desorption Ionization• Analyte co-deposited with Matrix• Laser excites matrix which transfers energy to analyte• Produces singly charged species• Typically used for large biomolecules / polymers• MALDI is a high mass/pulsed source so usually combined with TOF
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5 Types of Mass Spectrometers
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5 Types of Mass Spectrometers
• Scanning (Filter)– Linear Quadrupole– Sector
• Pulsed (Batch)– Ion Trap– FT-ICR– Time-of-Flight
( Separation in Space)
( Separation in Time)
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Basics of Ion Physics
maF qEF
qVmvEK 2
21..
m – massa – accelerationB – Magnetic Fieldq – chargeE - electric fieldF – ForceK.E. – kinetic energyV – electric potentialv - velocity
qvBF
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Combine 1st two equations
qEma
mqEa
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mqEa
We can control this. (volts/meter)We can
measure this.
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mqEa
We can control this. (volts/meter)We can
measure this.
We can deduce This !
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0V -40V
+
0V
-40V
+
1 meter
mqEa
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Time of Flight MS
qVmvEK 2
21..
2
2
2lVt
qm
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Time of Flight (TOF)
+ Very high mass range + Both high resolution and high
sensitivity + Mass accuracy+ High scan speed+ Mechanically simple
m/z t2
- High vacuum critical- Demanding high voltage/ pulsed/ high
precision electronics- Expensive
Bruker, Waters-Micromass, JEOL, Analytica
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Time of Flight
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SECTOR MS
qvBrmvF
2
vrB
qm
2
22
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High resolution (60,000 at 10% valley).
MStation™ Double Focusing Magnetic Sector Mass SpectrometerFROM JEOL
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Very high reproducibility Best quantitative performance of all mass
spectrometer analyzers High resolution High sensitivity High dynamic range
- Large- Expensive- Not suited for pulsed sources
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FT-ICR
qvBrmvF
2
mqB
rv
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1347.734
1348.736
1349.741
mm
Resolution
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PROFILE Scan 35 from ...ta sept 24.04\0.01+0.036 extrste mode 1 609.xms
605.0 607.5 610.0 612.5 615.0 617.5m/z
0.0
0.5
1.0
1.5
kCounts
609.50 0.3541 1384
610.45 0.4533
471
611.45 0.3952
114
PROFILESpectrum 1A0.472 min. Scans: 3-67 Channel: 1 Ion: 2000 us RIC: 21543BP 609.50 (1384=100%) 0.01+0.036 extrste mode 1 609.xms
609
607
610
611612
Reserpine
Reserpine is used to treat high blood pressure. It works by decreasing your heart rate and relaxing the blood vessels so that blood can flow more easily through the body. It also is used to treat severe agitation in patients with mental disorders
Resolution ~ 1200
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LC/MS/MS with data dependent acquisition using Bruker’s simple, unified Compass software package
Exact mass MS analysis to sub-ppm levels for unambiguous determination of elemental chemical
composition. Automated software to confirm composition with m/z and isotopic pattern information
Exact mass MS(n) capability for detailed structural analysis and peptide sequencing
Qh-hybrid along with CID and ECD for “top-down” proteomics (Top↓Pro™) facilitates selected gas
phase ion enrichment
Extreme resolution capability for direct analysis of complex mixtures (> 600,000 FWHM)
Wide m/z range simultaneous detection of ions (e.g. 100 - 7,000 m/z)
Sub fmol sensitivity
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FT-ICR
The highest recorded mass resolution of all mass spectrometers
Powerful capabilities for ion chemistry and MS/MS experiments
Well-suited for use with pulsed ionization methods such as MALDI
Non-destructive ion detection; ion remeasurement
Stable mass calibration in superconducting magnet FTICR systems
• Limited dynamic range • High Vacuum Demands • Subject to space charge effects and ion molecule
reactions • Many parameters (excitation, trapping, detection
conditions) comprise the experiment sequence that defines the quality of the mass spectrum
• Generally low-energy CID, spectrum depends on collision energy, collision gas, and other parameters
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Ion Traps, Transmission Quadrupoles and Linear Traps
• Electrodynamic quadrupole fields– Paul (University of Bonn in 1953 – Nobel Prize 1989)
• 3D and 2D traps• Created a “high resolution quad” that was 5.82 m
long !• A quadrupole field is linearly dependant on the
coordinate axis• Ions are confined or rejected based on Voltage,
Frequency, Dimension, Mass and Charge
![Page 77: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/77.jpg)
Ion Traps and Quads
•Traps are Pulsed•Quads are Continuous•Both rely time varying electric fields (RF)
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+
+
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- -Splat
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• Forces on ion are simple to understand• As always
Where Fz = the force in the z direction
e = charge on the particle m = mass of the particle a = acceleration Ez= electric field
maeEF zz
Ion Trap + Quadrupole Theory
![Page 93: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/93.jpg)
ze
dtzdmmaF zZ
2
2
)cos(222
2
tVUrze
dtzdmmaF
oZ
zz eEmaF
![Page 94: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/94.jpg)
0)cos(222
2
ztVUmre
dtzd
o
0)cos(22
2
rtVUmre
dtrd
o
Ion Motion in an Ion Trap• After several pages of math, we can derive an equation
for ion motion as a function of time:
• These second order differentials are not trivial to solve.• Mathieu Equation ! ( solved in 1868 , sub type of Hill’s equations) • Graphical Solution – (Slightly different for Traps and Quads because of symmetry.)
NEED SOLUTIONS WHICH ARE BOUND AND STABLE IN TIME
![Page 95: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/95.jpg)
Stable Solutions to the Mathieu EquationFor a Quadrupole
2222z m4eV-
m8eU- a
oz
o rq
r
![Page 96: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/96.jpg)
Mathieu Equation for an ion trap
au
qu15
-15
15
5 10
10
5
0
-5
-10
20 25
z stable
z stable
r stable
r stable
au
qu15
-15
15
5 10
10
5
0
-5
-10
20 25
z stable
z stable
r stable
r stable
2222z m8eV-
m16eU- a
oz
o rq
r
![Page 97: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/97.jpg)
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
az
qz
z
r
1.41.20.80.60.40.2 1.0
1.00.8
0.60.4
0.00.2
0.4
0.6
0.8
1.0
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
az
qz
z
r
1.41.20.80.60.40.2 1.0 1.41.20.80.60.40.2 1.0
1.00.8
0.60.4
0.00.2
0.4
0.6
0.8
1.0
• Operated in RF only mode
• Light ions have a higher qz than heavier ions
• Ions stable in z axis when qz < 0.908
• Ions selectively ejected when RF amplitude is raised
• Light ions leave first, heavier ions later
2222z m8eV-
m16eU- a
oz
o rq
r
Stability Diagram ( Area 1)
![Page 98: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/98.jpg)
Stability Diagram for a Quad
2222z m4eV-
m8eU- a
oz
o rq
r
![Page 99: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/99.jpg)
Stability Diagram for a Quad
2222z m4eV-
m8eU- a
oz
o rq
r
200 100 50
V=200VU=0V
![Page 100: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/100.jpg)
Stability Diagram for a Quad
2222z m4eV-
m8eU- a
oz
o rq
r
V=200VU=50V
200100
50
![Page 101: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/101.jpg)
Stability Diagram for a Quad
2222z m4eV-
m8eU- a
oz
o rq
r
V=200VU=100V100
200
50
![Page 102: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/102.jpg)
Stability Diagram for a Quad
2222z m4eV-
m8eU- a
oz
o rq
r
150
200
50
V=400VU=200V
![Page 103: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/103.jpg)
Stability Diagram for a TRAP
Quad operates by selectively passing one m/z at a time.
Trap operates by collecting all ions simultaneously and then ramping them out one at a time.
2222z m8eV-
m16eU- a
oz
o rq
r
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
az
qz
z
r
1.41.20.80.60.40.2 1.0
1.00.8
0.60.4
0.00.2
0.4
0.6
0.8
1.0
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
az
qz
z
r
1.41.20.80.60.40.2 1.0 1.41.20.80.60.40.2 1.0
1.00.8
0.60.4
0.00.2
0.4
0.6
0.8
1.0
![Page 104: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/104.jpg)
Stability Diagram for a Trap
2222z m8eV-
m16eU- a
oz
o rq
r
200 100 50
V=200VU=0V
Eject when q=0.908
![Page 105: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/105.jpg)
Stability Diagram for a Trap
2222z m8eV-
m16eU- a
oz
o rq
r
200 100 50
V=300VU=0V
Eject when q=0.908
![Page 106: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/106.jpg)
Stability Diagram for a Trap
2222z m8eV-
m16eU- a
oz
o rq
r
200 100 50
V=400VU=0V
Eject when q=0.908
![Page 107: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/107.jpg)
Mass Spectrum on a Quad or Trap
Ramp RF (in trap) or ramp RF/DC in Quad
RF
Spectrum
![Page 108: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/108.jpg)
2222z m8eV-
m16eU- a
oz
o rq
r
Stability Diagram for a Trap
?m
![Page 109: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/109.jpg)
Potential Well Model
Need for helium buffer gas
22
2
42
o
rz mzeVDD
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222
21
2
u
uuuq
a
Secular Frequency• Ion Motion in Trap contains many frequency
components• These depend on a and q parameters
– (When q < 0.40)
![Page 111: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/111.jpg)
0 0.2 0.4 0.6 0.8 1
m/z= 500q = 0.1816ω = 50.5 kHz
m/z= 1000q = 0.0908ω = 25.1 kHz
m/z= 1500q = 0.0605ω = 16.7 kHz
Low MassCut Off100 m/z
m/z= 106q = 0.850ω = 301.9 kHz
![Page 112: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/112.jpg)
0 0.2 0.4 0.6 0.8 1
m/z= 500q = 0.1816ω = 50.5 kHz
m/z= 1000q = 0.0908ω = 25.1 kHz
m/z= 1500q = 0.0605ω = 16.7 kHz
Low MassCut Off100 m/z
m/z= 106q = 0.850ω = 301.9 kHz
Varian Eject
![Page 113: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/113.jpg)
frequency
Amplitude
Fourier Transform
Notched Broad Band Waveform
![Page 114: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/114.jpg)
0 0.2 0.4 0.6 0.8 1
m/z= 500q = 0.1816ω = 50.5 kHz
m/z= 1000q = 0.0908ω = 25.1 kHz
m/z= 1500q = 0.0605ω = 16.7 kHz
Low MassCut Off100 m/z
m/z= 106q = 0.850ω = 301.9 kHz
Frequency Notch
180kHz 240kHz
![Page 115: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/115.jpg)
Practical Mass Spectrometer
Load Time Ion Ejection
Notched Waveform
Dipole Ejection
Mass Spectrum
![Page 116: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/116.jpg)
Ion trap
BenefitsHigh sensitivity Multi-stage mass spectrometry (analogous to FTICR experiments) Compact mass analyzerCheap and Easy to build
Limitations•Poor quantitation •Poor inherent dynamic range •Subject to space charge effects and ion molecule reactions •Collision energy not well-defined in CID MS/MS •Many parameters (excitation, trapping, detection conditions) comprise the experiment sequence that defines the quality of the mass spectrum
![Page 117: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/117.jpg)
Transmission Quadrupole Mass Spectrometer
BenefitsClassical mass spectra Good reproducibility Relatively small and low-cost systems Potentially good conversion efficiency for MS/MS
Limitations•Limited resolution •Peak heights variable as a function of mass (mass discrimination). Peak height vs. mass response must be 'tuned'. •Not well suited for pulsed ionization methods •Low-energy collision-induced dissociation (CID) MS/MS spectra in triple quadrupole and hybrid mass spectrometers depend strongly on energy, collision gas, pressure, and other factors.
![Page 118: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/118.jpg)
Linear Trap
+ =
Newest Generation MS•Many of the advantages of ion traps, without normal trap limitations.•Less Space Charge Problems•MSN
•Great loading Efficiency
![Page 119: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/119.jpg)
![Page 120: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/120.jpg)
MS/MS • In a transmission Quadrupole, MS/MS is
done in Space– need three quads ( Triple Quad)
• In an Ion trap MS/MS is done in time.
Pass only 195
RF ONLY-Pass Everything-Collisions with Ar cause fragmentation
Scan from 100-195 Look at daughter ions
Q1 Q2 Q3
![Page 121: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/121.jpg)
vs.
Triple Quad
Ion Trap
![Page 122: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/122.jpg)
Why MS/MS
• Unknown Identification• Potentially two compounds of interest
have the same mass ( and same retention time)
• Quantitation improvements ( background signal reduced)
![Page 123: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/123.jpg)
Problem: Thiabendazole in Grapefruit Extract
• Antifungal agent, thiabendazole (TBZ) must be below 10 ppb in the processed grapefruit
• Major matrix interferent: Similar retention time Similar spectrum Concentration much greater than TBZ
Interferent
![Page 124: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/124.jpg)
Interferent
![Page 125: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/125.jpg)
MS, MS/MS, and MS/MS/MS of TBZMatrix peak
Matrix peak
No matrix peak
MS (500 pg)
MS/MS (10 pg)
MS/MS/MS (10 pg)
20180-220
20117465-220
![Page 126: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/126.jpg)
SelectScanningProduct Ion Scan
SelectPrecursor ion Scan
Scanning Neutral Loss Scan
Scanning
Scanning
Quadrupole 1MS 1
Quadrupole 2Collision Cell
Quadrupole 3MS 1
![Page 127: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/127.jpg)
Real Life System
![Page 128: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/128.jpg)
PROFILE Scan 35 from ...ta sept 24.04\0.01+0.036 extrste mode 1 609.xms
605.0 607.5 610.0 612.5 615.0 617.5m/z
0.0
0.5
1.0
1.5
kCounts
609.50 0.3541 1384
610.45 0.4533
471
611.45 0.3952
114
PROFILESpectrum 1A0.472 min. Scans: 3-67 Channel: 1 Ion: 2000 us RIC: 21543BP 609.50 (1384=100%) 0.01+0.036 extrste mode 1 609.xms
609
607
610
611612
Reserpine
Reserpine is used to treat high blood pressure. It works by decreasing your heart rate and relaxing the blood vessels so that blood can flow more easily through the body. It also is used to treat severe agitation in patients with mental disorders
![Page 129: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/129.jpg)
PROFILE Scan 85 from ...ultip charge ions\4500-cytochrome c-6-17-04.xms
500 750 1000 1250 1500 1750 2000m/z
0.0
0.5
1.0
1.5
2.0
2.5
kCounts
721.00 1.3347
238
765.65 0.6099 1186
816.43 0.3790 2316
874.45 0.4061 1507
941.55 0.4655
693
1020.13 0.4678
413 1112.72 0.4881
247 1223.87 0.6065
183
1359.76 0.5506
236
1529.57 0.5139
456
1747.75 0.7672
180
PROFILESpectrum 1A4.898 min. Scans: 10-160 Channel: 1 Ion: 500 us RIC: 159835BP 816.43 (2316=100%) 4500-cytochrome c-6-17-04.xms
Cytochrome C – MW 12220
+17
+16
+15
+14
+13
+12+11
+10+9
+8
+7
m/z = mass/charge
nHnHMW
![Page 130: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/130.jpg)
Market Segments and Where Varian Sits
![Page 131: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/131.jpg)
Single QuadrupoleSingle Quadrupole$204 M$204 M
Triple QuadrupoleTriple Quadrupole$ 14 M$ 14 M
Ion TrapIon Trap$50 M$50 M
SectorSector$5 M$5 M
TOFTOF$7 M $7 M
GC/MS mass analyzer type
GC/MS Initial Sales $280M
![Page 132: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/132.jpg)
18%
33%25%
8%
3%
13%Single QuadrupoleSingle Quadrupole
$114 M$114 M
Triple QuadrupoleTriple Quadrupole$221 M$221 MIon TrapIon Trap
$140 M$140 M
Sector/FTICRSector/FTICR$30 M$30 M
Q-TOFQ-TOF$128 M$128 M
API TOFAPI TOF$65 M$65 M
LC/MS mass analyzer type
2004 LC/MS Initial Sales $698M
![Page 133: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/133.jpg)
Agilent Bruker JEOL MicroMass
Sciex Thermo Varian
Single Quad 1 2 1 1 1Triple Quad 2 4 4 1Sector 3 1 1FT-ICR 2 13D Trap 3 3 2 1Linear Trap 1 1TOF 1 1 1 2
TOF/TOF 2
Q-TOF 2 4 1TOTAL (LC/MS) 5 10 4 11 6 10 3
![Page 134: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/134.jpg)
The High-end LC/MS VendorsHigh-end TQ (55%) Waters, Thermo, ABI
High-end Ion Traps (23%) Bruker/Agilent, Thermo
LTQ -Thermo
LC-TOF, TOF-TOF, Q-TOF (13%)
Q-Trap (5%)Magnetic sector (4%)
High-end LC/MS Vendor Market Share
![Page 135: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/135.jpg)
Markets served by the high-end LC/MS
Academic, Food/AG, Indep.Test 40M (5%) 14M (15%) 16M (6%)
Total Market $330M
Varian participates in less than 25% of the market, with a 1% overall market share
![Page 136: Intro to Mass Spec](https://reader031.vdocuments.mx/reader031/viewer/2022022415/577ccf331a28ab9e788f2400/html5/thumbnails/136.jpg)
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that weighs molecules ! (by measuring the mass to charge ratio of ions)
SourceEICIESIAPCIAPPIMALDI
DispersionTOFFT-ICRSectorQuadTrap
DetectorFaraday CupChanneltronMCP